From e5a1cb85cbbbc399eca4be11adb2a92f0ed9bd44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:17:02 +0100 Subject: [PATCH 01/54] start titles improvements --- R/attributes.R | 32 ++++++++++++++++---------------- R/iterators.R | 2 +- _pkgdown.yml | 9 +++------ man/delete_edge_attr.Rd | 4 ++-- man/delete_graph_attr.Rd | 4 ++-- man/delete_vertex_attr.Rd | 4 ++-- man/edge_attr-set.Rd | 4 ++-- man/edge_attr.Rd | 4 ++-- man/edge_attr_names.Rd | 4 ++-- man/graph_attr-set.Rd | 4 ++-- man/graph_attr.Rd | 4 ++-- man/graph_attr_names.Rd | 4 ++-- man/igraph-dollar.Rd | 4 ++-- man/igraph-vs-attributes.Rd | 4 ++-- man/roxygen/meta.R | 7 +++++++ man/set_edge_attr.Rd | 4 ++-- man/set_graph_attr.Rd | 4 ++-- man/set_vertex_attr.Rd | 4 ++-- man/vertex_attr-set.Rd | 4 ++-- man/vertex_attr.Rd | 4 ++-- man/vertex_attr_names.Rd | 4 ++-- src/Makevars | 4 ++-- 22 files changed, 63 insertions(+), 59 deletions(-) create mode 100644 man/roxygen/meta.R diff --git a/R/attributes.R b/R/attributes.R index 1c0c7f7722..8dbb74294f 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -43,7 +43,7 @@ #' @return A list of graph attributes, or a single graph attribute. #' #' @aliases get.graph.attribute graph.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -72,7 +72,7 @@ graph_attr <- function(graph, name) { #' @return The graph, with the attribute(s) added. #' #' @aliases graph.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -102,7 +102,7 @@ graph_attr <- function(graph, name) { #' @param value New value of the attribute. #' @return The graph with the new graph attribute added or set. #' -#' @family graph attributes +#' @family attributes #' @aliases set.graph.attribute #' #' @export @@ -152,7 +152,7 @@ graph.attributes <- function(graph) { #' all vertex attributes, if `name` is missing. #' #' @aliases get.vertex.attribute vertex.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -197,7 +197,7 @@ vertex_attr <- function(graph, name, index = V(graph)) { #' @return The graph, with the vertex attribute(s) added or set. #' #' @aliases vertex.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -229,7 +229,7 @@ vertex_attr <- function(graph, name, index = V(graph)) { #' @return The graph, with the vertex attribute added or set. #' #' @aliases set.vertex.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -363,7 +363,7 @@ vertex.attributes <- function(graph, index = V(graph)) { #' edge attributes if `name` is missing. #' #' @aliases get.edge.attribute edge.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -407,7 +407,7 @@ edge_attr <- function(graph, name, index = E(graph)) { #' @return The graph, with the edge attribute(s) added or set. #' #' @aliases edge.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -439,7 +439,7 @@ edge_attr <- function(graph, name, index = E(graph)) { #' @return The graph, with the edge attribute added or set. #' #' @aliases set.edge.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -567,7 +567,7 @@ edge.attributes <- function(graph, index = E(graph)) { #' @return Character vector, the names of the graph attributes. #' #' @aliases list.graph.attributes attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -590,7 +590,7 @@ graph_attr_names <- function(graph) { #' @return Character vector, the names of the vertex attributes. #' #' @aliases list.vertex.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -617,7 +617,7 @@ vertex_attr_names <- function(graph) { #' @return Character vector, the names of the edge attributes. #' #' @aliases list.edge.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -643,7 +643,7 @@ edge_attr_names <- function(graph) { #' @return The graph, with the specified attribute removed. #' #' @aliases remove.graph.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -673,7 +673,7 @@ delete_graph_attr <- function(graph, name) { #' @return The graph, with the specified vertex attribute removed. #' #' @aliases remove.vertex.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -704,7 +704,7 @@ delete_vertex_attr <- function(graph, name) { #' @return The graph, with the specified edge attribute removed. #' #' @aliases remove.edge.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -971,7 +971,7 @@ NULL #' @method $ igraph #' @name igraph-dollar #' @export -#' @family graph attributes +#' @family attributes #' @examples #' g <- make_ring(10) #' g$name diff --git a/R/iterators.R b/R/iterators.R index c5cae425fe..16c37e2f82 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -1063,7 +1063,7 @@ simple_es_index <- function(x, i, na_ok = FALSE) { #' #' @export #' @family vertex and edge sequences -#' @family graph attributes +#' @family attributes #' @examples #' g <- make_( #' ring(10), diff --git a/_pkgdown.yml b/_pkgdown.yml index 34935546c0..ee985f1056 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,16 +4,16 @@ template: bootstrap: 5 reference: -- title: Adjacency +- title: Adjacency matrices - contents: - has_concept("adjacency") -- title: Graph attributes +- title: Vertex, edge and graph attributes - contents: - has_concept("graph attributes") - title: Structural queries - contents: - has_concept("structural queries") -- title: Bipartite +- title: Bipartite graphs - contents: - has_concept("bipartite") - title: Centrality @@ -112,9 +112,6 @@ reference: - title: Vertex and edge sequence operations - contents: - has_concept("vertex and edge sequence operations") -- title: Graph attributes -- contents: - - has_concept("graph attributes") - title: Graph layouts - contents: - has_concept("graph layouts") diff --git a/man/delete_edge_attr.Rd b/man/delete_edge_attr.Rd index 0f6c708d60..365f561b97 100644 --- a/man/delete_edge_attr.Rd +++ b/man/delete_edge_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_edge_attr(g, "name") edge_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, @@ -44,4 +44,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/delete_graph_attr.Rd b/man/delete_graph_attr.Rd index 8bea2ada25..10d981c7ed 100644 --- a/man/delete_graph_attr.Rd +++ b/man/delete_graph_attr.Rd @@ -25,7 +25,7 @@ g2 <- delete_graph_attr(g, "name") graph_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, @@ -43,4 +43,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/delete_vertex_attr.Rd b/man/delete_vertex_attr.Rd index b3ccb76527..f7d83846b4 100644 --- a/man/delete_vertex_attr.Rd +++ b/man/delete_vertex_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_vertex_attr(g, "name") vertex_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{edge_attr<-}()}, @@ -44,4 +44,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_attr-set.Rd b/man/edge_attr-set.Rd index 1894fa936f..859a7a7dd4 100644 --- a/man/edge_attr-set.Rd +++ b/man/edge_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -55,4 +55,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_attr.Rd b/man/edge_attr.Rd index 19d7ac4c26..f6ace0583b 100644 --- a/man/edge_attr.Rd +++ b/man/edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g, edge.width = E(g)$weight) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -50,4 +50,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_attr_names.Rd b/man/edge_attr_names.Rd index 1b5b1c2670..4f549c3095 100644 --- a/man/edge_attr_names.Rd +++ b/man/edge_attr_names.Rd @@ -23,7 +23,7 @@ edge_attr_names(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -41,4 +41,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_attr-set.Rd b/man/graph_attr-set.Rd index ff1f6cdf4f..342d31b824 100644 --- a/man/graph_attr-set.Rd +++ b/man/graph_attr-set.Rd @@ -34,7 +34,7 @@ graph_attr(g) <- list( plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -52,4 +52,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_attr.Rd b/man/graph_attr.Rd index 57cb7e108c..864e71482a 100644 --- a/man/graph_attr.Rd +++ b/man/graph_attr.Rd @@ -26,7 +26,7 @@ graph_attr(g) graph_attr(g, "name") } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -44,4 +44,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_attr_names.Rd b/man/graph_attr_names.Rd index a0af577ff3..5909263778 100644 --- a/man/graph_attr_names.Rd +++ b/man/graph_attr_names.Rd @@ -22,7 +22,7 @@ g <- make_ring(10) graph_attr_names(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -40,4 +40,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/igraph-dollar.Rd b/man/igraph-dollar.Rd index 106de6af00..ecadd45a29 100644 --- a/man/igraph-dollar.Rd +++ b/man/igraph-dollar.Rd @@ -29,7 +29,7 @@ g$name <- "10-ring" g$name } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -47,4 +47,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/igraph-vs-attributes.Rd b/man/igraph-vs-attributes.Rd index 5f730900b6..e63221834a 100644 --- a/man/igraph-vs-attributes.Rd +++ b/man/igraph-vs-attributes.Rd @@ -87,7 +87,7 @@ Other vertex and edge sequences: \code{\link{print.igraph.es}()}, \code{\link{print.igraph.vs}()} -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -105,5 +105,5 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} \concept{vertex and edge sequences} diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R new file mode 100644 index 0000000000..a7b9855a8a --- /dev/null +++ b/man/roxygen/meta.R @@ -0,0 +1,7 @@ +list( + rd_family_title = list( + adjacency = "Adjacency matrices", + attributes = "Vertex, edge and graph attributes", + bipartite = "Bipartite graphs" + ) +) diff --git a/man/set_edge_attr.Rd b/man/set_edge_attr.Rd index 8dac8f8fff..f3a7669848 100644 --- a/man/set_edge_attr.Rd +++ b/man/set_edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -50,4 +50,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/set_graph_attr.Rd b/man/set_graph_attr.Rd index 554fa10150..33ce770ad3 100644 --- a/man/set_graph_attr.Rd +++ b/man/set_graph_attr.Rd @@ -27,7 +27,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -45,4 +45,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/set_vertex_attr.Rd b/man/set_vertex_attr.Rd index 38ba253b9e..0150dc0c29 100644 --- a/man/set_vertex_attr.Rd +++ b/man/set_vertex_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -50,4 +50,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_attr-set.Rd b/man/vertex_attr-set.Rd index d4a88dcb59..da55dc1a79 100644 --- a/man/vertex_attr-set.Rd +++ b/man/vertex_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -55,4 +55,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_attr.Rd b/man/vertex_attr.Rd index 28519fb02f..18cb13f18a 100644 --- a/man/vertex_attr.Rd +++ b/man/vertex_attr.Rd @@ -33,7 +33,7 @@ vertex_attr(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -51,4 +51,4 @@ Other graph attributes: \code{\link{vertex_attr<-}()}, \code{\link{vertex_attr_names}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_attr_names.Rd b/man/vertex_attr_names.Rd index 42cb85c43c..327d58c1ed 100644 --- a/man/vertex_attr_names.Rd +++ b/man/vertex_attr_names.Rd @@ -24,7 +24,7 @@ vertex_attr_names(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -42,4 +42,4 @@ Other graph attributes: \code{\link{vertex_attr<-}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/src/Makevars b/src/Makevars index d9535e9849..fc864eb796 100644 --- a/src/Makevars +++ b/src/Makevars @@ -5,10 +5,10 @@ PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT \ + -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ -DINTERNAL_ARPACK \ -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) all: $(SHLIB) From 995c283f8740d958edf8bcb7083a198477061292 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:19:31 +0100 Subject: [PATCH 02/54] more of the same --- _pkgdown.yml | 2 +- man/alpha_centrality.Rd | 2 +- man/arpack.Rd | 4 ++-- man/betweenness.Rd | 6 +++--- man/bipartite_mapping.Rd | 2 +- man/bipartite_projection.Rd | 2 +- man/closeness.Rd | 2 +- man/diversity.Rd | 2 +- man/eigen_centrality.Rd | 2 +- man/harmonic_centrality.Rd | 2 +- man/page_rank.Rd | 2 +- man/power_centrality.Rd | 2 +- man/roxygen/meta.R | 3 ++- man/spectrum.Rd | 2 +- man/strength.Rd | 2 +- man/subgraph_centrality.Rd | 2 +- 16 files changed, 20 insertions(+), 19 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index ee985f1056..7f0e3c3802 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -16,7 +16,7 @@ reference: - title: Bipartite graphs - contents: - has_concept("bipartite") -- title: Centrality +- title: Centrality measures - contents: - has_concept("centrality") - title: Centralization related diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 02dd447d4a..6f980120ec 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -93,7 +93,7 @@ measures of centrality for asymmetric relations'' \emph{Social Networks}, \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=power_centrality]{power_centrality()}} -Other centrality: +Centrality measures \code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, diff --git a/man/arpack.Rd b/man/arpack.Rd index 79742d3b0d..aa876dbfb0 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -218,7 +218,7 @@ Matrices. \emph{Linear Algebra and its Applications}, vol 88/89, pp 575-595, \code{\link[=hub_score]{hub_score()}}, \code{\link[=cluster_leading_eigen]{cluster_leading_eigen()}} are some of the functions in igraph that use ARPACK. -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -231,7 +231,7 @@ Other centrality: \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 9c6d5f4a74..64f6f71118 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -133,7 +133,7 @@ of Mathematical Sociology} 25(2):163-177, 2001. \seealso{ \code{\link[=closeness]{closeness()}}, \code{\link[=degree]{degree()}}, \code{\link[=harmonic_centrality]{harmonic_centrality()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, @@ -146,7 +146,7 @@ Other centrality: \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, @@ -159,7 +159,7 @@ Other centrality: \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/bipartite_mapping.Rd b/man/bipartite_mapping.Rd index 85a7a9c2a0..5a07465514 100644 --- a/man/bipartite_mapping.Rd +++ b/man/bipartite_mapping.Rd @@ -52,7 +52,7 @@ g3 <- add_edges(g3, c(1, 3)) bipartite_mapping(g3) } \seealso{ -Other bipartite: +Bipartite graphs \code{\link{bipartite_projection}()} } \author{ diff --git a/man/bipartite_projection.Rd b/man/bipartite_projection.Rd index da319fb469..f0f256ca49 100644 --- a/man/bipartite_projection.Rd +++ b/man/bipartite_projection.Rd @@ -90,7 +90,7 @@ print(proj2[[2]], g = TRUE, e = TRUE) } \seealso{ -Other bipartite: +Bipartite graphs \code{\link{bipartite_mapping}()} } \author{ diff --git a/man/closeness.Rd b/man/closeness.Rd index d510ed8497..1ee2c66ef9 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -88,7 +88,7 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239. \seealso{ \code{\link[=betweenness]{betweenness()}}, \code{\link[=degree]{degree()}}, \code{\link[=harmonic_centrality]{harmonic_centrality()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{diversity}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index 0ca30dd19d..4eea01e17e 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -53,7 +53,7 @@ Nathan Eagle, Michael Macy and Rob Claxton: Network Diversity and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010. } \seealso{ -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index 894b422c05..f81fabbf74 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -103,7 +103,7 @@ Bonacich, P. (1987). Power and Centrality: A Family of Measures. \emph{American Journal of Sociology}, 92, 1170-1182. } \seealso{ -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index 28ae15984d..f6cd880126 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -69,7 +69,7 @@ M. Marchiori and V. Latora, Harmony in the small-world, \seealso{ \code{\link[=betweenness]{betweenness()}}, \code{\link[=closeness]{closeness()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/page_rank.Rd b/man/page_rank.Rd index 49bbab41b8..eebd971080 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -109,7 +109,7 @@ Conference, Brisbane, Australia, April 1998. Other centrality scores: \code{\link[=closeness]{closeness()}}, \code{\link[=betweenness]{betweenness()}}, \code{\link[=degree]{degree()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index 8902cf613a..cbc97928f6 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -135,7 +135,7 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.'' \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=alpha_centrality]{alpha_centrality()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R index a7b9855a8a..9c257fe6b7 100644 --- a/man/roxygen/meta.R +++ b/man/roxygen/meta.R @@ -2,6 +2,7 @@ list( rd_family_title = list( adjacency = "Adjacency matrices", attributes = "Vertex, edge and graph attributes", - bipartite = "Bipartite graphs" + bipartite = "Bipartite graphs", + centrality = "Centrality measures" ) ) diff --git a/man/spectrum.Rd b/man/spectrum.Rd index d8c718c60d..5408d3c59c 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -78,7 +78,7 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values \seealso{ \code{\link[=as_adj]{as_adj()}} to create a (sparse) adjacency matrix. -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/strength.Rd b/man/strength.Rd index 534db0944b..a3cc75a6a7 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -55,7 +55,7 @@ Natl. Acad. Sci. USA 101, 3747 (2004) \seealso{ \code{\link[=degree]{degree()}} for the unweighted version. -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index eec184cf71..9c9ac33501 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -45,7 +45,7 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005). \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}}, \code{\link[=page_rank]{page_rank()}} -Other centrality: +Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, From 61a2adb7bf9bda1952a5800aa7ea9924fd73a95f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:22:44 +0100 Subject: [PATCH 03/54] merging --- _pkgdown.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 7f0e3c3802..7983139ed6 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -25,12 +25,6 @@ reference: - title: Cliques - contents: - has_concept("cliques") -- title: Cocitation -- contents: - - has_concept("cocitation") -- title: Cohesive blocks -- contents: - - has_concept("cohesive.blocks") - title: Coloring - contents: - has_concept("coloring") @@ -193,6 +187,8 @@ reference: - title: Structural properties - contents: - has_concept("structural.properties") + - has_concept("cocitation") + - has_concept("cohesive.blocks") - title: Structural queries - contents: - has_concept("structural queries") From bb194200974f47c1b3491e65b300989338952965 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:25:05 +0100 Subject: [PATCH 04/54] more of the same --- _pkgdown.yml | 14 +++++------- man/articulation_points.Rd | 4 ++-- man/as_membership.Rd | 2 +- man/biconnected_components.Rd | 2 +- man/cluster_edge_betweenness.Rd | 2 +- man/cluster_fast_greedy.Rd | 2 +- man/cluster_fluid_communities.Rd | 2 +- man/cluster_infomap.Rd | 2 +- man/cluster_label_prop.Rd | 2 +- man/cluster_leading_eigen.Rd | 2 +- man/cluster_leiden.Rd | 2 +- man/cluster_louvain.Rd | 2 +- man/cluster_optimal.Rd | 2 +- man/cluster_spinglass.Rd | 2 +- man/cluster_walktrap.Rd | 2 +- man/communities.Rd | 34 +++++++++++++++--------------- man/compare.Rd | 2 +- man/components.Rd | 2 +- man/contract.Rd | 2 +- man/decompose.Rd | 2 +- man/groups.Rd | 2 +- man/make_clusters.Rd | 2 +- man/modularity.igraph.Rd | 4 ++-- man/plot_dendrogram.communities.Rd | 4 ++-- man/roxygen/meta.R | 5 ++++- man/split_join_distance.Rd | 2 +- 26 files changed, 52 insertions(+), 53 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 7983139ed6..92be1c08f4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -19,19 +19,20 @@ reference: - title: Centrality measures - contents: - has_concept("centrality") + - has_concept("efficiency") - title: Centralization related - contents: - has_concept("centralization related") - title: Cliques - contents: - has_concept("cliques") -- title: Coloring +- title: Graph coloring - contents: - has_concept("coloring") -- title: Community +- title: Community detection - contents: - has_concept("community") -- title: Components +- title: Connected components - contents: - has_concept("components") - title: Console @@ -43,18 +44,12 @@ reference: - title: Deterministic constructors - contents: - has_concept("deterministic constructors") -- title: Decomposition -- contents: - - has_concept("decomposition") - title: Graphical degree sequences - contents: - has_concept("graphical degree sequences") - title: Demo - contents: - has_concept("demo") -- title: Efficiency -- contents: - - has_concept("efficiency") - title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") @@ -189,6 +184,7 @@ reference: - has_concept("structural.properties") - has_concept("cocitation") - has_concept("cohesive.blocks") + - has_concept("decomposition") - title: Structural queries - contents: - has_concept("structural queries") diff --git a/man/articulation_points.Rd b/man/articulation_points.Rd index 4a15c428fe..3b65008811 100644 --- a/man/articulation_points.Rd +++ b/man/articulation_points.Rd @@ -47,12 +47,12 @@ bridges(g) \code{\link[=is_connected]{is_connected()}}, \code{\link[=vertex_connectivity]{vertex_connectivity()}}, \code{\link[=edge_connectivity]{edge_connectivity()}} -Other components: +Connected components \code{\link{biconnected_components}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} -Other components: +Connected components \code{\link{biconnected_components}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} diff --git a/man/as_membership.Rd b/man/as_membership.Rd index 20379373b5..e09a84f744 100644 --- a/man/as_membership.Rd +++ b/man/as_membership.Rd @@ -27,7 +27,7 @@ compare(correct, fc) compare(correct, membership(fc)) } \seealso{ -Other community: +Community detection \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/biconnected_components.Rd b/man/biconnected_components.Rd index cf73788922..3fe8dd3016 100644 --- a/man/biconnected_components.Rd +++ b/man/biconnected_components.Rd @@ -46,7 +46,7 @@ bc <- biconnected_components(g) \code{\link[=articulation_points]{articulation_points()}}, \code{\link[=components]{components()}}, \code{\link[=is_connected]{is_connected()}}, \code{\link[=vertex_connectivity]{vertex_connectivity()}} -Other components: +Connected components \code{\link{articulation_points}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} diff --git a/man/cluster_edge_betweenness.Rd b/man/cluster_edge_betweenness.Rd index 53c8a161df..3adcce94f1 100644 --- a/man/cluster_edge_betweenness.Rd +++ b/man/cluster_edge_betweenness.Rd @@ -110,7 +110,7 @@ methods. See \code{\link[=communities]{communities()}} for extracting the results of the community detection. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_fast_greedy}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/cluster_fast_greedy.Rd b/man/cluster_fast_greedy.Rd index 51c15daa95..2df29dfed6 100644 --- a/man/cluster_fast_greedy.Rd +++ b/man/cluster_fast_greedy.Rd @@ -69,7 +69,7 @@ See also \code{\link[=cluster_walktrap]{cluster_walktrap()}}, \code{\link[=cluster_edge_betweenness]{cluster_edge_betweenness()}}, \code{\link[=cluster_louvain]{cluster_louvain()}} \code{\link[=cluster_leiden]{cluster_leiden()}} for other methods. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/cluster_fluid_communities.Rd b/man/cluster_fluid_communities.Rd index a7d593a296..9627a4dd2d 100644 --- a/man/cluster_fluid_communities.Rd +++ b/man/cluster_fluid_communities.Rd @@ -48,7 +48,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_louvain]{cluster_louvain()}}, \code{\link[=cluster_leiden]{cluster_leiden()}} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_infomap.Rd b/man/cluster_infomap.Rd index 5e7043cfec..f092b83f40 100644 --- a/man/cluster_infomap.Rd +++ b/man/cluster_infomap.Rd @@ -68,7 +68,7 @@ equation, \emph{Eur. Phys. J. Special Topics} 178, 13 (2009). \seealso{ Other community finding methods and \code{\link[=communities]{communities()}}. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_label_prop.Rd b/man/cluster_label_prop.Rd index 72c48d897e..67737483fe 100644 --- a/man/cluster_label_prop.Rd +++ b/man/cluster_label_prop.Rd @@ -70,7 +70,7 @@ Rev E} 76, 036106. (2007) \code{\link[=cluster_spinglass]{cluster_spinglass()}}, \code{\link[=cluster_louvain]{cluster_louvain()}} and \code{\link[=cluster_leiden]{cluster_leiden()}} for other community detection methods. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_leading_eigen.Rd b/man/cluster_leading_eigen.Rd index 86fcbbeb6f..f0fc6a1955 100644 --- a/man/cluster_leading_eigen.Rd +++ b/man/cluster_leading_eigen.Rd @@ -122,7 +122,7 @@ of matrices, Physical Review E 74 036104, 2006. \code{\link[=cluster_edge_betweenness]{cluster_edge_betweenness()}}, \code{\link[=cluster_fast_greedy]{cluster_fast_greedy()}}, \code{\link[=as.dendrogram]{as.dendrogram()}} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_leiden.Rd b/man/cluster_leiden.Rd index 5f14d9beca..d0ec9dd9d7 100644 --- a/man/cluster_leiden.Rd +++ b/man/cluster_leiden.Rd @@ -130,7 +130,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_optimal]{cluster_optimal()}} \code{\link[=cluster_walktrap]{cluster_walktrap()}} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_louvain.Rd b/man/cluster_louvain.Rd index 10e0cd206e..a94f74111f 100644 --- a/man/cluster_louvain.Rd +++ b/man/cluster_louvain.Rd @@ -76,7 +76,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_label_prop]{cluster_label_prop()}} \code{\link[=cluster_leiden]{cluster_leiden()}} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_optimal.Rd b/man/cluster_optimal.Rd index c6d160fc9e..433afd7b86 100644 --- a/man/cluster_optimal.Rd +++ b/man/cluster_optimal.Rd @@ -75,7 +75,7 @@ Martin Hoefer, Zoran Nikoloski, Dorothea Wagner: On Modularity Clustering, \code{\link[=modularity]{modularity()}}. See also \code{\link[=cluster_fast_greedy]{cluster_fast_greedy()}} for a fast greedy optimizer. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_spinglass.Rd b/man/cluster_spinglass.Rd index c628c808ac..2e0a631783 100644 --- a/man/cluster_spinglass.Rd +++ b/man/cluster_spinglass.Rd @@ -146,7 +146,7 @@ positive and negative links, \url{https://arxiv.org/abs/0811.2329} (2008). \seealso{ \code{\link[=communities]{communities()}}, \code{\link[=components]{components()}} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_walktrap.Rd b/man/cluster_walktrap.Rd index 39ddd05941..17c1630ab4 100644 --- a/man/cluster_walktrap.Rd +++ b/man/cluster_walktrap.Rd @@ -75,7 +75,7 @@ vector, merge matrix, modularity score, etc. and \code{\link[=cluster_leiden]{cluster_leiden()}} for other community detection methods. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/communities.Rd b/man/communities.Rd index 4dc5b0e01e..cad7ebc725 100644 --- a/man/communities.Rd +++ b/man/communities.Rd @@ -275,7 +275,7 @@ The different methods for finding communities, they all return a \code{\link[=cluster_optimal]{cluster_optimal()}}, \code{\link[=cluster_spinglass]{cluster_spinglass()}}, \code{\link[=cluster_walktrap]{cluster_walktrap()}}. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -296,7 +296,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -317,7 +317,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -338,7 +338,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -359,7 +359,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -380,7 +380,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -401,7 +401,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -422,7 +422,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -443,7 +443,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -464,7 +464,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -485,7 +485,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -506,7 +506,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -527,7 +527,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -548,7 +548,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -569,7 +569,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -590,7 +590,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -611,7 +611,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/compare.Rd b/man/compare.Rd index f91f163de0..281e95ce15 100644 --- a/man/compare.Rd +++ b/man/compare.Rd @@ -76,7 +76,7 @@ See \code{\link[=cluster_walktrap]{cluster_walktrap()}}, \code{\link[=cluster_leiden]{cluster_leiden()}} for various community detection methods. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/components.Rd b/man/components.Rd index 2252a2747d..264977ca37 100644 --- a/man/components.Rd +++ b/man/components.Rd @@ -80,7 +80,7 @@ groups(clu) \seealso{ \code{\link[=decompose]{decompose()}}, \code{\link[=subcomponent]{subcomponent()}}, \code{\link[=groups]{groups()}} -Other components: +Connected components \code{\link{articulation_points}()}, \code{\link{biconnected_components}()}, \code{\link{decompose}()} diff --git a/man/contract.Rd b/man/contract.Rd index 1a44bb52b9..51bf2d41e6 100644 --- a/man/contract.Rd +++ b/man/contract.Rd @@ -46,7 +46,7 @@ print(g2, g = TRUE, v = TRUE, e = TRUE) } \seealso{ -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/decompose.Rd b/man/decompose.Rd index 25be6adfea..4bf6567e71 100644 --- a/man/decompose.Rd +++ b/man/decompose.Rd @@ -42,7 +42,7 @@ sapply(components, diameter) \code{\link[=is_connected]{is_connected()}} to decide whether a graph is connected, \code{\link[=components]{components()}} to calculate the connected components of a graph. -Other components: +Connected components \code{\link{articulation_points}()}, \code{\link{biconnected_components}()}, \code{\link{component_distribution}()} diff --git a/man/groups.Rd b/man/groups.Rd index d6c853ca4c..f18005a25e 100644 --- a/man/groups.Rd +++ b/man/groups.Rd @@ -40,7 +40,7 @@ groups(components(g2)) \code{\link[=components]{components()}} and the various community finding functions. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/make_clusters.Rd b/man/make_clusters.Rd index c243783a99..2ff44996a9 100644 --- a/man/make_clusters.Rd +++ b/man/make_clusters.Rd @@ -38,7 +38,7 @@ This is useful to integrate the results of community finding algorithms that are not included in igraph. } \seealso{ -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/modularity.igraph.Rd b/man/modularity.igraph.Rd index 5645b19549..9e90f9ac1e 100644 --- a/man/modularity.igraph.Rd +++ b/man/modularity.igraph.Rd @@ -104,7 +104,7 @@ structure in very large networks, \emph{Physical Review E} 2004, 70, 066111 \code{\link[=cluster_louvain]{cluster_louvain()}} and \code{\link[=cluster_leiden]{cluster_leiden()}} for various community detection methods. -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -125,7 +125,7 @@ Other community: \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/plot_dendrogram.communities.Rd b/man/plot_dendrogram.communities.Rd index e0807686bd..c3f254662a 100644 --- a/man/plot_dendrogram.communities.Rd +++ b/man/plot_dendrogram.communities.Rd @@ -101,7 +101,7 @@ plot_dendrogram(fc) } \seealso{ -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -122,7 +122,7 @@ Other community: \code{\link{modularity.igraph}()}, \code{\link{split_join_distance}()} -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R index 9c257fe6b7..4e8aa31f8d 100644 --- a/man/roxygen/meta.R +++ b/man/roxygen/meta.R @@ -3,6 +3,9 @@ list( adjacency = "Adjacency matrices", attributes = "Vertex, edge and graph attributes", bipartite = "Bipartite graphs", - centrality = "Centrality measures" + centrality = "Centrality measures", + coloring = "Graph coloring", + community = "Community detection", + components = "Connected components" ) ) diff --git a/man/split_join_distance.Rd b/man/split_join_distance.Rd index eca8343865..a51355238c 100644 --- a/man/split_join_distance.Rd +++ b/man/split_join_distance.Rd @@ -42,7 +42,7 @@ Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. } \seealso{ -Other community: +Community detection \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, From 22b405662fe7ce9baf92d480fa59789740920034 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:31:57 +0100 Subject: [PATCH 05/54] more reorg --- _pkgdown.yml | 44 ++++++++++------------------------ man/ego.Rd | 2 +- man/erdos.renyi.game.Rd | 2 +- man/graph_from_graphdb.Rd | 2 +- man/plot.sir.Rd | 2 +- man/read_graph.Rd | 2 +- man/roxygen/meta.R | 6 ++++- man/sample_bipartite.Rd | 4 ++-- man/sample_degseq.Rd | 4 ++-- man/sample_dot_product.Rd | 4 ++-- man/sample_gnm.Rd | 4 ++-- man/sample_gnp.Rd | 4 ++-- man/sample_grg.Rd | 4 ++-- man/sample_growing.Rd | 4 ++-- man/sample_hierarchical_sbm.Rd | 4 ++-- man/sample_islands.Rd | 2 +- man/sample_k_regular.Rd | 2 +- man/sample_last_cit.Rd | 12 +++++----- man/sample_pa.Rd | 4 ++-- man/sample_pa_age.Rd | 4 ++-- man/sample_pref.Rd | 8 +++---- man/sample_sbm.Rd | 4 ++-- man/sample_smallworld.Rd | 4 ++-- man/sample_traits_callaway.Rd | 8 +++---- man/sir.Rd | 6 ++--- man/write_graph.Rd | 2 +- 26 files changed, 66 insertions(+), 82 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 92be1c08f4..4f83fce54f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -16,6 +16,7 @@ reference: - title: Bipartite graphs - contents: - has_concept("bipartite") + - has_concept("incidence") - title: Centrality measures - contents: - has_concept("centrality") @@ -26,6 +27,7 @@ reference: - title: Cliques - contents: - has_concept("cliques") + - has_concept("glet") - title: Graph coloring - contents: - has_concept("coloring") @@ -56,10 +58,10 @@ reference: - title: Env and data - contents: - has_concept("env-and-data") -- title: Epi +- title: Processes on graphs - contents: - has_concept("epi") -- title: Eulerian +- title: Graph cycles - contents: - has_concept("eulerian") - title: Fit @@ -68,21 +70,15 @@ reference: - title: Flow - contents: - has_concept("flow") -- title: Foreign +- title: Foreign format readers - contents: - has_concept("foreign") -- title: Games +- title: Random graph models (games) - contents: - has_concept("games") -- title: Glet -- contents: - - has_concept("glet") - title: Hierarchical random graph functions - contents: - has_concept("hierarchical random graph functions") -- title: Incidence -- contents: - - has_concept("incidence") - title: Structural queries - contents: - has_concept("structural queries") @@ -92,48 +88,28 @@ reference: - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") -- title: Structural queries -- contents: - - has_concept("structural queries") - title: Vertex and edge sequences - contents: - has_concept("vertex and edge sequences") -- title: Vertex and edge sequence operations -- contents: - has_concept("vertex and edge sequence operations") -- title: Graph layouts +- title: Visualization - contents: - has_concept("graph layouts") -- title: Layout modifiers -- contents: - has_concept("layout modifiers") -- title: Layout drl -- contents: - has_concept("layout_drl") + - has_concept("palettes") - title: Constructor modifiers - contents: - has_concept("constructor modifiers") -- title: Deterministic constructors -- contents: - - has_concept("deterministic constructors") -- title: Minimum spanning tree -- contents: - - has_concept("minimum.spanning.tree") - title: Graph motifs - contents: - has_concept("graph motifs") -- title: Nexus -- contents: - - has_concept("nexus") - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") - title: Other - contents: - has_concept("other") -- title: Palettes -- contents: - - has_concept("palettes") - title: Igraph options - contents: - has_concept("igraph options") @@ -200,6 +176,7 @@ reference: - title: Trees - contents: - has_concept("trees") + - has_concept("minimum.spanning.tree") - title: Triangles - contents: - has_concept("triangles") @@ -209,3 +186,6 @@ reference: - title: Others - contents: - lacks_concepts(c("adjacency", "graph attributes", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) +- title: Internal +- contents: + - has_concept("nexus") diff --git a/man/ego.Rd b/man/ego.Rd index c242b9e2c7..64bc03c465 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -108,7 +108,7 @@ g <- connect(g, 2) } \seealso{ -Other games: +Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_degseq}()}, diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index f00a3afc1b..241f887176 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -67,7 +67,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_pa]{sample_pa()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_degseq}()}, diff --git a/man/graph_from_graphdb.Rd b/man/graph_from_graphdb.Rd index 77414d3dc0..77824ec73e 100644 --- a/man/graph_from_graphdb.Rd +++ b/man/graph_from_graphdb.Rd @@ -95,7 +95,7 @@ of graphs and its use for benchmarking graph isomorphism algorithms, \seealso{ \code{\link[=read_graph]{read_graph()}}, \code{\link[=graph.isomorphic.vf2]{graph.isomorphic.vf2()}} -Other foreign: +Foreign format readers \code{\link{read_graph}()}, \code{\link{write_graph}()} } diff --git a/man/plot.sir.Rd b/man/plot.sir.Rd index a4e3d6a120..c8b32d88b8 100644 --- a/man/plot.sir.Rd +++ b/man/plot.sir.Rd @@ -85,7 +85,7 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=sir]{sir()}} for running the actual simulation. -Other epi: +Processes on graphs \code{\link{time_bins.sir}()} } \author{ diff --git a/man/read_graph.Rd b/man/read_graph.Rd index 189cafa9a8..3b69485609 100644 --- a/man/read_graph.Rd +++ b/man/read_graph.Rd @@ -59,7 +59,7 @@ default value is \code{TRUE}.} } \seealso{ \code{\link[=write_graph]{write_graph()}} -Other foreign: +Foreign format readers \code{\link{graph_from_graphdb}()}, \code{\link{write_graph}()} } diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R index 4e8aa31f8d..f5980055b7 100644 --- a/man/roxygen/meta.R +++ b/man/roxygen/meta.R @@ -6,6 +6,10 @@ list( centrality = "Centrality measures", coloring = "Graph coloring", community = "Community detection", - components = "Connected components" + components = "Connected components", + epi = "Processes on graphs", + eulerian = "Graph cycles", + foreign = "Foreign format readers", + games = "Random graph models (games)" ) ) diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index a66c984662..4ced6d0ce1 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -76,7 +76,7 @@ sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} and \code{\link[=sample_gnm]{sample_gnm()}} for the unipartite version. -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_degseq}()}, @@ -96,7 +96,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index b307a4a55b..28d25e6df5 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -108,7 +108,7 @@ all(degree(g5) == degs) \code{\link[=simplify]{simplify()}} to get rid of the multiple and/or loops edges, \code{\link[=realize_degseq]{realize_degseq()}} for a deterministic variant. -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -128,7 +128,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index ec5c38f1f5..5a0278020f 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -56,7 +56,7 @@ for social networks. Dissertation, Johns Hopkins University, Maryland, USA, \code{\link[=sample_dirichlet]{sample_dirichlet()}}, \code{\link[=sample_sphere_surface]{sample_sphere_surface()}} and \code{\link[=sample_sphere_volume]{sample_sphere_volume()}} for sampling position vectors. -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -76,7 +76,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 11b61e39b3..075988365c 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -46,7 +46,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_pa]{sample_pa()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -66,7 +66,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index 5063a8a15b..701441c506 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -45,7 +45,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_gnm]{sample_gnm()}}, \code{\link[=sample_pa]{sample_pa()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -65,7 +65,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 904fc07f78..9dd1088a0d 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -47,7 +47,7 @@ g2 <- sample_grg(1000, 0.05, torus = TRUE) \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -67,7 +67,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index b92e347d0e..b085ea1cc2 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -44,7 +44,7 @@ g2 <- sample_growing(500, citation = TRUE) \seealso{ \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -64,7 +64,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index 151bf680f1..43fd3fce22 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -58,7 +58,7 @@ if (require(Matrix)) { \seealso{ \code{\link[=sbm.game]{sbm.game()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -78,7 +78,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 163f7a4be1..9ec6aad7d2 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -36,7 +36,7 @@ oc \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 1a85cf37a3..9a4deb2431 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -48,7 +48,7 @@ sapply(k10, plot, vertex.label = NA) \code{\link[=sample_degseq]{sample_degseq()}} for a generator with prescribed degree sequence. -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index b5e204308f..3f6b9ae864 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -82,7 +82,7 @@ but the probability of an edge depends on the (potentially) cited vertex only. } \seealso{ -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -102,7 +102,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -122,7 +122,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -142,7 +142,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -162,7 +162,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -182,7 +182,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index c73939c7b6..e83b456701 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -130,7 +130,7 @@ de Solla Price, D. J. 1965. Networks of Scientific Papers \emph{Science}, \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -150,7 +150,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index 41035703fc..f90688e4c3 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -140,7 +140,7 @@ max(degree(g3)) \seealso{ \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -160,7 +160,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index e75f9ef767..80ad19cf5a 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -101,7 +101,7 @@ tkplot(g, layout = layout_in_circle) \code{\link[=sample_traits]{sample_traits()}}. \code{\link[=sample_traits_callaway]{sample_traits_callaway()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -121,7 +121,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -141,7 +141,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -161,7 +161,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index f1880ceb2e..41748c9fa4 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -55,7 +55,7 @@ and evaluation. \emph{Social Networks}, 14, 5--61. \seealso{ \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_gnm]{sample_gnm()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -75,7 +75,7 @@ Other games: \code{\link{sample_smallworld}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 7a5432ed11..70f5276d0e 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -56,7 +56,7 @@ Duncan J Watts and Steven H Strogatz: Collective dynamics of \seealso{ \code{\link[=make_lattice]{make_lattice()}}, \code{\link[=rewire]{rewire()}} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -76,7 +76,7 @@ Other games: \code{\link{sample_sbm}()}, \code{\link{sample_traits_callaway}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index de163ff57a..bb8db02fcd 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -80,7 +80,7 @@ g1 <- sample_traits_callaway(1000, 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2)) } \seealso{ -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -100,7 +100,7 @@ Other games: \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -120,7 +120,7 @@ Other games: \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, @@ -140,7 +140,7 @@ Other games: \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()} -Other games: +Random graph models (games) \code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, diff --git a/man/sir.Rd b/man/sir.Rd index bb8a7438ab..53e0c056fa 100644 --- a/man/sir.Rd +++ b/man/sir.Rd @@ -106,13 +106,13 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=plot.sir]{plot.sir()}} to conveniently plot the results -Other epi: +Processes on graphs \code{\link{plot.sir}()} -Other epi: +Processes on graphs \code{\link{plot.sir}()} -Other epi: +Processes on graphs \code{\link{plot.sir}()} } \author{ diff --git a/man/write_graph.Rd b/man/write_graph.Rd index 3be2c656c5..f5c9882970 100644 --- a/man/write_graph.Rd +++ b/man/write_graph.Rd @@ -58,7 +58,7 @@ networks. \emph{J Mol Biol.} 2004 Jun 25;340(1):179-90. \seealso{ \code{\link[=read_graph]{read_graph()}} -Other foreign: +Foreign format readers \code{\link{graph_from_graphdb}()}, \code{\link{read_graph}()} } From 1d5addd6c8cfa10af642f7e5b4ee1207058e656c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:39:42 +0100 Subject: [PATCH 06/54] more reorg --- _pkgdown.yml | 32 ++++++++++---------------------- man/roxygen/meta.R | 4 +++- man/scg.Rd | 2 +- man/scg_group.Rd | 2 +- man/scg_semi_proj.Rd | 2 +- man/stochastic_matrix.Rd | 2 +- 6 files changed, 17 insertions(+), 27 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 4f83fce54f..7b4fbf4917 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -61,6 +61,7 @@ reference: - title: Processes on graphs - contents: - has_concept("epi") + - has_concept("random_walk") - title: Graph cycles - contents: - has_concept("eulerian") @@ -98,6 +99,9 @@ reference: - has_concept("layout modifiers") - has_concept("layout_drl") - has_concept("palettes") + - has_concept("plot") + - has_concept("plot.common") + - has_concept("plot.shapes") - title: Constructor modifiers - contents: - has_concept("constructor modifiers") @@ -110,40 +114,28 @@ reference: - title: Other - contents: - has_concept("other") -- title: Igraph options +- title: igraph options - contents: - has_concept("igraph options") - title: Paths - contents: - has_concept("paths") -- title: Plot -- contents: - - has_concept("plot") -- title: Plot common -- contents: - - has_concept("plot.common") -- title: Plot shapes -- contents: - - has_concept("plot.shapes") - title: Print - contents: - has_concept("print") - title: Printer callbacks - contents: - has_concept("printer callbacks") -- title: Random walk -- contents: - - has_concept("random_walk") - title: Rewiring functions - contents: - has_concept("rewiring functions") - title: Scan statistics - contents: - has_concept("scan statistics") -- title: Scg +- title: Spectral Coarse Graining - contents: - has_concept("scg") -- title: Sgm +- title: Graph matching - contents: - has_concept("sgm") - title: Similarity @@ -152,24 +144,23 @@ reference: - title: Simple - contents: - has_concept("simple") -- title: Socnet +- title: Interactive functions - contents: - has_concept("socnet") + - has_concept("tkplot") - title: Structural properties - contents: - has_concept("structural.properties") - has_concept("cocitation") - has_concept("cohesive.blocks") - has_concept("decomposition") + - has_concept("triangles") - title: Structural queries - contents: - has_concept("structural queries") - title: Test - contents: - has_concept("test") -- title: Tkplot -- contents: - - has_concept("tkplot") - title: Graph isomorphism - contents: - has_concept("graph isomorphism") @@ -177,9 +168,6 @@ reference: - contents: - has_concept("trees") - has_concept("minimum.spanning.tree") -- title: Triangles -- contents: - - has_concept("triangles") - title: Versions - contents: - has_concept("versions") diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R index f5980055b7..35d8ab7f7a 100644 --- a/man/roxygen/meta.R +++ b/man/roxygen/meta.R @@ -10,6 +10,8 @@ list( epi = "Processes on graphs", eulerian = "Graph cycles", foreign = "Foreign format readers", - games = "Random graph models (games)" + games = "Random graph models (games)", + scg = "Spectral Coarse Graining", + sgm = "Graph matching" ) ) diff --git a/man/scg.Rd b/man/scg.Rd index 2987ab97e3..09e49ae357 100644 --- a/man/scg.Rd +++ b/man/scg.Rd @@ -240,7 +240,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for an introduction. \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} and \code{\link[=scg_semi_proj]{scg_semi_proj()}}. -Other scg: +Spectral Coarse Graining \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_group.Rd b/man/scg_group.Rd index 4947332912..6fa5abe19b 100644 --- a/man/scg_group.Rd +++ b/man/scg_group.Rd @@ -135,7 +135,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for a detailed introduction. \code{\link[=scg]{scg()}}, \code{\link[=scg_eps]{scg_eps()}} -Other scg: +Spectral Coarse Graining \code{\link{scg_semi_proj}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_semi_proj.Rd b/man/scg_semi_proj.Rd index 7e3983a065..6887229958 100644 --- a/man/scg_semi_proj.Rd +++ b/man/scg_semi_proj.Rd @@ -100,7 +100,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for a detailed introduction. \code{\link[=scg]{scg()}}, \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} -Other scg: +Spectral Coarse Graining \code{\link{scg_group}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/stochastic_matrix.Rd b/man/stochastic_matrix.Rd index 95ee1ff1a2..66fa4bc2a2 100644 --- a/man/stochastic_matrix.Rd +++ b/man/stochastic_matrix.Rd @@ -53,7 +53,7 @@ max(abs(rowSums(W)) - 1) \seealso{ \code{\link[=as_adj]{as_adj()}} -Other scg: +Spectral Coarse Graining \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{scg}()} From 331e2c96fe889741a02c20bf454a81b20449bd1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:52:42 +0100 Subject: [PATCH 07/54] fix case --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 7b4fbf4917..4325332323 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -174,6 +174,6 @@ reference: - title: Others - contents: - lacks_concepts(c("adjacency", "graph attributes", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) -- title: Internal +- title: internal - contents: - has_concept("nexus") From 3d85f97e679a2ccf1df8a1a51a61e8410df76152 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 10:59:01 +0100 Subject: [PATCH 08/54] undo automatic changes --- src/Makevars | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Makevars b/src/Makevars index fc864eb796..d9535e9849 100644 --- a/src/Makevars +++ b/src/Makevars @@ -5,10 +5,10 @@ PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ + -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT \ -DINTERNAL_ARPACK \ -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) all: $(SHLIB) From 9ec21d59eb1e17c19e01a876ca06a1e05ad87322 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:09:22 +0100 Subject: [PATCH 09/54] rename family tag too --- R/epi.R | 10 +++++----- R/eulerian.R | 8 ++++---- man/has_eulerian_path.Rd | 2 +- man/plot.sir.Rd | 2 +- man/roxygen/meta.R | 4 ++-- man/sir.Rd | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/R/epi.R b/R/epi.R index b60c2a5913..dbfbaa4cba 100644 --- a/R/epi.R +++ b/R/epi.R @@ -19,7 +19,7 @@ # ################################################################### -#' @family epi +#' @family processes #' @export time_bins <- function(x, middle = TRUE) { UseMethod("time_bins") @@ -27,7 +27,7 @@ time_bins <- function(x, middle = TRUE) { #' @method time_bins sir #' @rdname sir -#' @family epi +#' @family processes #' @export #' @importFrom stats IQR time_bins.sir <- function(x, middle = TRUE) { @@ -52,7 +52,7 @@ time_bins.sir <- function(x, middle = TRUE) { #' @importFrom stats median #' @method median sir #' @rdname sir -#' @family epi +#' @family processes #' @export median.sir <- function(x, na.rm = FALSE, ...) { sir <- x @@ -73,7 +73,7 @@ median.sir <- function(x, na.rm = FALSE, ...) { #' @importFrom stats quantile #' @method quantile sir #' @rdname sir -#' @family epi +#' @family processes #' @export quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) { sir <- x @@ -144,7 +144,7 @@ quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) { #' @references Bailey, Norman T. J. (1975). The mathematical theory of #' infectious diseases and its applications (2nd ed.). London: Griffin. #' @method plot sir -#' @family epi +#' @family processes #' @export #' @importFrom graphics plot lines #' @keywords graphs diff --git a/R/eulerian.R b/R/eulerian.R index 1a5f26f8c8..d92657672e 100644 --- a/R/eulerian.R +++ b/R/eulerian.R @@ -59,21 +59,21 @@ #' has_eulerian_cycle(g) #' try(eulerian_cycle(g)) #' -#' @family eulerian +#' @family cycles #' @export has_eulerian_path <- function(graph) is_eulerian(graph)$has_path #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export has_eulerian_cycle <- function(graph) is_eulerian(graph)$has_cycle #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export eulerian_path <- eulerian_path #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export eulerian_cycle <- eulerian_cycle diff --git a/man/has_eulerian_path.Rd b/man/has_eulerian_path.Rd index d28dbbc40f..d5e041fdb8 100644 --- a/man/has_eulerian_path.Rd +++ b/man/has_eulerian_path.Rd @@ -56,5 +56,5 @@ has_eulerian_cycle(g) try(eulerian_cycle(g)) } -\concept{eulerian} +\concept{cycles} \keyword{graphs} diff --git a/man/plot.sir.Rd b/man/plot.sir.Rd index c8b32d88b8..f8d69ada43 100644 --- a/man/plot.sir.Rd +++ b/man/plot.sir.Rd @@ -92,5 +92,5 @@ Processes on graphs Eric Kolaczyk (\url{http://math.bu.edu/people/kolaczyk/}) and Gabor Csardi \email{csardi.gabor@gmail.com}. } -\concept{epi} +\concept{processes} \keyword{graphs} diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R index 35d8ab7f7a..6faddc1d86 100644 --- a/man/roxygen/meta.R +++ b/man/roxygen/meta.R @@ -7,8 +7,8 @@ list( coloring = "Graph coloring", community = "Community detection", components = "Connected components", - epi = "Processes on graphs", - eulerian = "Graph cycles", + processes = "Processes on graphs", + cycles = "Graph cycles", foreign = "Foreign format readers", games = "Random graph models (games)", scg = "Spectral Coarse Graining", diff --git a/man/sir.Rd b/man/sir.Rd index 53e0c056fa..8e62895a78 100644 --- a/man/sir.Rd +++ b/man/sir.Rd @@ -119,5 +119,5 @@ Processes on graphs Gabor Csardi \email{csardi.gabor@gmail.com}. Eric Kolaczyk (\url{http://math.bu.edu/people/kolaczyk/}) wrote the initial version in R. } -\concept{epi} +\concept{processes} \keyword{graphs} From 814233d2bcd562148d7a1dc86a78f24c44d76e1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:13:51 +0100 Subject: [PATCH 10/54] regroup constructors --- _pkgdown.yml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 4325332323..49492ffe62 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,6 +4,16 @@ template: bootstrap: 5 reference: +- title: Construction +- subtitle: Deterministic constructors +- contents: + - has_concept("deterministic constructors") +- subtitle: Constructor modifiers +- contents: + - has_concept("constructor modifiers") +- subtitle: Convert to igraph +- contents: + - as.igraph - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -43,9 +53,6 @@ reference: - title: Conversion - contents: - has_concept("conversion") -- title: Deterministic constructors -- contents: - - has_concept("deterministic constructors") - title: Graphical degree sequences - contents: - has_concept("graphical degree sequences") @@ -102,9 +109,6 @@ reference: - has_concept("plot") - has_concept("plot.common") - has_concept("plot.shapes") -- title: Constructor modifiers -- contents: - - has_concept("constructor modifiers") - title: Graph motifs - contents: - has_concept("graph motifs") From 9a5950406a54d5878a8a283c1cc61e862e9712e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:18:30 +0100 Subject: [PATCH 11/54] oops --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 49492ffe62..61b066d9bc 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -19,7 +19,7 @@ reference: - has_concept("adjacency") - title: Vertex, edge and graph attributes - contents: - - has_concept("graph attributes") + - has_concept("attributes") - title: Structural queries - contents: - has_concept("structural queries") From c155d6419e4b9b57a9dc69a2b1d00fe80f578319 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:35:29 +0100 Subject: [PATCH 12/54] more regrouping --- R/iterators.R | 1 + _pkgdown.yml | 2 ++ man/E.Rd | 1 + man/V.Rd | 1 + man/as_ids.Rd | 14 ++++++++++++++ man/igraph-es-attributes.Rd | 2 ++ man/igraph-es-indexing.Rd | 1 + man/igraph-es-indexing2.Rd | 1 + man/igraph-vs-attributes.Rd | 1 + man/igraph-vs-indexing.Rd | 1 + man/igraph-vs-indexing2.Rd | 1 + man/print.igraph.es.Rd | 1 + man/print.igraph.vs.Rd | 1 + 13 files changed, 28 insertions(+) diff --git a/R/iterators.R b/R/iterators.R index 16c37e2f82..ae6d548b40 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -1789,6 +1789,7 @@ rev.igraph.es <- rev.igraph.vs #' V(g)$name <- letters[1:10] #' as_ids(V(g)) #' as_ids(E(g)) +#' @family vertex and edge sequences as_ids <- function(seq) { UseMethod("as_ids") } diff --git a/_pkgdown.yml b/_pkgdown.yml index 61b066d9bc..66db9f739b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -14,6 +14,7 @@ reference: - subtitle: Convert to igraph - contents: - as.igraph + - graph_from_lcf - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -159,6 +160,7 @@ reference: - has_concept("cohesive.blocks") - has_concept("decomposition") - has_concept("triangles") + - starts_with("assortativity") - title: Structural queries - contents: - has_concept("structural queries") diff --git a/man/E.Rd b/man/E.Rd index 716a8ec029..51ebe64ad3 100644 --- a/man/E.Rd +++ b/man/E.Rd @@ -71,6 +71,7 @@ E(g2) \seealso{ Other vertex and edge sequences: \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/V.Rd b/man/V.Rd index 4d1e49048b..ef1cd750cc 100644 --- a/man/V.Rd +++ b/man/V.Rd @@ -64,6 +64,7 @@ V(g2) \seealso{ Other vertex and edge sequences: \code{\link{E}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/as_ids.Rd b/man/as_ids.Rd index 8d38ef8bfa..6574521678 100644 --- a/man/as_ids.Rd +++ b/man/as_ids.Rd @@ -41,3 +41,17 @@ V(g)$name <- letters[1:10] as_ids(V(g)) as_ids(E(g)) } +\seealso{ +Other vertex and edge sequences: +\code{\link{E}()}, +\code{\link{V}()}, +\code{\link{igraph-es-attributes}}, +\code{\link{igraph-es-indexing2}}, +\code{\link{igraph-es-indexing}}, +\code{\link{igraph-vs-attributes}}, +\code{\link{igraph-vs-indexing2}}, +\code{\link{igraph-vs-indexing}}, +\code{\link{print.igraph.es}()}, +\code{\link{print.igraph.vs}()} +} +\concept{vertex and edge sequences} diff --git a/man/igraph-es-attributes.Rd b/man/igraph-es-attributes.Rd index b7ecb446de..e111087e95 100644 --- a/man/igraph-es-attributes.Rd +++ b/man/igraph-es-attributes.Rd @@ -75,6 +75,7 @@ plot(g) Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, @@ -86,6 +87,7 @@ Other vertex and edge sequences: Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-es-indexing.Rd b/man/igraph-es-indexing.Rd index 8d4663a1fa..093de589a1 100644 --- a/man/igraph-es-indexing.Rd +++ b/man/igraph-es-indexing.Rd @@ -129,6 +129,7 @@ E(g)[.env$x] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-es-indexing2.Rd b/man/igraph-es-indexing2.Rd index 0e72acc4ec..d65c5f83b9 100644 --- a/man/igraph-es-indexing2.Rd +++ b/man/igraph-es-indexing2.Rd @@ -42,6 +42,7 @@ E(g)[[.inc("A")]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-vs-attributes.Rd b/man/igraph-vs-attributes.Rd index e63221834a..ffca5e8108 100644 --- a/man/igraph-vs-attributes.Rd +++ b/man/igraph-vs-attributes.Rd @@ -79,6 +79,7 @@ plot(g) Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/igraph-vs-indexing.Rd b/man/igraph-vs-indexing.Rd index 0db1978020..3c0dedba8f 100644 --- a/man/igraph-vs-indexing.Rd +++ b/man/igraph-vs-indexing.Rd @@ -144,6 +144,7 @@ V(g)[.env$x] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/igraph-vs-indexing2.Rd b/man/igraph-vs-indexing2.Rd index 8fec612ec5..854638f60a 100644 --- a/man/igraph-vs-indexing2.Rd +++ b/man/igraph-vs-indexing2.Rd @@ -41,6 +41,7 @@ V(g)[[1:5]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/print.igraph.es.Rd b/man/print.igraph.es.Rd index 5e5f15c1fb..24352a9918 100644 --- a/man/print.igraph.es.Rd +++ b/man/print.igraph.es.Rd @@ -57,6 +57,7 @@ E(g4)[[1:5]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/print.igraph.vs.Rd b/man/print.igraph.vs.Rd index 947944cfba..78ea896804 100644 --- a/man/print.igraph.vs.Rd +++ b/man/print.igraph.vs.Rd @@ -55,6 +55,7 @@ V(g4)[[2:5, 7:8]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, From db8e05e4c607c63a715321b951edefc0e7687ef2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:40:07 +0100 Subject: [PATCH 13/54] add authority_score() to centrality family --- R/centrality.R | 1 + man/alpha_centrality.Rd | 1 + man/arpack.Rd | 2 ++ man/authority_score.Rd | 15 +++++++++++++++ man/betweenness.Rd | 3 +++ man/closeness.Rd | 1 + man/diversity.Rd | 1 + man/eigen_centrality.Rd | 1 + man/harmonic_centrality.Rd | 1 + man/page_rank.Rd | 1 + man/power_centrality.Rd | 1 + man/spectrum.Rd | 1 + man/strength.Rd | 1 + man/subgraph_centrality.Rd | 1 + 14 files changed, 31 insertions(+) diff --git a/R/centrality.R b/R/centrality.R index d5320940e5..8aab24c196 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -955,6 +955,7 @@ hub_score <- hub_score #' g2 <- make_ring(10) #' hub_score(g2)$vector #' authority_score(g2)$vector +#' @family centrality authority_score <- authority_score diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 6f980120ec..8b3262501f 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -95,6 +95,7 @@ measures of centrality for asymmetric relations'' \emph{Social Networks}, Centrality measures \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/arpack.Rd b/man/arpack.Rd index aa876dbfb0..ea4af7ed49 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -220,6 +220,7 @@ functions in igraph that use ARPACK. Centrality measures \code{\link{alpha_centrality}()}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, @@ -233,6 +234,7 @@ Centrality measures Centrality measures \code{\link{alpha_centrality}()}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/authority_score.Rd b/man/authority_score.Rd index e1d040a658..db2b980bc2 100644 --- a/man/authority_score.Rd +++ b/man/authority_score.Rd @@ -65,4 +65,19 @@ as IBM Research Report RJ 10076, May 1997. eigenvector centrality, \code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for the underlining machinery of the computation. + +Centrality measures +\code{\link{alpha_centrality}()}, +\code{\link{arpack_defaults}}, +\code{\link{closeness}()}, +\code{\link{diversity}()}, +\code{\link{eigen_centrality}()}, +\code{\link{estimate_betweenness}()}, +\code{\link{harmonic_centrality}()}, +\code{\link{page_rank}()}, +\code{\link{power_centrality}()}, +\code{\link{spectrum}()}, +\code{\link{strength}()}, +\code{\link{subgraph_centrality}()} } +\concept{centrality} diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 64f6f71118..44e36a9489 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -136,6 +136,7 @@ of Mathematical Sociology} 25(2):163-177, 2001. Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, @@ -149,6 +150,7 @@ Centrality measures Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, @@ -162,6 +164,7 @@ Centrality measures Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/closeness.Rd b/man/closeness.Rd index 1ee2c66ef9..335c5e3894 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -91,6 +91,7 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239. Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index 4eea01e17e..ecbb4b513a 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -56,6 +56,7 @@ and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010. Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index f81fabbf74..02561bdaff 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -106,6 +106,7 @@ Measures. \emph{American Journal of Sociology}, 92, 1170-1182. Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{estimate_betweenness}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index f6cd880126..0f45a636dc 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -72,6 +72,7 @@ M. Marchiori and V. Latora, Harmony in the small-world, Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/page_rank.Rd b/man/page_rank.Rd index eebd971080..6a262f3874 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -112,6 +112,7 @@ Other centrality scores: \code{\link[=closeness]{closeness()}}, Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index cbc97928f6..ca739b311d 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -138,6 +138,7 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.'' Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/spectrum.Rd b/man/spectrum.Rd index 5408d3c59c..42253588f0 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -81,6 +81,7 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/strength.Rd b/man/strength.Rd index a3cc75a6a7..bc81b73102 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -58,6 +58,7 @@ Natl. Acad. Sci. USA 101, 3747 (2004) Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index 9c9ac33501..b4196dba50 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -48,6 +48,7 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005). Centrality measures \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, From f566e658bba33fa966d0a9fee028e8abd217d1f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:45:00 +0100 Subject: [PATCH 14/54] create topology title with isomorphism and automorphism as subtitles --- R/topology.R | 3 +++ _pkgdown.yml | 6 +++++- man/automorphism_group.Rd | 4 ++++ man/canonical_permutation.Rd | 11 +++++++++++ man/count_automorphisms.Rd | 4 ++++ man/count_isomorphisms.Rd | 1 + man/count_subgraph_isomorphisms.Rd | 1 + man/graph_from_isomorphism_class.Rd | 1 + man/isomorphic.Rd | 1 + man/isomorphism_class.Rd | 1 + man/isomorphisms.Rd | 1 + man/subgraph_isomorphic.Rd | 1 + man/subgraph_isomorphisms.Rd | 1 + 13 files changed, 35 insertions(+), 1 deletion(-) diff --git a/R/topology.R b/R/topology.R index af564f4f91..0a39ea1f1b 100644 --- a/R/topology.R +++ b/R/topology.R @@ -778,6 +778,7 @@ graph_from_isomorphism_class <- graph_from_isomorphism_class #' el1 <- el1[order(el1[, 1], el1[, 2]), ] #' el2 <- el2[order(el2[, 1], el2[, 2]), ] #' all(el1 == el2) +#' @family graph isomorphism #' @export canonical_permutation <- canonical_permutation @@ -881,6 +882,7 @@ permute <- permute #' ## matching by colors, leading to only 4 automorphisms #' g <- make_full_graph(4) #' count_automorphisms(g, colors = c(1, 2, 1, 2)) +#' @family graph automorphism #' @export count_automorphisms <- count_automorphisms @@ -939,5 +941,6 @@ count_automorphisms <- count_automorphisms #' ## "turns" the ring by one vertex to the left or right #' g <- make_ring(10) #' automorphism_group(g) +#' @family graph automorphism #' @export automorphism_group <- automorphism_group diff --git a/_pkgdown.yml b/_pkgdown.yml index 66db9f739b..c7acfb56e9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -167,9 +167,13 @@ reference: - title: Test - contents: - has_concept("test") -- title: Graph isomorphism +- title: Topology +- subtitle: Graph isomorphism - contents: - has_concept("graph isomorphism") +- subtitle: Graph automorphism +- contents: + - has_concept("graph automorphism") - title: Trees - contents: - has_concept("trees") diff --git a/man/automorphism_group.Rd b/man/automorphism_group.Rd index e6db9ccc2b..1def2b4d48 100644 --- a/man/automorphism_group.Rd +++ b/man/automorphism_group.Rd @@ -72,10 +72,14 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \seealso{ \code{\link[=canonical_permutation]{canonical_permutation()}}, \code{\link[=permute]{permute()}}, \code{\link[=count_automorphisms]{count_automorphisms()}} + +Other graph automorphism: +\code{\link{count_automorphisms}()} } \author{ Tommi Junttila (\url{http://users.ics.aalto.fi/tjunttil/}) for BLISS, Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph glue code and Tamas Nepusz \email{ntamas@gmail.com} for this manual page. } +\concept{graph automorphism} \keyword{graphs} diff --git a/man/canonical_permutation.Rd b/man/canonical_permutation.Rd index 8d28d06996..8d714e0991 100644 --- a/man/canonical_permutation.Rd +++ b/man/canonical_permutation.Rd @@ -89,9 +89,20 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \code{\link[=permute]{permute()}} to apply a permutation to a graph, \code{\link[=graph.isomorphic]{graph.isomorphic()}} for deciding graph isomorphism, possibly based on canonical labels. + +Other graph isomorphism: +\code{\link{count_isomorphisms}()}, +\code{\link{count_subgraph_isomorphisms}()}, +\code{\link{graph_from_isomorphism_class}()}, +\code{\link{isomorphic}()}, +\code{\link{isomorphism_class}()}, +\code{\link{isomorphisms}()}, +\code{\link{subgraph_isomorphic}()}, +\code{\link{subgraph_isomorphisms}()} } \author{ Tommi Junttila for BLISS, Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph and R interfaces. } +\concept{graph isomorphism} \keyword{graphs} diff --git a/man/count_automorphisms.Rd b/man/count_automorphisms.Rd index 195450cd0e..f980a2d8fe 100644 --- a/man/count_automorphisms.Rd +++ b/man/count_automorphisms.Rd @@ -71,10 +71,14 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \code{\link[=canonical_permutation]{canonical_permutation()}}, \code{\link[=permute]{permute()}}, and \code{\link[=automorphism_group]{automorphism_group()}} for a compact representation of all automorphisms + +Other graph automorphism: +\code{\link{automorphism_group}()} } \author{ Tommi Junttila (\url{http://users.ics.aalto.fi/tjunttil/}) for BLISS and Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph glue code and this manual page. } +\concept{graph automorphism} \keyword{graphs} diff --git a/man/count_isomorphisms.Rd b/man/count_isomorphisms.Rd index 23b82102fd..e449bb8253 100644 --- a/man/count_isomorphisms.Rd +++ b/man/count_isomorphisms.Rd @@ -46,6 +46,7 @@ on Graphbased Representations in Pattern Recognition}, 149--159, 2001. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, \code{\link{isomorphic}()}, diff --git a/man/count_subgraph_isomorphisms.Rd b/man/count_subgraph_isomorphisms.Rd index 5fd84c027b..6aae8240b4 100644 --- a/man/count_subgraph_isomorphisms.Rd +++ b/man/count_subgraph_isomorphisms.Rd @@ -78,6 +78,7 @@ C. Solnon: AllDifferent-based Filtering for Subgraph Isomorphism, } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, \code{\link{isomorphic}()}, diff --git a/man/graph_from_isomorphism_class.Rd b/man/graph_from_isomorphism_class.Rd index 86292c8798..df9b0f5a04 100644 --- a/man/graph_from_isomorphism_class.Rd +++ b/man/graph_from_isomorphism_class.Rd @@ -27,6 +27,7 @@ vertices and undirected graphd with 3 to 6 vertices. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{isomorphic}()}, diff --git a/man/isomorphic.Rd b/man/isomorphic.Rd index 5ed05c3a65..745a45c710 100644 --- a/man/isomorphic.Rd +++ b/man/isomorphic.Rd @@ -134,6 +134,7 @@ on Graphbased Representations in Pattern Recognition}, 149--159, 2001. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/isomorphism_class.Rd b/man/isomorphism_class.Rd index 45da27910a..5a485b06df 100644 --- a/man/isomorphism_class.Rd +++ b/man/isomorphism_class.Rd @@ -34,6 +34,7 @@ isomorphic(g1, g2) } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/isomorphisms.Rd b/man/isomorphisms.Rd index 75d004639e..95ffdf50ed 100644 --- a/man/isomorphisms.Rd +++ b/man/isomorphisms.Rd @@ -26,6 +26,7 @@ Calculate all isomorphic mappings between the vertices of two graphs } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/subgraph_isomorphic.Rd b/man/subgraph_isomorphic.Rd index 129f79b07f..cd5fa41a31 100644 --- a/man/subgraph_isomorphic.Rd +++ b/man/subgraph_isomorphic.Rd @@ -116,6 +116,7 @@ C. Solnon: AllDifferent-based Filtering for Subgraph Isomorphism, } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/subgraph_isomorphisms.Rd b/man/subgraph_isomorphisms.Rd index 021996d440..a36b15020b 100644 --- a/man/subgraph_isomorphisms.Rd +++ b/man/subgraph_isomorphisms.Rd @@ -68,6 +68,7 @@ supply \code{NULL} for both of these arguments.} \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, From 2c71a3761b141067ae4ba016bb5a6a169c2ea5ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 11:55:02 +0100 Subject: [PATCH 15/54] add more family tags in operators.R --- R/operators.R | 20 +++++++++++++++++ _pkgdown.yml | 2 +- man/add_edges.Rd | 11 ++++++++++ man/add_vertices.Rd | 11 ++++++++++ man/complementer.Rd | 23 ++++++++++++++++++++ man/compose.Rd | 23 ++++++++++++++++++++ man/delete_edges.Rd | 11 ++++++++++ man/delete_vertices.Rd | 11 ++++++++++ man/difference.Rd | 23 ++++++++++++++++++++ man/difference.igraph.Rd | 23 ++++++++++++++++++++ man/disjoint_union.Rd | 23 ++++++++++++++++++++ man/edge.Rd | 32 +++++++++++++++++++++++++++ man/igraph-minus.Rd | 11 ++++++++++ man/intersection.Rd | 23 ++++++++++++++++++++ man/intersection.igraph.Rd | 23 ++++++++++++++++++++ man/path.Rd | 11 ++++++++++ man/plus-.igraph.Rd | 11 ++++++++++ man/rep.igraph.Rd | 44 ++++++++++++++++++++++++++++++++++++++ man/reverse_edges.Rd | 44 ++++++++++++++++++++++++++++++++++++++ man/union.Rd | 23 ++++++++++++++++++++ man/union.igraph.Rd | 23 ++++++++++++++++++++ man/vertex.Rd | 34 ++++++++++++++++++++++++++++- 22 files changed, 458 insertions(+), 2 deletions(-) diff --git a/R/operators.R b/R/operators.R index e4a54bcda6..5a645efb1c 100644 --- a/R/operators.R +++ b/R/operators.R @@ -177,6 +177,7 @@ disjoint_union <- function(...) { #' @export #' @rdname disjoint_union +#' @family functions for manipulating graph structure "%du%" <- function(x, y) { disjoint_union(x, y) } @@ -297,12 +298,14 @@ disjoint_union <- function(...) { #' the function that implements `union()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export union <- function(...) { UseMethod("union") } #' @method union default +#' @family functions for manipulating graph structure #' @export union.default <- function(...) { base::union(...) @@ -343,6 +346,7 @@ union.default <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method union igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -361,6 +365,7 @@ union.igraph <- function(..., byname = "auto") { ) } +#' @family functions for manipulating graph structure #' @export "%u%" <- function(x, y) { union(x, y) @@ -379,6 +384,7 @@ union.igraph <- function(..., byname = "auto") { #' the function that implements `intersection()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export intersection <- function(...) { UseMethod("intersection") @@ -421,6 +427,7 @@ intersection <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method intersection igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -440,6 +447,7 @@ intersection.igraph <- function(..., byname = "auto", ) } +#' @family functions for manipulating graph structure #' @export "%s%" <- function(x, y) { intersection(x, y) @@ -458,6 +466,7 @@ intersection.igraph <- function(..., byname = "auto", #' the function that implements `difference()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export difference <- function(...) { UseMethod("difference") @@ -496,6 +505,7 @@ difference <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method difference igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -552,6 +562,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) { } } +#' @family functions for manipulating graph structure #' @export "%m%" <- function(x, y) { difference(x, y) @@ -576,6 +587,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) { #' @param loops Logical constant, whether to generate loop edges. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -651,6 +663,7 @@ complementer <- function(graph, loops = FALSE) { #' but not both graphs are named. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -727,6 +740,7 @@ compose <- function(g1, g2, byname = "auto") { res } +#' @family functions for manipulating graph structure #' @export "%c%" <- function(x, y) { compose(x, y) @@ -777,6 +791,7 @@ edge <- function(...) { structure(list(...), class = "igraph.edge") } +#' @family functions for manipulating graph structure #' @export #' @rdname edge edges <- edge @@ -813,6 +828,7 @@ vertex <- function(...) { structure(list(...), class = "igraph.vertex") } +#' @family functions for manipulating graph structure #' @export #' @rdname vertex vertices <- vertex @@ -1123,6 +1139,7 @@ path <- function(...) { #' currently ignored. #' #' @method rep igraph +#' @family functions for manipulating graph structure #' @export #' #' @examples @@ -1142,6 +1159,7 @@ rep.igraph <- function(x, n, mark = TRUE, ...) { #' @rdname rep.igraph #' @method * igraph +#' @family functions for manipulating graph structure #' @export `*.igraph` <- function(x, n) { if (!is_igraph(x) && is_igraph(n)) { @@ -1173,11 +1191,13 @@ rep.igraph <- function(x, n, mark = TRUE, ...) { #' #' g <- make_graph(~ 1 -+ 2, 2 -+ 3, 3 -+ 4) #' reverse_edges(g, 2) +#' @family functions for manipulating graph structure #' @export reverse_edges <- reverse_edges #' @rdname reverse_edges #' @param x The input graph. #' @method t igraph +#' @family functions for manipulating graph structure #' @export t.igraph <- function(x) reverse_edges(x) diff --git a/_pkgdown.yml b/_pkgdown.yml index c7acfb56e9..1056269fe8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -183,7 +183,7 @@ reference: - has_concept("versions") - title: Others - contents: - - lacks_concepts(c("adjacency", "graph attributes", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) + - lacks_concepts(c("adjacency", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) - title: internal - contents: - has_concept("nexus") diff --git a/man/add_edges.Rd b/man/add_edges.Rd index 804028b90e..94b57d37cb 100644 --- a/man/add_edges.Rd +++ b/man/add_edges.Rd @@ -51,11 +51,22 @@ plot(g) Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/add_vertices.Rd b/man/add_vertices.Rd index d692626e80..de2979130e 100644 --- a/man/add_vertices.Rd +++ b/man/add_vertices.Rd @@ -46,11 +46,22 @@ plot(g) Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/complementer.Rd b/man/complementer.Rd index 21a95c4b3b..ac8f7b6a31 100644 --- a/man/complementer.Rd +++ b/man/complementer.Rd @@ -40,8 +40,31 @@ gu <- union(g, gc) gu graph.isomorphic(gu, make_full_graph(vcount(g))) +} +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/compose.Rd b/man/compose.Rd index e03bc87675..15bd33bba9 100644 --- a/man/compose.Rd +++ b/man/compose.Rd @@ -70,8 +70,31 @@ gc <- compose(g1, g2) print_all(gc) print_all(simplify(gc)) +} +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/delete_edges.Rd b/man/delete_edges.Rd index c907ca1ec8..b35fa9b6c6 100644 --- a/man/delete_edges.Rd +++ b/man/delete_edges.Rd @@ -39,10 +39,21 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/delete_vertices.Rd b/man/delete_vertices.Rd index beb5f88a68..ecd16181f4 100644 --- a/man/delete_vertices.Rd +++ b/man/delete_vertices.Rd @@ -34,10 +34,21 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/difference.Rd b/man/difference.Rd index b256d9a1ca..aa2ffc2512 100644 --- a/man/difference.Rd +++ b/man/difference.Rd @@ -21,3 +21,26 @@ and igraph vertex and edge sequences. See \code{\link[=difference.igraph]{difference.igraph()}}, and \code{\link[=difference.igraph.vs]{difference.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/difference.igraph.Rd b/man/difference.igraph.Rd index 0582635bea..a84560564d 100644 --- a/man/difference.igraph.Rd +++ b/man/difference.igraph.Rd @@ -60,7 +60,30 @@ G <- wheel \%m\% sstar print_all(G) plot(G, layout = layout_nicely(wheel)) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/disjoint_union.Rd b/man/disjoint_union.Rd index 6f362d602e..f16f7bf875 100644 --- a/man/disjoint_union.Rd +++ b/man/disjoint_union.Rd @@ -51,7 +51,30 @@ g2 <- make_ring(10) V(g2)$name <- letters[11:20] print_all(g1 \%du\% g2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/edge.Rd b/man/edge.Rd index 9e25de22cb..a015be3489 100644 --- a/man/edge.Rd +++ b/man/edge.Rd @@ -55,10 +55,42 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/igraph-minus.Rd b/man/igraph-minus.Rd index 46df8249f0..115f53b3de 100644 --- a/man/igraph-minus.Rd +++ b/man/igraph-minus.Rd @@ -61,10 +61,21 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/intersection.Rd b/man/intersection.Rd index 40e6910b7a..b85da21edf 100644 --- a/man/intersection.Rd +++ b/man/intersection.Rd @@ -21,3 +21,26 @@ sequences. See \code{\link[=intersection.igraph]{intersection.igraph()}}, and \code{\link[=intersection.igraph.vs]{intersection.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/intersection.igraph.Rd b/man/intersection.igraph.Rd index 4f97995efe..1219bcaf31 100644 --- a/man/intersection.igraph.Rd +++ b/man/intersection.igraph.Rd @@ -58,7 +58,30 @@ net1 <- graph_from_literal( net2 <- graph_from_literal(D - A:F:Y, B - A - X - F - H - Z, F - Y) print_all(net1 \%s\% net2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/path.Rd b/man/path.Rd index 5fa00017dd..8a9de91239 100644 --- a/man/path.Rd +++ b/man/path.Rd @@ -49,10 +49,21 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/plus-.igraph.Rd b/man/plus-.igraph.Rd index aab9a78957..abfae59451 100644 --- a/man/plus-.igraph.Rd +++ b/man/plus-.igraph.Rd @@ -105,11 +105,22 @@ plot(g) Other functions for manipulating graph structure: \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/rep.igraph.Rd b/man/rep.igraph.Rd index beba58c15b..1fa3c6e3d5 100644 --- a/man/rep.igraph.Rd +++ b/man/rep.igraph.Rd @@ -28,3 +28,47 @@ of times, as unconnected components. \examples{ rings <- make_ring(5) * 5 } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/reverse_edges.Rd b/man/reverse_edges.Rd index 5af0656fef..ad949f2850 100644 --- a/man/reverse_edges.Rd +++ b/man/reverse_edges.Rd @@ -31,3 +31,47 @@ all edges, this operation is also known as graph transpose. g <- make_graph(~ 1 -+ 2, 2 -+ 3, 3 -+ 4) reverse_edges(g, 2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/union.Rd b/man/union.Rd index 46d6f04a27..b0de5cf2d1 100644 --- a/man/union.Rd +++ b/man/union.Rd @@ -21,3 +21,26 @@ sequences. See \code{\link[=union.igraph]{union.igraph()}}, and \code{\link[=union.igraph.vs]{union.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/union.igraph.Rd b/man/union.igraph.Rd index c5c14c328d..a9ea1b0eb8 100644 --- a/man/union.igraph.Rd +++ b/man/union.igraph.Rd @@ -55,7 +55,30 @@ net1 <- graph_from_literal( net2 <- graph_from_literal(D - A:F:Y, B - A - X - F - H - Z, F - Y) print_all(net1 \%u\% net2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/vertex.Rd b/man/vertex.Rd index b5f1d5dc54..5467d790cd 100644 --- a/man/vertex.Rd +++ b/man/vertex.Rd @@ -42,10 +42,42 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, -\code{\link{path}()} +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()} } \concept{functions for manipulating graph structure} From be0a104a3543472880ca0b3de8703d9cbc13dc35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:04:41 +0100 Subject: [PATCH 16/54] add two functions to modifiers --- R/make.R | 2 ++ man/dot-apply_modifiers.Rd | 12 ++++++++++++ man/dot-extract_constructor_and_modifiers.Rd | 12 ++++++++++++ man/simplified.Rd | 2 ++ man/with_edge_.Rd | 2 ++ man/with_graph_.Rd | 2 ++ man/with_vertex_.Rd | 2 ++ man/without_attr.Rd | 2 ++ man/without_loops.Rd | 2 ++ man/without_multiples.Rd | 2 ++ 10 files changed, 40 insertions(+) diff --git a/R/make.R b/R/make.R index 3b2d405b16..a6d9694bba 100644 --- a/R/make.R +++ b/R/make.R @@ -34,6 +34,7 @@ #' @param .variant Constructor variant; must be one of \sQuote{make}, #' \sQuote{graph} or \sQuote{sample}. Used in cases when the same constructor #' specification has deterministic and random variants. +#' @family constructor modifiers #' @return A named list with three items: \sQuote{cons} for the constructor #' function, \sQuote{mods} for the modifiers and \sQuote{args} for the #' remaining, unparsed arguments. @@ -83,6 +84,7 @@ #' #' @param graph The graph to apply the modifiers to #' @param mods The modifiers to apply +#' @family constructor modifiers #' @return The modified graph .apply_modifiers <- function(graph, mods) { for (m in mods) { diff --git a/man/dot-apply_modifiers.Rd b/man/dot-apply_modifiers.Rd index bab4f19786..062de7e0de 100644 --- a/man/dot-apply_modifiers.Rd +++ b/man/dot-apply_modifiers.Rd @@ -18,3 +18,15 @@ The modified graph This is a helper function for the common parts of \code{make_()} and \code{sample_()}. } +\seealso{ +Other constructor modifiers: +\code{\link{.extract_constructor_and_modifiers}()}, +\code{\link{simplified}()}, +\code{\link{with_edge_}()}, +\code{\link{with_graph_}()}, +\code{\link{with_vertex_}()}, +\code{\link{without_attr}()}, +\code{\link{without_loops}()}, +\code{\link{without_multiples}()} +} +\concept{constructor modifiers} diff --git a/man/dot-extract_constructor_and_modifiers.Rd b/man/dot-extract_constructor_and_modifiers.Rd index 15b2a21db9..a9fc68bce9 100644 --- a/man/dot-extract_constructor_and_modifiers.Rd +++ b/man/dot-extract_constructor_and_modifiers.Rd @@ -26,3 +26,15 @@ remaining, unparsed arguments. This is a helper function for the common parts of \code{make_()} and \code{sample_()}. } +\seealso{ +Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{simplified}()}, +\code{\link{with_edge_}()}, +\code{\link{with_graph_}()}, +\code{\link{with_vertex_}()}, +\code{\link{without_attr}()}, +\code{\link{without_loops}()}, +\code{\link{without_multiples}()} +} +\concept{constructor modifiers} diff --git a/man/simplified.Rd b/man/simplified.Rd index 6a54cdf4fc..0ff9616874 100644 --- a/man/simplified.Rd +++ b/man/simplified.Rd @@ -15,6 +15,8 @@ sample_(pa(10, m = 3, algorithm = "bag"), simplified()) } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{with_edge_}()}, \code{\link{with_graph_}()}, \code{\link{with_vertex_}()}, diff --git a/man/with_edge_.Rd b/man/with_edge_.Rd index 57cf889742..258046812e 100644 --- a/man/with_edge_.Rd +++ b/man/with_edge_.Rd @@ -24,6 +24,8 @@ make_( } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_graph_}()}, \code{\link{with_vertex_}()}, diff --git a/man/with_graph_.Rd b/man/with_graph_.Rd index f44aef642b..ac0c5e97c6 100644 --- a/man/with_graph_.Rd +++ b/man/with_graph_.Rd @@ -17,6 +17,8 @@ make_(ring(10), with_graph_(name = "10-ring")) } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_edge_}()}, \code{\link{with_vertex_}()}, diff --git a/man/with_vertex_.Rd b/man/with_vertex_.Rd index 2f053a6f55..9dbb56968a 100644 --- a/man/with_vertex_.Rd +++ b/man/with_vertex_.Rd @@ -25,6 +25,8 @@ make_( } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_edge_}()}, \code{\link{with_graph_}()}, diff --git a/man/without_attr.Rd b/man/without_attr.Rd index 418bc1c7e6..c853dbb4eb 100644 --- a/man/without_attr.Rd +++ b/man/without_attr.Rd @@ -18,6 +18,8 @@ g2 } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_edge_}()}, \code{\link{with_graph_}()}, diff --git a/man/without_loops.Rd b/man/without_loops.Rd index 778cf76d31..139ae85e91 100644 --- a/man/without_loops.Rd +++ b/man/without_loops.Rd @@ -16,6 +16,8 @@ make_(full_graph(5, loops = TRUE), without_loops()) } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_edge_}()}, \code{\link{with_graph_}()}, diff --git a/man/without_multiples.Rd b/man/without_multiples.Rd index 8f35859255..4a1c181b24 100644 --- a/man/without_multiples.Rd +++ b/man/without_multiples.Rd @@ -15,6 +15,8 @@ sample_(pa(10, m = 3, algorithm = "bag"), without_multiples()) } \seealso{ Other constructor modifiers: +\code{\link{.apply_modifiers}()}, +\code{\link{.extract_constructor_and_modifiers}()}, \code{\link{simplified}()}, \code{\link{with_edge_}()}, \code{\link{with_graph_}()}, From f660b1b72e6195673d8542007e0fe5be61b06482 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:08:11 +0100 Subject: [PATCH 17/54] add missing family tag --- R/motifs.R | 1 + man/count_motifs.Rd | 1 + man/dyad_census.Rd | 6 ++++++ man/motifs.Rd | 1 + man/sample_motifs.Rd | 1 + src/Makevars | 4 ++-- 6 files changed, 12 insertions(+), 2 deletions(-) diff --git a/R/motifs.R b/R/motifs.R index b3e1c4e165..b09b02d48b 100644 --- a/R/motifs.R +++ b/R/motifs.R @@ -195,6 +195,7 @@ sample_motifs <- function(graph, size = 3, cut.prob = rep(0, size), #' #' g <- sample_pa(100) #' dyad_census(g) +#' @family graph motifs #' @export dyad_census <- dyad_census diff --git a/man/count_motifs.Rd b/man/count_motifs.Rd index b33d1e9957..8b736dd916 100644 --- a/man/count_motifs.Rd +++ b/man/count_motifs.Rd @@ -37,6 +37,7 @@ sample_motifs(g, 3) \code{\link[=isomorphism_class]{isomorphism_class()}} Other graph motifs: +\code{\link{dyad_census}()}, \code{\link{motifs}()}, \code{\link{sample_motifs}()} } diff --git a/man/dyad_census.Rd b/man/dyad_census.Rd index a880a5878f..a3f261eb78 100644 --- a/man/dyad_census.Rd +++ b/man/dyad_census.Rd @@ -37,8 +37,14 @@ Applications.} Cambridge: Cambridge University Press. 1994. \seealso{ \code{\link[=triad_census]{triad_census()}} for the same classification, but with triples. + +Other graph motifs: +\code{\link{count_motifs}()}, +\code{\link{motifs}()}, +\code{\link{sample_motifs}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{graph motifs} \keyword{graphs} diff --git a/man/motifs.Rd b/man/motifs.Rd index a87ad35f62..2b7bd5d667 100644 --- a/man/motifs.Rd +++ b/man/motifs.Rd @@ -44,6 +44,7 @@ sample_motifs(g, 3) Other graph motifs: \code{\link{count_motifs}()}, +\code{\link{dyad_census}()}, \code{\link{sample_motifs}()} } \concept{graph motifs} diff --git a/man/sample_motifs.Rd b/man/sample_motifs.Rd index 72f3428e79..fc767cd154 100644 --- a/man/sample_motifs.Rd +++ b/man/sample_motifs.Rd @@ -52,6 +52,7 @@ sample_motifs(g, 3) Other graph motifs: \code{\link{count_motifs}()}, +\code{\link{dyad_census}()}, \code{\link{motifs}()} } \concept{graph motifs} diff --git a/src/Makevars b/src/Makevars index d9535e9849..fc864eb796 100644 --- a/src/Makevars +++ b/src/Makevars @@ -5,10 +5,10 @@ PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT \ + -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ -DINTERNAL_ARPACK \ -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) all: $(SHLIB) From a0a44698a4144e235b6fa5ffa64a9a1544df5f28 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:10:04 +0100 Subject: [PATCH 18/54] embedding family --- R/embedding.R | 2 ++ _pkgdown.yml | 9 +++++---- man/dim_select.Rd | 4 ++++ man/embed_adjacency_matrix.Rd | 4 ++++ 4 files changed, 15 insertions(+), 4 deletions(-) diff --git a/R/embedding.R b/R/embedding.R index deb923e296..96a6d4b7ba 100644 --- a/R/embedding.R +++ b/R/embedding.R @@ -88,6 +88,7 @@ #' }) #' RDP <- sample_dot_product(lpvs) #' embed <- embed_adjacency_matrix(RDP, 5) +#' @family embedding #' @export embed_adjacency_matrix <- embed_adjacency_matrix @@ -148,6 +149,7 @@ embed_adjacency_matrix <- embed_adjacency_matrix #' RDP.graph.3 <- sample_dot_product(lpvs.sph) #' dim_select(embed_adjacency_matrix(RDP.graph.3, 10)$D) #' +#' @family embedding #' @export dim_select <- dim_select diff --git a/_pkgdown.yml b/_pkgdown.yml index 1056269fe8..8667df0be1 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -140,6 +140,9 @@ reference: - title: Spectral Coarse Graining - contents: - has_concept("scg") +- title: Embedding +- contents: + - has_concept("embedding") - title: Graph matching - contents: - has_concept("sgm") @@ -164,9 +167,6 @@ reference: - title: Structural queries - contents: - has_concept("structural queries") -- title: Test -- contents: - - has_concept("test") - title: Topology - subtitle: Graph isomorphism - contents: @@ -183,7 +183,8 @@ reference: - has_concept("versions") - title: Others - contents: - - lacks_concepts(c("adjacency", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) + - lacks_concepts(c("adjacency", "attributes", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) - title: internal - contents: - has_concept("nexus") + - has_concept("test") diff --git a/man/dim_select.Rd b/man/dim_select.Rd index 5526b12f31..6c916654f7 100644 --- a/man/dim_select.Rd +++ b/man/dim_select.Rd @@ -68,8 +68,12 @@ Statistics and Data Analysis}, Vol. 51, 918--930. } \seealso{ \code{\link[=embed_adjacency_matrix]{embed_adjacency_matrix()}} + +Other embedding: +\code{\link{embed_adjacency_matrix}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{embedding} \keyword{graphs} diff --git a/man/embed_adjacency_matrix.Rd b/man/embed_adjacency_matrix.Rd index ceb518b384..3fde7ccf5b 100644 --- a/man/embed_adjacency_matrix.Rd +++ b/man/embed_adjacency_matrix.Rd @@ -93,5 +93,9 @@ Consistent Adjacency Spectral Embedding for Stochastic Blockmodel Graphs, } \seealso{ \code{\link[=sample_dot_product]{sample_dot_product()}} + +Other embedding: +\code{\link{dim_select}()} } +\concept{embedding} \keyword{graphs} From 236337d8f96b40edb492cfbf884574ae6a4491e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:17:36 +0100 Subject: [PATCH 19/54] tweaks --- _pkgdown.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 8667df0be1..4d173d33f3 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -15,6 +15,10 @@ reference: - contents: - as.igraph - graph_from_lcf + - graph_ +- title: Utilities +- contents: + - graph_id - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -68,11 +72,11 @@ reference: - has_concept("env-and-data") - title: Processes on graphs - contents: - - has_concept("epi") + - has_concept("processes") - has_concept("random_walk") - title: Graph cycles - contents: - - has_concept("eulerian") + - has_concept("cycles") - title: Fit - contents: - has_concept("fit") @@ -183,7 +187,7 @@ reference: - has_concept("versions") - title: Others - contents: - - lacks_concepts(c("adjacency", "attributes", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) + - lacks_concepts(c("adjacency", "attributes", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "processes", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) - title: internal - contents: - has_concept("nexus") From 06cced46fd9eb6066e3dc894e02d64dad799b1eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:22:14 +0100 Subject: [PATCH 20/54] add hub_score in centrality --- R/centrality.R | 1 + man/alpha_centrality.Rd | 1 + man/arpack.Rd | 2 ++ man/authority_score.Rd | 1 + man/betweenness.Rd | 3 +++ man/closeness.Rd | 1 + man/diversity.Rd | 1 + man/eigen_centrality.Rd | 1 + man/harmonic_centrality.Rd | 1 + man/hub_score.Rd | 16 ++++++++++++++++ man/page_rank.Rd | 1 + man/power_centrality.Rd | 1 + man/spectrum.Rd | 1 + man/strength.Rd | 1 + man/subgraph_centrality.Rd | 1 + 15 files changed, 33 insertions(+) diff --git a/R/centrality.R b/R/centrality.R index 8aab24c196..d1ee482c51 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -904,6 +904,7 @@ diversity <- diversity #' ## A ring #' g2 <- make_ring(10) #' hub_score(g2)$vector +#' @family centrality hub_score <- hub_score diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 8b3262501f..4c477513c8 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -101,6 +101,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/arpack.Rd b/man/arpack.Rd index ea4af7ed49..aa58a943a8 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -226,6 +226,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, @@ -240,6 +241,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/authority_score.Rd b/man/authority_score.Rd index db2b980bc2..b7c7c9add6 100644 --- a/man/authority_score.Rd +++ b/man/authority_score.Rd @@ -74,6 +74,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 44e36a9489..cc5ab996a2 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -141,6 +141,7 @@ Centrality measures \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, @@ -155,6 +156,7 @@ Centrality measures \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, @@ -169,6 +171,7 @@ Centrality measures \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/closeness.Rd b/man/closeness.Rd index 335c5e3894..b7587d2da0 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -96,6 +96,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index ecbb4b513a..1be804a923 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -61,6 +61,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index 02561bdaff..df989a0679 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -111,6 +111,7 @@ Centrality measures \code{\link{diversity}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index 0f45a636dc..bc2249e8f8 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -77,6 +77,7 @@ Centrality measures \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/hub_score.Rd b/man/hub_score.Rd index 7981918ccc..69e993d124 100644 --- a/man/hub_score.Rd +++ b/man/hub_score.Rd @@ -63,4 +63,20 @@ as IBM Research Report RJ 10076, May 1997. \code{\link[=eigen_centrality]{eigen_centrality()}} for eigenvector centrality, \code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for the underlining machinery of the computation. + +Centrality measures +\code{\link{alpha_centrality}()}, +\code{\link{arpack_defaults}}, +\code{\link{authority_score}()}, +\code{\link{closeness}()}, +\code{\link{diversity}()}, +\code{\link{eigen_centrality}()}, +\code{\link{estimate_betweenness}()}, +\code{\link{harmonic_centrality}()}, +\code{\link{page_rank}()}, +\code{\link{power_centrality}()}, +\code{\link{spectrum}()}, +\code{\link{strength}()}, +\code{\link{subgraph_centrality}()} } +\concept{centrality} diff --git a/man/page_rank.Rd b/man/page_rank.Rd index 6a262f3874..c3e8ea81e5 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -118,6 +118,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, \code{\link{strength}()}, diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index ca739b311d..e06107d313 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -144,6 +144,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{spectrum}()}, \code{\link{strength}()}, diff --git a/man/spectrum.Rd b/man/spectrum.Rd index 42253588f0..b5ee09d396 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -87,6 +87,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{strength}()}, diff --git a/man/strength.Rd b/man/strength.Rd index bc81b73102..86fd457bc9 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -64,6 +64,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index b4196dba50..cb5128c0bd 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -54,6 +54,7 @@ Centrality measures \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, From 22a8294b870790bff76101db83064454c7eeab80 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 12:57:44 +0100 Subject: [PATCH 21/54] no more "other" --- R/aaa-auto.R | 1 + R/attributes.R | 2 ++ R/flow.R | 1 + R/motifs.R | 1 + R/paths.R | 1 + R/scg.R | 2 ++ _pkgdown.yml | 42 +++++++++++++++++++++++++---- man/all_simple_paths.Rd | 1 + man/bipartite_mapping.Rd | 3 ++- man/bipartite_projection.Rd | 3 ++- man/delete_edge_attr.Rd | 1 + man/delete_graph_attr.Rd | 1 + man/delete_vertex_attr.Rd | 1 + man/distances.Rd | 1 + man/dominator_tree.Rd | 1 + man/eccentricity.Rd | 1 + man/edge_attr-set.Rd | 1 + man/edge_attr.Rd | 1 + man/edge_attr_names.Rd | 1 + man/edge_connectivity.Rd | 1 + man/graph_attr-set.Rd | 1 + man/graph_attr.Rd | 1 + man/graph_attr_names.Rd | 1 + man/igraph-attribute-combination.Rd | 20 ++++++++++++++ man/igraph-dollar.Rd | 1 + man/igraph-vs-attributes.Rd | 1 + man/is_dag.Rd | 1 + man/is_min_separator.Rd | 1 + man/is_separator.Rd | 1 + man/make_bipartite_graph.Rd | 5 ++++ man/max_cardinality.Rd | 8 ++++++ man/max_flow.Rd | 1 + man/min_cut.Rd | 1 + man/min_separators.Rd | 1 + man/min_st_separators.Rd | 14 ++++++++++ man/radius.Rd | 3 ++- man/scg-method.Rd | 9 +++++++ man/scg.Rd | 2 ++ man/scg_eps.Rd | 8 ++++++ man/scg_group.Rd | 2 ++ man/scg_semi_proj.Rd | 2 ++ man/set_edge_attr.Rd | 1 + man/set_graph_attr.Rd | 1 + man/set_vertex_attr.Rd | 1 + man/st_cuts.Rd | 1 + man/st_min_cuts.Rd | 1 + man/stochastic_matrix.Rd | 2 ++ man/triad_census.Rd | 1 + man/vertex_attr-set.Rd | 1 + man/vertex_attr.Rd | 1 + man/vertex_attr_names.Rd | 1 + man/vertex_connectivity.Rd | 2 ++ src/Makevars | 4 +-- 53 files changed, 158 insertions(+), 10 deletions(-) diff --git a/R/aaa-auto.R b/R/aaa-auto.R index 287beb96fa..0c0694749d 100644 --- a/R/aaa-auto.R +++ b/R/aaa-auto.R @@ -2143,6 +2143,7 @@ embed_adjacency_matrix <- function(graph, no, weights=NULL, which=c("lm", "la", res } +#' @family embedding #' @export embed_laplacian_matrix <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), type=c("default", "D-A", "DAD", "I-DAD", "OAP"), scaled=TRUE, options=igraph.arpack.default) { # Argument checks diff --git a/R/attributes.R b/R/attributes.R index 8dbb74294f..24e4af01bb 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -809,6 +809,7 @@ is_weighted <- function(graph) { } #' @rdname make_bipartite_graph +#' @family bipartite #' @export is_bipartite <- function(graph) { if (!is_igraph(graph)) { @@ -895,6 +896,7 @@ igraph.i.attribute.combination <- function(comb) { #' new edge should be sum of the weights of the corresponding edges in the old #' graph; and that the rest of the attributes should be ignored (=dropped). #' +#' @family attributes #' @name igraph-attribute-combination #' @aliases attribute.combination #' @section Predefined combination functions: The following combination diff --git a/R/flow.R b/R/flow.R index 089774d93f..ed77178013 100644 --- a/R/flow.R +++ b/R/flow.R @@ -614,6 +614,7 @@ dominator_tree <- function(graph, root, mode = c("out", "in", "all", "total")) { #' #' chvatal <- make_graph("chvatal") #' min_st_separators(chvatal) +#' @family flow min_st_separators <- min_st_separators diff --git a/R/motifs.R b/R/motifs.R index b09b02d48b..76cdb735a3 100644 --- a/R/motifs.R +++ b/R/motifs.R @@ -236,5 +236,6 @@ dyad_census <- dyad_census #' #' g <- sample_gnm(15, 45, directed = TRUE) #' triad_census(g) +#' @family motifs #' @export triad_census <- triad_census diff --git a/R/paths.R b/R/paths.R index b85f53fcaf..a6c28c7f6d 100644 --- a/R/paths.R +++ b/R/paths.R @@ -157,6 +157,7 @@ is_dag <- is_dag #' ) #' max_cardinality(g2) #' is_chordal(g2, fillin = TRUE) +#' @family paths max_cardinality <- max_cardinality diff --git a/R/scg.R b/R/scg.R index e3d856d9fa..3bc9d02ec9 100644 --- a/R/scg.R +++ b/R/scg.R @@ -26,6 +26,7 @@ #' graphs. #' #' @name scg-method +#' @family scg #' @section Introduction: The SCG functions provide a framework, called #' Spectral Coarse Graining (SCG), for reducing large graphs while preserving #' their *spectral-related features*, that is features closely related @@ -841,4 +842,5 @@ myscg <- function(graph, matrix, sparsemat, ev, nt, groups = NULL, #' km <- kmeans(v, 5) #' sum(km$withinss) #' scg_eps(cbind(v), km$cluster)^2 +#' @family scg scg_eps <- scg_eps diff --git a/_pkgdown.yml b/_pkgdown.yml index 4d173d33f3..f7b10518c3 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -7,6 +7,8 @@ reference: - title: Construction - subtitle: Deterministic constructors - contents: + - starts_with("make_") + - realize_degseq - has_concept("deterministic constructors") - subtitle: Constructor modifiers - contents: @@ -17,8 +19,18 @@ reference: - graph_from_lcf - graph_ - title: Utilities +- subtitle: Utilities - contents: - graph_id + - identical_graphs + - is_igraph + - is_named + - is_weighted +- subtitle: Printing +- contents: + - head_print + - indent_print + - printr - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -64,9 +76,19 @@ reference: - title: Demo - contents: - has_concept("demo") -- title: Latent position vector samplers +- title: Sampling +- subtitle: Latent position vector samplers - contents: - has_concept("latent position vector samplers") +- subtitle: Other samplers +- contents: + - sample_ + - sample_correlated_gnp_pair + - sample_fitness + - sample_fitness_pl + - sample_forestfire + - sample_tree + - sample_correlated_gnp - title: Env and data - contents: - has_concept("env-and-data") @@ -112,11 +134,16 @@ reference: - has_concept("layout_drl") - has_concept("palettes") - has_concept("plot") + - igraph.plotting + - plot_dendrogram.igraphHRG + - plot_dendrogram - has_concept("plot.common") - has_concept("plot.shapes") -- title: Graph motifs + - vertex.shape.pie +- title: Graph motifs and subgraphs - contents: - has_concept("graph motifs") + - triad_census - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -147,6 +174,7 @@ reference: - title: Embedding - contents: - has_concept("embedding") + - embed_laplacian_matrix - title: Graph matching - contents: - has_concept("sgm") @@ -175,6 +203,7 @@ reference: - subtitle: Graph isomorphism - contents: - has_concept("graph isomorphism") + - permute - subtitle: Graph automorphism - contents: - has_concept("graph automorphism") @@ -185,10 +214,13 @@ reference: - title: Versions - contents: - has_concept("versions") -- title: Others -- contents: - - lacks_concepts(c("adjacency", "attributes", "graph automorphism", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "processes", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) - title: internal - contents: + - igraph-package - has_concept("nexus") - has_concept("test") + - layout.reingold.tilford + - layout.fruchterman.reingold.grid + - layout.spring + - layout.svd + - "%>%" diff --git a/man/all_simple_paths.Rd b/man/all_simple_paths.Rd index 3613d4a84e..2a4f3a0d3c 100644 --- a/man/all_simple_paths.Rd +++ b/man/all_simple_paths.Rd @@ -57,6 +57,7 @@ Other paths: \code{\link{distance_table}()}, \code{\link{eccentricity}()}, \code{\link{is_dag}()}, +\code{\link{max_cardinality}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/bipartite_mapping.Rd b/man/bipartite_mapping.Rd index 5a07465514..d5a3f0c599 100644 --- a/man/bipartite_mapping.Rd +++ b/man/bipartite_mapping.Rd @@ -53,7 +53,8 @@ bipartite_mapping(g3) } \seealso{ Bipartite graphs -\code{\link{bipartite_projection}()} +\code{\link{bipartite_projection}()}, +\code{\link{is_bipartite}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/bipartite_projection.Rd b/man/bipartite_projection.Rd index f0f256ca49..dc009fb2f9 100644 --- a/man/bipartite_projection.Rd +++ b/man/bipartite_projection.Rd @@ -91,7 +91,8 @@ print(proj2[[2]], g = TRUE, e = TRUE) } \seealso{ Bipartite graphs -\code{\link{bipartite_mapping}()} +\code{\link{bipartite_mapping}()}, +\code{\link{is_bipartite}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/delete_edge_attr.Rd b/man/delete_edge_attr.Rd index 365f561b97..933d737cd9 100644 --- a/man/delete_edge_attr.Rd +++ b/man/delete_edge_attr.Rd @@ -35,6 +35,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/delete_graph_attr.Rd b/man/delete_graph_attr.Rd index 10d981c7ed..cb185a78dd 100644 --- a/man/delete_graph_attr.Rd +++ b/man/delete_graph_attr.Rd @@ -34,6 +34,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/delete_vertex_attr.Rd b/man/delete_vertex_attr.Rd index f7d83846b4..3852e56e99 100644 --- a/man/delete_vertex_attr.Rd +++ b/man/delete_vertex_attr.Rd @@ -35,6 +35,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/distances.Rd b/man/distances.Rd index 85507de472..2d5e278300 100644 --- a/man/distances.Rd +++ b/man/distances.Rd @@ -263,6 +263,7 @@ Other paths: \code{\link{all_simple_paths}()}, \code{\link{eccentricity}()}, \code{\link{is_dag}()}, +\code{\link{max_cardinality}()}, \code{\link{radius}()} Other structural.properties: diff --git a/man/dominator_tree.Rd b/man/dominator_tree.Rd index cae1865969..817f5a2147 100644 --- a/man/dominator_tree.Rd +++ b/man/dominator_tree.Rd @@ -73,6 +73,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/eccentricity.Rd b/man/eccentricity.Rd index 9f7a5f1683..ed00536c23 100644 --- a/man/eccentricity.Rd +++ b/man/eccentricity.Rd @@ -50,6 +50,7 @@ Other paths: \code{\link{all_simple_paths}()}, \code{\link{distance_table}()}, \code{\link{is_dag}()}, +\code{\link{max_cardinality}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/edge_attr-set.Rd b/man/edge_attr-set.Rd index 859a7a7dd4..7b14870552 100644 --- a/man/edge_attr-set.Rd +++ b/man/edge_attr-set.Rd @@ -46,6 +46,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/edge_attr.Rd b/man/edge_attr.Rd index f6ace0583b..3782d28951 100644 --- a/man/edge_attr.Rd +++ b/man/edge_attr.Rd @@ -41,6 +41,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/edge_attr_names.Rd b/man/edge_attr_names.Rd index 4f549c3095..c51a641cb8 100644 --- a/man/edge_attr_names.Rd +++ b/man/edge_attr_names.Rd @@ -32,6 +32,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/edge_connectivity.Rd b/man/edge_connectivity.Rd index 4aa7618b1c..1be9805cc6 100644 --- a/man/edge_connectivity.Rd +++ b/man/edge_connectivity.Rd @@ -88,6 +88,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/graph_attr-set.Rd b/man/graph_attr-set.Rd index 342d31b824..8f0e6d340c 100644 --- a/man/graph_attr-set.Rd +++ b/man/graph_attr-set.Rd @@ -43,6 +43,7 @@ Vertex, edge and graph attributes \code{\link{edge_attr}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/graph_attr.Rd b/man/graph_attr.Rd index 864e71482a..24da90ff98 100644 --- a/man/graph_attr.Rd +++ b/man/graph_attr.Rd @@ -35,6 +35,7 @@ Vertex, edge and graph attributes \code{\link{edge_attr}()}, \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/graph_attr_names.Rd b/man/graph_attr_names.Rd index 5909263778..8a91c0b3b1 100644 --- a/man/graph_attr_names.Rd +++ b/man/graph_attr_names.Rd @@ -31,6 +31,7 @@ Vertex, edge and graph attributes \code{\link{edge_attr}()}, \code{\link{graph_attr<-}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/igraph-attribute-combination.Rd b/man/igraph-attribute-combination.Rd index 444554ab5d..2afea5b1b7 100644 --- a/man/igraph-attribute-combination.Rd +++ b/man/igraph-attribute-combination.Rd @@ -105,8 +105,28 @@ simplify(g, edge.attr.comb = list( \code{\link[=graph_attr]{graph_attr()}}, \code{\link[=vertex_attr]{vertex_attr()}}, \code{\link[=edge_attr]{edge_attr()}} on how to use graph/vertex/edge attributes in general. \code{\link[=igraph_options]{igraph_options()}} on igraph parameters. + +Vertex, edge and graph attributes +\code{\link{delete_edge_attr}()}, +\code{\link{delete_graph_attr}()}, +\code{\link{delete_vertex_attr}()}, +\code{\link{edge_attr<-}()}, +\code{\link{edge_attr_names}()}, +\code{\link{edge_attr}()}, +\code{\link{graph_attr<-}()}, +\code{\link{graph_attr_names}()}, +\code{\link{graph_attr}()}, +\code{\link{igraph-dollar}}, +\code{\link{igraph-vs-attributes}}, +\code{\link{set_edge_attr}()}, +\code{\link{set_graph_attr}()}, +\code{\link{set_vertex_attr}()}, +\code{\link{vertex_attr<-}()}, +\code{\link{vertex_attr_names}()}, +\code{\link{vertex_attr}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{attributes} \keyword{graphs} diff --git a/man/igraph-dollar.Rd b/man/igraph-dollar.Rd index ecadd45a29..141eb013e5 100644 --- a/man/igraph-dollar.Rd +++ b/man/igraph-dollar.Rd @@ -39,6 +39,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, \code{\link{set_graph_attr}()}, diff --git a/man/igraph-vs-attributes.Rd b/man/igraph-vs-attributes.Rd index ffca5e8108..bbc9f5e79f 100644 --- a/man/igraph-vs-attributes.Rd +++ b/man/igraph-vs-attributes.Rd @@ -98,6 +98,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{set_edge_attr}()}, \code{\link{set_graph_attr}()}, diff --git a/man/is_dag.Rd b/man/is_dag.Rd index 30613bc0c0..cd5eec83c6 100644 --- a/man/is_dag.Rd +++ b/man/is_dag.Rd @@ -34,6 +34,7 @@ Other paths: \code{\link{all_simple_paths}()}, \code{\link{distance_table}()}, \code{\link{eccentricity}()}, +\code{\link{max_cardinality}()}, \code{\link{radius}()} } \author{ diff --git a/man/is_min_separator.Rd b/man/is_min_separator.Rd index 0c8b4f1ccf..e1317d9f39 100644 --- a/man/is_min_separator.Rd +++ b/man/is_min_separator.Rd @@ -70,6 +70,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/is_separator.Rd b/man/is_separator.Rd index 303ab93120..c560724a2b 100644 --- a/man/is_separator.Rd +++ b/man/is_separator.Rd @@ -40,6 +40,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/make_bipartite_graph.Rd b/man/make_bipartite_graph.Rd index a719369985..c431c006b8 100644 --- a/man/make_bipartite_graph.Rd +++ b/man/make_bipartite_graph.Rd @@ -66,8 +66,13 @@ print(g, v = TRUE) } \seealso{ \code{\link[=graph]{graph()}} to create one-mode networks + +Bipartite graphs +\code{\link{bipartite_mapping}()}, +\code{\link{bipartite_projection}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{bipartite} \keyword{graphs} diff --git a/man/max_cardinality.Rd b/man/max_cardinality.Rd index c549e872e5..a78cdc0e19 100644 --- a/man/max_cardinality.Rd +++ b/man/max_cardinality.Rd @@ -58,8 +58,16 @@ of Computation} 13, 566--579. } \seealso{ \code{\link[=is_chordal]{is_chordal()}} + +Other paths: +\code{\link{all_simple_paths}()}, +\code{\link{distance_table}()}, +\code{\link{eccentricity}()}, +\code{\link{is_dag}()}, +\code{\link{radius}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{paths} \keyword{graphs} diff --git a/man/max_flow.Rd b/man/max_flow.Rd index 71bafb0585..c6892b0457 100644 --- a/man/max_flow.Rd +++ b/man/max_flow.Rd @@ -83,6 +83,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_cut.Rd b/man/min_cut.Rd index 051ff98664..798dfdce4f 100644 --- a/man/min_cut.Rd +++ b/man/min_cut.Rd @@ -90,6 +90,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{max_flow}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_separators.Rd b/man/min_separators.Rd index 456d6150a3..bfefead44f 100644 --- a/man/min_separators.Rd +++ b/man/min_separators.Rd @@ -89,6 +89,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{max_flow}()}, \code{\link{min_cut}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_st_separators.Rd b/man/min_st_separators.Rd index 799b7728e3..4c92986954 100644 --- a/man/min_st_separators.Rd +++ b/man/min_st_separators.Rd @@ -42,7 +42,21 @@ the Minimal Separators of a Graph, In: Peter Widmayer, Gabriele Neyer and Stephan Eidenbenz (editors): \emph{Graph-theoretic concepts in computer science}, 1665, 167--172, 1999. Springer. } +\seealso{ +Other flow: +\code{\link{dominator_tree}()}, +\code{\link{edge_connectivity}()}, +\code{\link{is_min_separator}()}, +\code{\link{is_separator}()}, +\code{\link{max_flow}()}, +\code{\link{min_cut}()}, +\code{\link{min_separators}()}, +\code{\link{st_cuts}()}, +\code{\link{st_min_cuts}()}, +\code{\link{vertex_connectivity}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{flow} \keyword{graphs} diff --git a/man/radius.Rd b/man/radius.Rd index d55f09441f..aadd142ab6 100644 --- a/man/radius.Rd +++ b/man/radius.Rd @@ -50,6 +50,7 @@ Other paths: \code{\link{all_simple_paths}()}, \code{\link{distance_table}()}, \code{\link{eccentricity}()}, -\code{\link{is_dag}()} +\code{\link{is_dag}()}, +\code{\link{max_cardinality}()} } \concept{paths} diff --git a/man/scg-method.Rd b/man/scg-method.Rd index 15bee51f41..00b2cbc4e3 100644 --- a/man/scg-method.Rd +++ b/man/scg-method.Rd @@ -45,8 +45,17 @@ D. Gfeller, and P. De Los Rios, Spectral Coarse Graining of Complex Networks, \emph{Physical Review Letters}, \strong{99}(3), 2007. \url{https://arxiv.org/abs/0706.0812} } +\seealso{ +Spectral Coarse Graining +\code{\link{scg_eps}()}, +\code{\link{scg_group}()}, +\code{\link{scg_semi_proj}()}, +\code{\link{scg}()}, +\code{\link{stochastic_matrix}()} +} \author{ David Morton de Lachapelle, \url{http://people.epfl.ch/david.morton}. } +\concept{scg} \keyword{graphs} diff --git a/man/scg.Rd b/man/scg.Rd index 09e49ae357..fa77e9bd11 100644 --- a/man/scg.Rd +++ b/man/scg.Rd @@ -241,6 +241,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_group]{scg_group()}} and \code{\link[=scg_semi_proj]{scg_semi_proj()}}. Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_eps.Rd b/man/scg_eps.Rd index 7c3f89a1ab..d317f1fb1c 100644 --- a/man/scg_eps.Rd +++ b/man/scg_eps.Rd @@ -57,8 +57,16 @@ Matrix Analysis and Applications}, 2008. } \seealso{ \link{scg-method} and \code{\link[=scg]{scg()}}. + +Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_group}()}, +\code{\link{scg_semi_proj}()}, +\code{\link{scg}()}, +\code{\link{stochastic_matrix}()} } \author{ David Morton de Lachapelle, \url{http://people.epfl.ch/david.morton}. } +\concept{scg} diff --git a/man/scg_group.Rd b/man/scg_group.Rd index 6fa5abe19b..24aa1fada7 100644 --- a/man/scg_group.Rd +++ b/man/scg_group.Rd @@ -136,6 +136,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_eps]{scg_eps()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_semi_proj}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_semi_proj.Rd b/man/scg_semi_proj.Rd index 6887229958..8df8cb9f99 100644 --- a/man/scg_semi_proj.Rd +++ b/man/scg_semi_proj.Rd @@ -101,6 +101,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/set_edge_attr.Rd b/man/set_edge_attr.Rd index f3a7669848..d188cdc00b 100644 --- a/man/set_edge_attr.Rd +++ b/man/set_edge_attr.Rd @@ -42,6 +42,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_graph_attr}()}, diff --git a/man/set_graph_attr.Rd b/man/set_graph_attr.Rd index 33ce770ad3..0675b57342 100644 --- a/man/set_graph_attr.Rd +++ b/man/set_graph_attr.Rd @@ -37,6 +37,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/set_vertex_attr.Rd b/man/set_vertex_attr.Rd index 0150dc0c29..3c0ef7f9fd 100644 --- a/man/set_vertex_attr.Rd +++ b/man/set_vertex_attr.Rd @@ -42,6 +42,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/st_cuts.Rd b/man/st_cuts.Rd index d5a714d181..68f3e27c91 100644 --- a/man/st_cuts.Rd +++ b/man/st_cuts.Rd @@ -60,6 +60,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} } diff --git a/man/st_min_cuts.Rd b/man/st_min_cuts.Rd index ac514cb64c..f9377611ba 100644 --- a/man/st_min_cuts.Rd +++ b/man/st_min_cuts.Rd @@ -70,6 +70,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{vertex_connectivity}()} } diff --git a/man/stochastic_matrix.Rd b/man/stochastic_matrix.Rd index 66fa4bc2a2..74bd73bb93 100644 --- a/man/stochastic_matrix.Rd +++ b/man/stochastic_matrix.Rd @@ -54,6 +54,8 @@ max(abs(rowSums(W)) - 1) \code{\link[=as_adj]{as_adj()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{scg}()} diff --git a/man/triad_census.Rd b/man/triad_census.Rd index e636bda87c..8476f006c5 100644 --- a/man/triad_census.Rd +++ b/man/triad_census.Rd @@ -52,4 +52,5 @@ Mifflin. \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{motifs} \keyword{graphs} diff --git a/man/vertex_attr-set.Rd b/man/vertex_attr-set.Rd index da55dc1a79..90469b00ba 100644 --- a/man/vertex_attr-set.Rd +++ b/man/vertex_attr-set.Rd @@ -47,6 +47,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/vertex_attr.Rd b/man/vertex_attr.Rd index 18cb13f18a..04b04357df 100644 --- a/man/vertex_attr.Rd +++ b/man/vertex_attr.Rd @@ -43,6 +43,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/vertex_attr_names.Rd b/man/vertex_attr_names.Rd index 327d58c1ed..d62dcfd92e 100644 --- a/man/vertex_attr_names.Rd +++ b/man/vertex_attr_names.Rd @@ -34,6 +34,7 @@ Vertex, edge and graph attributes \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, diff --git a/man/vertex_connectivity.Rd b/man/vertex_connectivity.Rd index 60cf959cbd..379cbdc24a 100644 --- a/man/vertex_connectivity.Rd +++ b/man/vertex_connectivity.Rd @@ -104,6 +104,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()} @@ -115,6 +116,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()} } diff --git a/src/Makevars b/src/Makevars index fc864eb796..d9535e9849 100644 --- a/src/Makevars +++ b/src/Makevars @@ -5,10 +5,10 @@ PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ + -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT \ -DINTERNAL_ARPACK \ -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) all: $(SHLIB) From ea8a1656a4b881f3bd7ffd5714904406bba3f9ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 13:33:17 +0100 Subject: [PATCH 22/54] tweaks --- R/community.R | 1 - R/games.R | 6 ++- R/make.R | 2 + _pkgdown.yml | 81 +++++++++++++----------------- man/as_membership.Rd | 1 - man/cluster_edge_betweenness.Rd | 1 - man/cluster_fast_greedy.Rd | 1 - man/cluster_fluid_communities.Rd | 1 - man/cluster_infomap.Rd | 1 - man/cluster_label_prop.Rd | 1 - man/cluster_leading_eigen.Rd | 1 - man/cluster_leiden.Rd | 1 - man/cluster_louvain.Rd | 1 - man/cluster_optimal.Rd | 1 - man/cluster_spinglass.Rd | 1 - man/cluster_walktrap.Rd | 1 - man/communities.Rd | 17 ------- man/compare.Rd | 1 - man/contract.Rd | 23 --------- man/ego.Rd | 21 -------- man/erdos.renyi.game.Rd | 10 +++- man/groups.Rd | 1 - man/make_clusters.Rd | 1 - man/modularity.igraph.Rd | 2 - man/plot_dendrogram.communities.Rd | 2 - man/sample_.Rd | 28 +++++++++++ man/sample_bipartite.Rd | 20 ++++++-- man/sample_correlated_gnp.Rd | 27 ++++++++++ man/sample_correlated_gnp_pair.Rd | 27 ++++++++++ man/sample_degseq.Rd | 20 ++++++-- man/sample_dot_product.Rd | 20 ++++++-- man/sample_fitness.Rd | 28 +++++++++++ man/sample_fitness_pl.Rd | 28 +++++++++++ man/sample_forestfire.Rd | 27 ++++++++++ man/sample_gnm.Rd | 20 ++++++-- man/sample_gnp.Rd | 20 ++++++-- man/sample_grg.Rd | 20 ++++++-- man/sample_growing.Rd | 20 ++++++-- man/sample_hierarchical_sbm.Rd | 20 ++++++-- man/sample_islands.Rd | 10 +++- man/sample_k_regular.Rd | 10 +++- man/sample_last_cit.Rd | 60 +++++++++++++++++----- man/sample_pa.Rd | 20 ++++++-- man/sample_pa_age.Rd | 20 ++++++-- man/sample_pref.Rd | 40 ++++++++++++--- man/sample_sbm.Rd | 20 ++++++-- man/sample_smallworld.Rd | 20 ++++++-- man/sample_traits_callaway.Rd | 40 ++++++++++++--- man/sample_tree.Rd | 28 +++++++++++ man/split_join_distance.Rd | 1 - 50 files changed, 564 insertions(+), 210 deletions(-) diff --git a/R/community.R b/R/community.R index 2bae7ed4e5..6318d2fffa 100644 --- a/R/community.R +++ b/R/community.R @@ -2548,6 +2548,5 @@ communities <- groups.communities #' ## combined using the 'toString' function. #' print(g2, g = TRUE, v = TRUE, e = TRUE) #' -#' @family community #' @export contract <- contract diff --git a/R/games.R b/R/games.R index 387fe39abc..d6a3d95b0e 100644 --- a/R/games.R +++ b/R/games.R @@ -1069,7 +1069,6 @@ asym_pref <- function(...) constructor_spec(sample_asym_pref, ...) #' @rdname ego -#' @family games #' @export connect <- function(graph, order, mode = c("all", "out", "in", "total")) { if (!is_igraph(graph)) { @@ -1661,6 +1660,7 @@ sample_k_regular <- sample_k_regular #' distribution in scale-free networks. *Phys Rev Lett* 87(27):278701, #' 2001. #' @keywords graphs +#' @family games #' @examples #' #' N <- 10000 @@ -1727,6 +1727,7 @@ sample_fitness <- sample_fitness #' Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation transitions in #' scale-free networks under the Achlioptas process. *Phys Rev Lett* #' 103:135702, 2009. +#' @family games #' @keywords graphs #' @examples #' @@ -1780,6 +1781,7 @@ sample_fitness_pl <- sample_fitness_pl #' time: densification laws, shrinking diameters and possible explanations. #' *KDD '05: Proceeding of the eleventh ACM SIGKDD international #' conference on Knowledge discovery in data mining*, 177--187, 2005. +#' @family games #' @keywords graphs #' @examples #' @@ -1821,6 +1823,7 @@ sample_forestfire <- sample_forestfire #' @references Lyzinski, V., Fishkind, D. E., Priebe, C. E. (2013). Seeded #' graph matching for correlated Erdos-Renyi graphs. #' +#' @family games #' @examples #' g <- sample_gnp(1000, .1) #' g2 <- sample_correlated_gnp(g, corr = 0.5) @@ -1857,6 +1860,7 @@ sample_correlated_gnp <- sample_correlated_gnp #' graph matching for correlated Erdos-Renyi graphs. #' #' @keywords graphs +#' @family games #' @examples #' gg <- sample_correlated_gnp_pair( #' n = 10, corr = .8, p = .5, diff --git a/R/make.R b/R/make.R index a6d9694bba..7d7df16800 100644 --- a/R/make.R +++ b/R/make.R @@ -204,6 +204,7 @@ make_ <- function(...) { #' ## Arguments are passed on from sample_ to sample_sbm #' blocky3 <- pref_matrix %>% #' sample_(sbm(), n = 20, block.sizes = c(10, 10)) +#' @family games sample_ <- function(...) { me <- attr(sys.function(), "name") %||% "construct" extracted <- .extract_constructor_and_modifiers(..., .operation = me, .variant = "sample") @@ -1207,6 +1208,7 @@ make_tree <- function(n, children = 2, mode = c("out", "in", "undirected")) { #' Prufer sequences does not support directed trees at the moment. #' @return A graph object. #' +#' @family games #' @keywords graphs #' @examples #' diff --git a/_pkgdown.yml b/_pkgdown.yml index f7b10518c3..544dff75e9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -18,6 +18,14 @@ reference: - as.igraph - graph_from_lcf - graph_ +- title: "Graph edition/modification" +- contents: + - permute + - contract + - connect +- subtitle: Rewiring functions +- contents: + - has_concept("rewiring functions") - title: Utilities - subtitle: Utilities - contents: @@ -37,17 +45,6 @@ reference: - title: Vertex, edge and graph attributes - contents: - has_concept("attributes") -- title: Structural queries -- contents: - - has_concept("structural queries") -- title: Bipartite graphs -- contents: - - has_concept("bipartite") - - has_concept("incidence") -- title: Centrality measures -- contents: - - has_concept("centrality") - - has_concept("efficiency") - title: Centralization related - contents: - has_concept("centralization related") @@ -80,15 +77,6 @@ reference: - subtitle: Latent position vector samplers - contents: - has_concept("latent position vector samplers") -- subtitle: Other samplers -- contents: - - sample_ - - sample_correlated_gnp_pair - - sample_fitness - - sample_fitness_pl - - sample_forestfire - - sample_tree - - sample_correlated_gnp - title: Env and data - contents: - has_concept("env-and-data") @@ -114,9 +102,6 @@ reference: - title: Hierarchical random graph functions - contents: - has_concept("hierarchical random graph functions") -- title: Structural queries -- contents: - - has_concept("structural queries") - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -140,10 +125,6 @@ reference: - has_concept("plot.common") - has_concept("plot.shapes") - vertex.shape.pie -- title: Graph motifs and subgraphs -- contents: - - has_concept("graph motifs") - - triad_census - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -153,18 +134,12 @@ reference: - title: igraph options - contents: - has_concept("igraph options") -- title: Paths -- contents: - - has_concept("paths") - title: Print - contents: - has_concept("print") - title: Printer callbacks - contents: - has_concept("printer callbacks") -- title: Rewiring functions -- contents: - - has_concept("rewiring functions") - title: Scan statistics - contents: - has_concept("scan statistics") @@ -175,12 +150,6 @@ reference: - contents: - has_concept("embedding") - embed_laplacian_matrix -- title: Graph matching -- contents: - - has_concept("sgm") -- title: Similarity -- contents: - - has_concept("similarity") - title: Simple - contents: - has_concept("simple") @@ -196,21 +165,43 @@ reference: - has_concept("decomposition") - has_concept("triangles") - starts_with("assortativity") -- title: Structural queries +- subtitle: Centrality measures +- contents: + - has_concept("centrality") +- subtitle: Paths +- contents: + - has_concept("paths") +- subtitle: Bipartite graphs +- contents: + - has_concept("bipartite") + - has_concept("incidence") +- subtitle: Efficiency +- contents: + - has_concept("efficiency") +- subtitle: Similarity +- contents: + - has_concept("similarity") +- subtitle: Trees +- contents: + - has_concept("trees") + - has_concept("minimum.spanning.tree") +- subtitle: Graph matching +- contents: + - has_concept("sgm") +- subtitle: Structural queries - contents: - has_concept("structural queries") +- title: Graph motifs and subgraphs +- contents: + - has_concept("graph motifs") + - triad_census - title: Topology - subtitle: Graph isomorphism - contents: - has_concept("graph isomorphism") - - permute - subtitle: Graph automorphism - contents: - has_concept("graph automorphism") -- title: Trees -- contents: - - has_concept("trees") - - has_concept("minimum.spanning.tree") - title: Versions - contents: - has_concept("versions") diff --git a/man/as_membership.Rd b/man/as_membership.Rd index e09a84f744..fc3d64d31c 100644 --- a/man/as_membership.Rd +++ b/man/as_membership.Rd @@ -40,7 +40,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_edge_betweenness.Rd b/man/cluster_edge_betweenness.Rd index 3adcce94f1..0829b4b459 100644 --- a/man/cluster_edge_betweenness.Rd +++ b/man/cluster_edge_betweenness.Rd @@ -123,7 +123,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_fast_greedy.Rd b/man/cluster_fast_greedy.Rd index 2df29dfed6..96ba6c2461 100644 --- a/man/cluster_fast_greedy.Rd +++ b/man/cluster_fast_greedy.Rd @@ -82,7 +82,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_fluid_communities.Rd b/man/cluster_fluid_communities.Rd index 9627a4dd2d..84369a92ae 100644 --- a/man/cluster_fluid_communities.Rd +++ b/man/cluster_fluid_communities.Rd @@ -61,7 +61,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_infomap.Rd b/man/cluster_infomap.Rd index f092b83f40..c6686d9877 100644 --- a/man/cluster_infomap.Rd +++ b/man/cluster_infomap.Rd @@ -81,7 +81,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_label_prop.Rd b/man/cluster_label_prop.Rd index 67737483fe..9921b49129 100644 --- a/man/cluster_label_prop.Rd +++ b/man/cluster_label_prop.Rd @@ -83,7 +83,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_leading_eigen.Rd b/man/cluster_leading_eigen.Rd index f0fc6a1955..9797582c90 100644 --- a/man/cluster_leading_eigen.Rd +++ b/man/cluster_leading_eigen.Rd @@ -135,7 +135,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_leiden.Rd b/man/cluster_leiden.Rd index d0ec9dd9d7..dc97b8b91a 100644 --- a/man/cluster_leiden.Rd +++ b/man/cluster_leiden.Rd @@ -143,7 +143,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_louvain.Rd b/man/cluster_louvain.Rd index a94f74111f..8a746e3dce 100644 --- a/man/cluster_louvain.Rd +++ b/man/cluster_louvain.Rd @@ -89,7 +89,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_optimal.Rd b/man/cluster_optimal.Rd index 433afd7b86..a5b9e5cb37 100644 --- a/man/cluster_optimal.Rd +++ b/man/cluster_optimal.Rd @@ -88,7 +88,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_spinglass.Rd b/man/cluster_spinglass.Rd index 2e0a631783..70d28a27dd 100644 --- a/man/cluster_spinglass.Rd +++ b/man/cluster_spinglass.Rd @@ -159,7 +159,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_walktrap.Rd b/man/cluster_walktrap.Rd index 17c1630ab4..99d51a045f 100644 --- a/man/cluster_walktrap.Rd +++ b/man/cluster_walktrap.Rd @@ -88,7 +88,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_spinglass}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/communities.Rd b/man/communities.Rd index cad7ebc725..81aa4af09d 100644 --- a/man/communities.Rd +++ b/man/communities.Rd @@ -289,7 +289,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -310,7 +309,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -331,7 +329,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -352,7 +349,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -373,7 +369,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -394,7 +389,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -415,7 +409,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -436,7 +429,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -457,7 +449,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -478,7 +469,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -499,7 +489,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -520,7 +509,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -541,7 +529,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -562,7 +549,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -583,7 +569,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -604,7 +589,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -625,7 +609,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, diff --git a/man/compare.Rd b/man/compare.Rd index 281e95ce15..8eef71fc43 100644 --- a/man/compare.Rd +++ b/man/compare.Rd @@ -89,7 +89,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/contract.Rd b/man/contract.Rd index 51bf2d41e6..1bf4e2ab7f 100644 --- a/man/contract.Rd +++ b/man/contract.Rd @@ -44,31 +44,8 @@ g2 <- contract(g, rep(1:5, each = 2), ## combined using the 'toString' function. print(g2, g = TRUE, v = TRUE, e = TRUE) -} -\seealso{ -Community detection -\code{\link{as_membership}()}, -\code{\link{cluster_edge_betweenness}()}, -\code{\link{cluster_fast_greedy}()}, -\code{\link{cluster_fluid_communities}()}, -\code{\link{cluster_infomap}()}, -\code{\link{cluster_label_prop}()}, -\code{\link{cluster_leading_eigen}()}, -\code{\link{cluster_leiden}()}, -\code{\link{cluster_louvain}()}, -\code{\link{cluster_optimal}()}, -\code{\link{cluster_spinglass}()}, -\code{\link{cluster_walktrap}()}, -\code{\link{compare}()}, -\code{\link{groups}()}, -\code{\link{make_clusters}()}, -\code{\link{membership}()}, -\code{\link{modularity.igraph}()}, -\code{\link{plot_dendrogram}()}, -\code{\link{split_join_distance}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{community} \keyword{graphs} diff --git a/man/ego.Rd b/man/ego.Rd index 64bc03c465..b5f9b94e89 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -108,26 +108,6 @@ g <- connect(g, 2) } \seealso{ -Random graph models (games) -\code{\link{erdos.renyi.game}()}, -\code{\link{sample_bipartite}()}, -\code{\link{sample_degseq}()}, -\code{\link{sample_dot_product}()}, -\code{\link{sample_gnm}()}, -\code{\link{sample_gnp}()}, -\code{\link{sample_grg}()}, -\code{\link{sample_growing}()}, -\code{\link{sample_hierarchical_sbm}()}, -\code{\link{sample_islands}()}, -\code{\link{sample_k_regular}()}, -\code{\link{sample_last_cit}()}, -\code{\link{sample_pa_age}()}, -\code{\link{sample_pa}()}, -\code{\link{sample_pref}()}, -\code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} - Other structural.properties: \code{\link{bfs}()}, \code{\link{component_distribution}()}, @@ -204,6 +184,5 @@ Other structural.properties: Gabor Csardi \email{csardi.gabor@gmail.com}, the first version was done by Vincent Matossian } -\concept{games} \concept{structural.properties} \keyword{graphs} diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 241f887176..16a0b7918a 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -68,10 +68,14 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -85,7 +89,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/groups.Rd b/man/groups.Rd index f18005a25e..a72ac54bb8 100644 --- a/man/groups.Rd +++ b/man/groups.Rd @@ -54,7 +54,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, \code{\link{modularity.igraph}()}, diff --git a/man/make_clusters.Rd b/man/make_clusters.Rd index 2ff44996a9..2d43b04272 100644 --- a/man/make_clusters.Rd +++ b/man/make_clusters.Rd @@ -52,7 +52,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{membership}()}, \code{\link{modularity.igraph}()}, diff --git a/man/modularity.igraph.Rd b/man/modularity.igraph.Rd index 9e90f9ac1e..be8a1d40be 100644 --- a/man/modularity.igraph.Rd +++ b/man/modularity.igraph.Rd @@ -118,7 +118,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, @@ -139,7 +138,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/plot_dendrogram.communities.Rd b/man/plot_dendrogram.communities.Rd index c3f254662a..4646891908 100644 --- a/man/plot_dendrogram.communities.Rd +++ b/man/plot_dendrogram.communities.Rd @@ -115,7 +115,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, @@ -136,7 +135,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/sample_.Rd b/man/sample_.Rd index 2f80ebe2b4..67173bc2b9 100644 --- a/man/sample_.Rd +++ b/man/sample_.Rd @@ -29,3 +29,31 @@ blocky2 <- pref_matrix \%>\% blocky3 <- pref_matrix \%>\% sample_(sbm(), n = 20, block.sizes = c(10, 10)) } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()} +} +\concept{games} diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index 4ced6d0ce1..c0cf409ffa 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -77,10 +77,14 @@ sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") \code{\link[=sample_gnp]{sample_gnp()}} and \code{\link[=sample_gnm]{sample_gnm()}} for the unipartite version. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,13 +98,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -114,7 +124,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_correlated_gnp.Rd b/man/sample_correlated_gnp.Rd index 89285aa7f5..de47064bc4 100644 --- a/man/sample_correlated_gnp.Rd +++ b/man/sample_correlated_gnp.Rd @@ -57,4 +57,31 @@ graph matching for correlated Erdos-Renyi graphs. \seealso{ \code{\link[=sample_correlated_gnp_pair]{sample_correlated_gnp_pair()}}, \code{\link[=sample_gnp]{sample_gnp()}} + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } +\concept{games} diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index 35d2793e26..5ca3163aaa 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -50,5 +50,32 @@ graph matching for correlated Erdos-Renyi graphs. \seealso{ \code{\link[=sample_correlated_gnp]{sample_correlated_gnp()}}, \code{\link[=sample_gnp]{sample_gnp()}}. + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } +\concept{games} \keyword{graphs} diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index 28d25e6df5..5bc1857403 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -109,10 +109,14 @@ all(degree(g5) == degs) \code{\link[=realize_degseq]{realize_degseq()}} for a deterministic variant. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -126,13 +130,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -146,7 +156,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index 5a0278020f..40f6368f9c 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -57,10 +57,14 @@ for social networks. Dissertation, Johns Hopkins University, Maryland, USA, and \code{\link[=sample_sphere_volume]{sample_sphere_volume()}} for sampling position vectors. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -74,13 +78,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,7 +104,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index 1736421078..408b230ce7 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -78,7 +78,35 @@ Goh K-I, Kahng B, Kim D: Universal behaviour of load distribution in scale-free networks. \emph{Phys Rev Lett} 87(27):278701, 2001. } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} +} \author{ Tamas Nepusz \email{ntamas@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index c487ec9a93..8d7957e574 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -87,7 +87,35 @@ Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation transitions in scale-free networks under the Achlioptas process. \emph{Phys Rev Lett} 103:135702, 2009. } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} +} \author{ Tamas Nepusz \email{ntamas@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index a13743708f..db2a553406 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -71,8 +71,35 @@ conference on Knowledge discovery in data mining}, 177--187, 2005. \seealso{ \code{\link[=barabasi.game]{barabasi.game()}} for the basic preferential attachment model. + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 075988365c..6a1b076510 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -47,11 +47,15 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -64,14 +68,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -84,7 +94,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index 701441c506..b0ce3e6939 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -46,11 +46,15 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_gnm]{sample_gnm()}}, \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -63,14 +67,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -83,7 +93,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 9dd1088a0d..58253883ef 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -48,11 +48,15 @@ g2 <- sample_grg(1000, 0.05, torus = TRUE) \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_growing}()}, @@ -65,14 +69,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_growing}()}, @@ -85,7 +95,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com}, first version was diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index b085ea1cc2..bb3b7014b2 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -45,11 +45,15 @@ g2 <- sample_growing(500, citation = TRUE) \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -62,14 +66,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -82,7 +92,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index 43fd3fce22..74de881742 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -59,11 +59,15 @@ if (require(Matrix)) { \code{\link[=sbm.game]{sbm.game()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -76,14 +80,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -96,7 +106,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 9ec6aad7d2..04dcf2d1f1 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -37,11 +37,15 @@ oc \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -54,7 +58,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Samuel Thiriot diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 9a4deb2431..6808ab72f4 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -49,11 +49,15 @@ sapply(k10, plot, vertex.label = NA) sequence. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -66,7 +70,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index 3f6b9ae864..ec1259857a 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -83,11 +83,15 @@ vertex only. } \seealso{ Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -100,14 +104,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -120,14 +130,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -140,14 +156,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -160,14 +182,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -180,14 +208,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -200,7 +234,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index e83b456701..1cc3d63a4e 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -131,11 +131,15 @@ de Solla Price, D. J. 1965. Networks of Scientific Papers \emph{Science}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -148,14 +152,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -168,7 +178,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index f90688e4c3..cd940e879d 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -141,11 +141,15 @@ max(degree(g3)) \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -158,14 +162,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -178,7 +188,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index 80ad19cf5a..cf50ad99b1 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -102,11 +102,15 @@ tkplot(g, layout = layout_in_circle) \code{\link[=sample_traits_callaway]{sample_traits_callaway()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -119,14 +123,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -139,14 +149,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -159,14 +175,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -179,7 +201,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} and Gabor Csardi diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index 41748c9fa4..3f7cf092f7 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -56,11 +56,15 @@ and evaluation. \emph{Social Networks}, 14, 5--61. \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_gnm]{sample_gnm()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -73,14 +77,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -93,7 +103,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 70f5276d0e..2106f3c476 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -57,11 +57,15 @@ Duncan J Watts and Steven H Strogatz: Collective dynamics of \code{\link[=make_lattice]{make_lattice()}}, \code{\link[=rewire]{rewire()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -74,14 +78,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,7 +104,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index bb8db02fcd..9546a9b46c 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -81,11 +81,15 @@ g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2 } \seealso{ Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -98,14 +102,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -118,14 +128,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -138,14 +154,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -158,7 +180,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_tree.Rd b/man/sample_tree.Rd index 6404bc0eb0..2cada8d411 100644 --- a/man/sample_tree.Rd +++ b/man/sample_tree.Rd @@ -35,4 +35,32 @@ given number of nodes with the same probability. g <- sample_tree(100, method = "lerw") } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_}()} +} +\concept{games} \keyword{graphs} diff --git a/man/split_join_distance.Rd b/man/split_join_distance.Rd index a51355238c..241059882b 100644 --- a/man/split_join_distance.Rd +++ b/man/split_join_distance.Rd @@ -56,7 +56,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, From 6819f354739e30e0ee9bf011af266b0a450873ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 13:36:25 +0100 Subject: [PATCH 23/54] tweaks --- _pkgdown.yml | 135 ++++++++++++++++++++++++++------------------------- 1 file changed, 68 insertions(+), 67 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 544dff75e9..52a35869ff 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -18,8 +18,22 @@ reference: - as.igraph - graph_from_lcf - graph_ -- title: "Graph edition/modification" +- title: Visualization - contents: + - has_concept("graph layouts") + - has_concept("layout modifiers") + - has_concept("layout_drl") + - has_concept("palettes") + - has_concept("plot") + - igraph.plotting + - plot_dendrogram.igraphHRG + - plot_dendrogram + - has_concept("plot.common") + - has_concept("plot.shapes") + - vertex.shape.pie +- title: Functions for manipulating graph structure +- contents: + - has_concept("functions for manipulating graph structure") - permute - contract - connect @@ -39,6 +53,58 @@ reference: - head_print - indent_print - printr +- title: Structural properties +- contents: + - has_concept("structural.properties") + - has_concept("cocitation") + - has_concept("cohesive.blocks") + - has_concept("decomposition") + - has_concept("triangles") + - starts_with("assortativity") +- subtitle: Centrality measures +- contents: + - has_concept("centrality") +- subtitle: Paths +- contents: + - has_concept("paths") +- subtitle: Bipartite graphs +- contents: + - has_concept("bipartite") + - has_concept("incidence") +- subtitle: Efficiency +- contents: + - has_concept("efficiency") +- subtitle: Similarity +- contents: + - has_concept("similarity") +- subtitle: Trees +- contents: + - has_concept("trees") + - has_concept("minimum.spanning.tree") +- subtitle: Graph matching +- contents: + - has_concept("sgm") +- subtitle: Structural queries +- contents: + - has_concept("structural queries") +- title: Graph motifs and subgraphs +- contents: + - has_concept("graph motifs") + - triad_census +- title: Topology +- subtitle: Graph isomorphism +- contents: + - has_concept("graph isomorphism") +- subtitle: Graph automorphism +- contents: + - has_concept("graph automorphism") +- title: Flow +- contents: + - has_concept("flow") +- title: Cliques +- contents: + - has_concept("cliques") + - has_concept("glet") - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -73,8 +139,7 @@ reference: - title: Demo - contents: - has_concept("demo") -- title: Sampling -- subtitle: Latent position vector samplers +- title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") - title: Env and data @@ -90,9 +155,6 @@ reference: - title: Fit - contents: - has_concept("fit") -- title: Flow -- contents: - - has_concept("flow") - title: Foreign format readers - contents: - has_concept("foreign") @@ -103,28 +165,12 @@ reference: - contents: - has_concept("hierarchical random graph functions") - title: Functions for manipulating graph structure -- contents: - - has_concept("functions for manipulating graph structure") -- title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") - title: Vertex and edge sequences - contents: - has_concept("vertex and edge sequences") - has_concept("vertex and edge sequence operations") -- title: Visualization -- contents: - - has_concept("graph layouts") - - has_concept("layout modifiers") - - has_concept("layout_drl") - - has_concept("palettes") - - has_concept("plot") - - igraph.plotting - - plot_dendrogram.igraphHRG - - plot_dendrogram - - has_concept("plot.common") - - has_concept("plot.shapes") - - vertex.shape.pie - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -157,51 +203,6 @@ reference: - contents: - has_concept("socnet") - has_concept("tkplot") -- title: Structural properties -- contents: - - has_concept("structural.properties") - - has_concept("cocitation") - - has_concept("cohesive.blocks") - - has_concept("decomposition") - - has_concept("triangles") - - starts_with("assortativity") -- subtitle: Centrality measures -- contents: - - has_concept("centrality") -- subtitle: Paths -- contents: - - has_concept("paths") -- subtitle: Bipartite graphs -- contents: - - has_concept("bipartite") - - has_concept("incidence") -- subtitle: Efficiency -- contents: - - has_concept("efficiency") -- subtitle: Similarity -- contents: - - has_concept("similarity") -- subtitle: Trees -- contents: - - has_concept("trees") - - has_concept("minimum.spanning.tree") -- subtitle: Graph matching -- contents: - - has_concept("sgm") -- subtitle: Structural queries -- contents: - - has_concept("structural queries") -- title: Graph motifs and subgraphs -- contents: - - has_concept("graph motifs") - - triad_census -- title: Topology -- subtitle: Graph isomorphism -- contents: - - has_concept("graph isomorphism") -- subtitle: Graph automorphism -- contents: - - has_concept("graph automorphism") - title: Versions - contents: - has_concept("versions") From 01633bd17f2e4530cec3fac06d58e7f9d3bf9164 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 13:42:48 +0100 Subject: [PATCH 24/54] more tweaking --- _pkgdown.yml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 52a35869ff..bb85c754b1 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -31,6 +31,9 @@ reference: - has_concept("plot.common") - has_concept("plot.shapes") - vertex.shape.pie +- subtitle: Graph coloring +- contents: + - has_concept("coloring") - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -53,6 +56,9 @@ reference: - head_print - indent_print - printr +- subtitle: Console +- contents: + - has_concept("console") - title: Structural properties - contents: - has_concept("structural.properties") @@ -105,6 +111,16 @@ reference: - contents: - has_concept("cliques") - has_concept("glet") +- title: Community detection +- contents: + - has_concept("community") +- title: Graph cycles +- contents: + - has_concept("cycles") +- title: Processes on graphs +- contents: + - has_concept("processes") + - has_concept("random_walk") - title: Adjacency matrices - contents: - has_concept("adjacency") @@ -118,18 +134,9 @@ reference: - contents: - has_concept("cliques") - has_concept("glet") -- title: Graph coloring -- contents: - - has_concept("coloring") -- title: Community detection -- contents: - - has_concept("community") - title: Connected components - contents: - has_concept("components") -- title: Console -- contents: - - has_concept("console") - title: Conversion - contents: - has_concept("conversion") @@ -145,13 +152,6 @@ reference: - title: Env and data - contents: - has_concept("env-and-data") -- title: Processes on graphs -- contents: - - has_concept("processes") - - has_concept("random_walk") -- title: Graph cycles -- contents: - - has_concept("cycles") - title: Fit - contents: - has_concept("fit") From 9fad8c5d7d41ed99f1f8fff63c17f6ebb1e4aa32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 13:48:52 +0100 Subject: [PATCH 25/54] force a build here --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 4fc3be5a2f..8c9d1bf5d0 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -2,7 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, config-draft] + branches: [main, master, reference-reorg] pull_request: branches: [main, master] release: From a70d980695278a0b2a1615bb98ed741e94d82abe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:04:30 +0100 Subject: [PATCH 26/54] place found for Adjacency matrices --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index bb85c754b1..e7ae279b42 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -18,6 +18,9 @@ reference: - as.igraph - graph_from_lcf - graph_ +- subtitle: Adjacency matrices +- contents: + - has_concept("adjacency") - title: Visualization - contents: - has_concept("graph layouts") @@ -121,9 +124,6 @@ reference: - contents: - has_concept("processes") - has_concept("random_walk") -- title: Adjacency matrices -- contents: - - has_concept("adjacency") - title: Vertex, edge and graph attributes - contents: - has_concept("attributes") From 163dd555815acb770be388a94b5ef87b233ec94e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:13:16 +0100 Subject: [PATCH 27/54] conversion under utilities --- _pkgdown.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index e7ae279b42..1f7b01ec4d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -48,12 +48,16 @@ reference: - has_concept("rewiring functions") - title: Utilities - subtitle: Utilities +- subtitle: Misc - contents: - graph_id - identical_graphs - is_igraph - is_named - is_weighted +- subtitle: Conversion +- contents: + - has_concept("conversion") - subtitle: Printing - contents: - head_print @@ -137,9 +141,6 @@ reference: - title: Connected components - contents: - has_concept("components") -- title: Conversion -- contents: - - has_concept("conversion") - title: Graphical degree sequences - contents: - has_concept("graphical degree sequences") From 431667af3588a757acae3bf7be2423cb718fcd0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:15:19 +0100 Subject: [PATCH 28/54] Env and data under utilities --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 1f7b01ec4d..044af8bc6a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -58,6 +58,9 @@ reference: - subtitle: Conversion - contents: - has_concept("conversion") +- subtitle: Env and data +- contents: + - has_concept("env-and-data") - subtitle: Printing - contents: - head_print @@ -150,9 +153,6 @@ reference: - title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") -- title: Env and data -- contents: - - has_concept("env-and-data") - title: Fit - contents: - has_concept("fit") From 02162af8cd2a9fe1956ee671047e074584241628 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:16:01 +0100 Subject: [PATCH 29/54] fit under utilities --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 044af8bc6a..d2a75a63f9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -61,6 +61,9 @@ reference: - subtitle: Env and data - contents: - has_concept("env-and-data") +- title: Fit +- contents: + - has_concept("fit") - subtitle: Printing - contents: - head_print @@ -153,9 +156,6 @@ reference: - title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") -- title: Fit -- contents: - - has_concept("fit") - title: Foreign format readers - contents: - has_concept("foreign") From 5c1e20b60572e482b75ae5bea2ac8378053b6abe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:16:44 +0100 Subject: [PATCH 30/54] clarify title --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index d2a75a63f9..24b697e52d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -156,7 +156,7 @@ reference: - title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") -- title: Foreign format readers +- title: I/O Read/Write Files - contents: - has_concept("foreign") - title: Random graph models (games) From f90f364072e9f755a7251126ad135c3d05d0735a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:17:37 +0100 Subject: [PATCH 31/54] rm dup --- _pkgdown.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 24b697e52d..51ea8e2571 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -165,9 +165,6 @@ reference: - title: Hierarchical random graph functions - contents: - has_concept("hierarchical random graph functions") -- title: Functions for manipulating graph structure -- contents: - - has_concept("functions for manipulating graph structure") - title: Vertex and edge sequences - contents: - has_concept("vertex and edge sequences") From bbeba617c20ff675f8ad0cf6605b16500050e98a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:20:06 +0100 Subject: [PATCH 32/54] rm "other" section --- _pkgdown.yml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 51ea8e2571..af58f10705 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -48,7 +48,7 @@ reference: - has_concept("rewiring functions") - title: Utilities - subtitle: Utilities -- subtitle: Misc +- subtitle: Graph ID, comparison, name, weight - contents: - graph_id - identical_graphs @@ -61,9 +61,6 @@ reference: - subtitle: Env and data - contents: - has_concept("env-and-data") -- title: Fit -- contents: - - has_concept("fit") - subtitle: Printing - contents: - head_print @@ -72,6 +69,12 @@ reference: - subtitle: Console - contents: - has_concept("console") +- subtitle: Misc +- contents: + - convex_hull + - running_mean + - sample_seq + - fit_power_law - title: Structural properties - contents: - has_concept("structural.properties") @@ -172,9 +175,6 @@ reference: - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") -- title: Other -- contents: - - has_concept("other") - title: igraph options - contents: - has_concept("igraph options") @@ -213,4 +213,5 @@ reference: - layout.fruchterman.reingold.grid - layout.spring - layout.svd + - srand - "%>%" From 317fb245cc6c41cba4246c4a7881b58807bfbc6b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 14:21:30 +0100 Subject: [PATCH 33/54] consolidate printing --- _pkgdown.yml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index af58f10705..1e83f7a272 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,6 +4,9 @@ template: bootstrap: 5 reference: +- title: igraph options +- contents: + - has_concept("igraph options") - title: Construction - subtitle: Deterministic constructors - contents: @@ -66,6 +69,8 @@ reference: - head_print - indent_print - printr + - has_concept("print") + - has_concept("printer callbacks") - subtitle: Console - contents: - has_concept("console") @@ -175,15 +180,7 @@ reference: - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") -- title: igraph options -- contents: - - has_concept("igraph options") -- title: Print -- contents: - - has_concept("print") -- title: Printer callbacks -- contents: - - has_concept("printer callbacks") + - title: Scan statistics - contents: - has_concept("scan statistics") From 03437f83370843ce1f5b1e3153905220ce2211c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 15:01:11 +0100 Subject: [PATCH 34/54] use feedback --- R/aaa-auto.R | 1 + R/make.R | 2 +- R/simple.R | 1 + _pkgdown.yml | 43 +++++++++++++++++-------------------- man/is_tree.Rd | 1 + man/make_from_prufer.Rd | 7 +++++- man/sample_spanning_tree.Rd | 1 + man/simplify.Rd | 1 + man/to_prufer.Rd | 1 + 9 files changed, 33 insertions(+), 25 deletions(-) diff --git a/R/aaa-auto.R b/R/aaa-auto.R index 0c0694749d..8dad23be60 100644 --- a/R/aaa-auto.R +++ b/R/aaa-auto.R @@ -1518,6 +1518,7 @@ count_triangles <- function(graph, vids=V(graph)) { res } +#' @family triangles #' @export triangles <- function(graph) { # Argument checks diff --git a/R/make.R b/R/make.R index 7d7df16800..c5e6944054 100644 --- a/R/make.R +++ b/R/make.R @@ -1245,7 +1245,7 @@ tree <- function(...) constructor_spec(list(make = make_tree, sample = sample_tr #' #' g <- make_tree(13, 3) #' to_prufer(g) -#' +#' @family trees #' @export make_from_prufer <- make_from_prufer diff --git a/R/simple.R b/R/simple.R index 507699910a..26e1843607 100644 --- a/R/simple.R +++ b/R/simple.R @@ -79,6 +79,7 @@ simplify <- simplify is_simple <- is_simple #' @family simple +#' @family isomorphism #' @export #' @rdname simplify simplify_and_colorize <- function(graph) { diff --git a/_pkgdown.yml b/_pkgdown.yml index 1e83f7a272..0c37e3ebff 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -21,6 +21,9 @@ reference: - as.igraph - graph_from_lcf - graph_ +- subtitle: "Random graph models (games)" +- contents: + - has_concept("games") - subtitle: Adjacency matrices - contents: - has_concept("adjacency") @@ -46,6 +49,7 @@ reference: - permute - contract - connect + - has_concept("simple") - subtitle: Rewiring functions - contents: - has_concept("rewiring functions") @@ -58,6 +62,7 @@ reference: - is_igraph - is_named - is_weighted + - is_chordal - subtitle: Conversion - contents: - has_concept("conversion") @@ -71,9 +76,6 @@ reference: - printr - has_concept("print") - has_concept("printer callbacks") -- subtitle: Console -- contents: - - has_concept("console") - subtitle: Misc - contents: - convex_hull @@ -85,12 +87,12 @@ reference: - has_concept("structural.properties") - has_concept("cocitation") - has_concept("cohesive.blocks") - - has_concept("decomposition") - has_concept("triangles") - starts_with("assortativity") -- subtitle: Centrality measures +- subtitle: Triangles and transitivity - contents: - - has_concept("centrality") + - matches("triangles") + - matches("transitivity") - subtitle: Paths - contents: - has_concept("paths") @@ -108,24 +110,27 @@ reference: - contents: - has_concept("trees") - has_concept("minimum.spanning.tree") -- subtitle: Graph matching -- contents: - - has_concept("sgm") - subtitle: Structural queries - contents: - has_concept("structural queries") +- subtitle: Centrality measures +- contents: + - has_concept("centrality") +- title: Centralization related +- contents: + - has_concept("centralization related") +- subtitle: Graph matching +- contents: + - has_concept("sgm") - title: Graph motifs and subgraphs - contents: - has_concept("graph motifs") - triad_census -- title: Topology -- subtitle: Graph isomorphism +- title: Graph isomorphism - contents: - has_concept("graph isomorphism") -- subtitle: Graph automorphism -- contents: - has_concept("graph automorphism") -- title: Flow +- title: Maximum flow and connectivity - contents: - has_concept("flow") - title: Cliques @@ -145,9 +150,6 @@ reference: - title: Vertex, edge and graph attributes - contents: - has_concept("attributes") -- title: Centralization related -- contents: - - has_concept("centralization related") - title: Cliques - contents: - has_concept("cliques") @@ -167,9 +169,6 @@ reference: - title: I/O Read/Write Files - contents: - has_concept("foreign") -- title: Random graph models (games) -- contents: - - has_concept("games") - title: Hierarchical random graph functions - contents: - has_concept("hierarchical random graph functions") @@ -191,9 +190,6 @@ reference: - contents: - has_concept("embedding") - embed_laplacian_matrix -- title: Simple -- contents: - - has_concept("simple") - title: Interactive functions - contents: - has_concept("socnet") @@ -212,3 +208,4 @@ reference: - layout.svd - srand - "%>%" + - has_concept("console") diff --git a/man/is_tree.Rd b/man/is_tree.Rd index 4bbfe66d9c..7d3b3debf1 100644 --- a/man/is_tree.Rd +++ b/man/is_tree.Rd @@ -47,6 +47,7 @@ is_tree(g, details = TRUE) } \seealso{ Other trees: +\code{\link{make_from_prufer}()}, \code{\link{sample_spanning_tree}()}, \code{\link{to_prufer}()} } diff --git a/man/make_from_prufer.Rd b/man/make_from_prufer.Rd index d8fe9fed7e..793c691210 100644 --- a/man/make_from_prufer.Rd +++ b/man/make_from_prufer.Rd @@ -32,9 +32,14 @@ only two vertices in the remaining graph. g <- make_tree(13, 3) to_prufer(g) - } \seealso{ \code{\link[=to_prufer]{to_prufer()}} to convert a graph into its Prufer sequence + +Other trees: +\code{\link{is_tree}()}, +\code{\link{sample_spanning_tree}()}, +\code{\link{to_prufer}()} } +\concept{trees} \keyword{graphs} diff --git a/man/sample_spanning_tree.Rd b/man/sample_spanning_tree.Rd index 93d29c9cba..9a02c09d20 100644 --- a/man/sample_spanning_tree.Rd +++ b/man/sample_spanning_tree.Rd @@ -37,6 +37,7 @@ forest <- subgraph.edges(g, edges) Other trees: \code{\link{is_tree}()}, +\code{\link{make_from_prufer}()}, \code{\link{to_prufer}()} } \concept{trees} diff --git a/man/simplify.Rd b/man/simplify.Rd index ebaa6482ae..055f33c730 100644 --- a/man/simplify.Rd +++ b/man/simplify.Rd @@ -75,5 +75,6 @@ is_simple(simplify(g)) \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{isomorphism} \concept{simple} \keyword{graphs} diff --git a/man/to_prufer.Rd b/man/to_prufer.Rd index 914280aa83..3a21d8aa30 100644 --- a/man/to_prufer.Rd +++ b/man/to_prufer.Rd @@ -35,6 +35,7 @@ Prufer sequence Other trees: \code{\link{is_tree}()}, +\code{\link{make_from_prufer}()}, \code{\link{sample_spanning_tree}()} } \concept{trees} From 9c52e652c63b80a5b3e213c22a6f028dd5813001 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 15:16:16 +0100 Subject: [PATCH 35/54] add 2 functions --- _pkgdown.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index 0c37e3ebff..89ab7060ae 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -109,6 +109,7 @@ reference: - subtitle: Trees - contents: - has_concept("trees") + - make_from_prufer - has_concept("minimum.spanning.tree") - subtitle: Structural queries - contents: @@ -129,6 +130,7 @@ reference: - title: Graph isomorphism - contents: - has_concept("graph isomorphism") + - simplify_and_colorize - has_concept("graph automorphism") - title: Maximum flow and connectivity - contents: From c878ec458498b29e49cb3ba84248ba7b8ff7bb04 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 15:21:56 +0100 Subject: [PATCH 36/54] add triangles --- R/aaa-auto.R | 1 + man/count_triangles.Rd | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/R/aaa-auto.R b/R/aaa-auto.R index 8dad23be60..f7bce518e9 100644 --- a/R/aaa-auto.R +++ b/R/aaa-auto.R @@ -1519,6 +1519,7 @@ count_triangles <- function(graph, vids=V(graph)) { } #' @family triangles +#' @rdname count_triangles #' @export triangles <- function(graph) { # Argument checks diff --git a/man/count_triangles.Rd b/man/count_triangles.Rd index 56ee5bc013..ea455b4ab6 100644 --- a/man/count_triangles.Rd +++ b/man/count_triangles.Rd @@ -1,11 +1,13 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/triangles.R -\name{count_triangles} +% Please edit documentation in R/aaa-auto.R, R/triangles.R +\name{triangles} +\alias{triangles} \alias{count_triangles} \alias{adjacent.triangles} -\alias{triangles} \title{Find triangles in graphs} \usage{ +triangles(graph) + count_triangles(graph, vids = V(graph)) } \arguments{ From ea64fbdd73aa024e12415e1a81e1d832a2c38399 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Feb 2023 15:23:21 +0100 Subject: [PATCH 37/54] move graph matching --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 89ab7060ae..b66b343850 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -120,9 +120,6 @@ reference: - title: Centralization related - contents: - has_concept("centralization related") -- subtitle: Graph matching -- contents: - - has_concept("sgm") - title: Graph motifs and subgraphs - contents: - has_concept("graph motifs") @@ -132,6 +129,9 @@ reference: - has_concept("graph isomorphism") - simplify_and_colorize - has_concept("graph automorphism") +- subtitle: Graph matching +- contents: + - has_concept("sgm") - title: Maximum flow and connectivity - contents: - has_concept("flow") From bc98edeec1f46b078ba9c69cca50ec9f8a894c77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:01:58 +0100 Subject: [PATCH 38/54] rm man/roxygen --- man/alpha_centrality.Rd | 2 +- man/arpack.Rd | 4 ++-- man/articulation_points.Rd | 4 ++-- man/as_membership.Rd | 2 +- man/authority_score.Rd | 2 +- man/betweenness.Rd | 6 ++--- man/biconnected_components.Rd | 2 +- man/bipartite_mapping.Rd | 2 +- man/bipartite_projection.Rd | 2 +- man/closeness.Rd | 2 +- man/cluster_edge_betweenness.Rd | 2 +- man/cluster_fast_greedy.Rd | 2 +- man/cluster_fluid_communities.Rd | 2 +- man/cluster_infomap.Rd | 2 +- man/cluster_label_prop.Rd | 2 +- man/cluster_leading_eigen.Rd | 2 +- man/cluster_leiden.Rd | 2 +- man/cluster_louvain.Rd | 2 +- man/cluster_optimal.Rd | 2 +- man/cluster_spinglass.Rd | 2 +- man/cluster_walktrap.Rd | 2 +- man/communities.Rd | 34 ++++++++++++++--------------- man/compare.Rd | 2 +- man/components.Rd | 2 +- man/decompose.Rd | 2 +- man/delete_edge_attr.Rd | 2 +- man/delete_graph_attr.Rd | 2 +- man/delete_vertex_attr.Rd | 2 +- man/diversity.Rd | 2 +- man/edge_attr-set.Rd | 2 +- man/edge_attr.Rd | 2 +- man/edge_attr_names.Rd | 2 +- man/eigen_centrality.Rd | 2 +- man/erdos.renyi.game.Rd | 2 +- man/graph_attr-set.Rd | 2 +- man/graph_attr.Rd | 2 +- man/graph_attr_names.Rd | 2 +- man/graph_from_graphdb.Rd | 2 +- man/groups.Rd | 2 +- man/harmonic_centrality.Rd | 2 +- man/hub_score.Rd | 2 +- man/igraph-attribute-combination.Rd | 2 +- man/igraph-dollar.Rd | 2 +- man/igraph-vs-attributes.Rd | 2 +- man/make_bipartite_graph.Rd | 2 +- man/make_clusters.Rd | 2 +- man/modularity.igraph.Rd | 4 ++-- man/page_rank.Rd | 2 +- man/plot.sir.Rd | 2 +- man/plot_dendrogram.communities.Rd | 4 ++-- man/power_centrality.Rd | 2 +- man/read_graph.Rd | 2 +- man/roxygen/meta.R | 17 --------------- man/sample_.Rd | 2 +- man/sample_bipartite.Rd | 4 ++-- man/sample_correlated_gnp.Rd | 2 +- man/sample_correlated_gnp_pair.Rd | 2 +- man/sample_degseq.Rd | 4 ++-- man/sample_dot_product.Rd | 4 ++-- man/sample_fitness.Rd | 2 +- man/sample_fitness_pl.Rd | 2 +- man/sample_forestfire.Rd | 2 +- man/sample_gnm.Rd | 4 ++-- man/sample_gnp.Rd | 4 ++-- man/sample_grg.Rd | 4 ++-- man/sample_growing.Rd | 4 ++-- man/sample_hierarchical_sbm.Rd | 4 ++-- man/sample_islands.Rd | 2 +- man/sample_k_regular.Rd | 2 +- man/sample_last_cit.Rd | 12 +++++----- man/sample_pa.Rd | 4 ++-- man/sample_pa_age.Rd | 4 ++-- man/sample_pref.Rd | 8 +++---- man/sample_sbm.Rd | 4 ++-- man/sample_smallworld.Rd | 4 ++-- man/sample_traits_callaway.Rd | 8 +++---- man/sample_tree.Rd | 2 +- man/scg-method.Rd | 2 +- man/scg.Rd | 2 +- man/scg_eps.Rd | 2 +- man/scg_group.Rd | 2 +- man/scg_semi_proj.Rd | 2 +- man/set_edge_attr.Rd | 2 +- man/set_graph_attr.Rd | 2 +- man/set_vertex_attr.Rd | 2 +- man/sir.Rd | 6 ++--- man/spectrum.Rd | 2 +- man/split_join_distance.Rd | 2 +- man/stochastic_matrix.Rd | 2 +- man/strength.Rd | 2 +- man/subgraph_centrality.Rd | 2 +- man/vertex_attr-set.Rd | 2 +- man/vertex_attr.Rd | 2 +- man/vertex_attr_names.Rd | 2 +- man/write_graph.Rd | 2 +- src/Makevars | 4 ++-- 96 files changed, 143 insertions(+), 160 deletions(-) delete mode 100644 man/roxygen/meta.R diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 4c477513c8..4ffb8d007a 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -93,7 +93,7 @@ measures of centrality for asymmetric relations'' \emph{Social Networks}, \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=power_centrality]{power_centrality()}} -Centrality measures +Other centrality: \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, diff --git a/man/arpack.Rd b/man/arpack.Rd index aa58a943a8..97536eb852 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -218,7 +218,7 @@ Matrices. \emph{Linear Algebra and its Applications}, vol 88/89, pp 575-595, \code{\link[=hub_score]{hub_score()}}, \code{\link[=cluster_leading_eigen]{cluster_leading_eigen()}} are some of the functions in igraph that use ARPACK. -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{authority_score}()}, \code{\link{closeness}()}, @@ -233,7 +233,7 @@ Centrality measures \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{authority_score}()}, \code{\link{closeness}()}, diff --git a/man/articulation_points.Rd b/man/articulation_points.Rd index 3b65008811..4a15c428fe 100644 --- a/man/articulation_points.Rd +++ b/man/articulation_points.Rd @@ -47,12 +47,12 @@ bridges(g) \code{\link[=is_connected]{is_connected()}}, \code{\link[=vertex_connectivity]{vertex_connectivity()}}, \code{\link[=edge_connectivity]{edge_connectivity()}} -Connected components +Other components: \code{\link{biconnected_components}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} -Connected components +Other components: \code{\link{biconnected_components}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} diff --git a/man/as_membership.Rd b/man/as_membership.Rd index fc3d64d31c..c57db5bcc6 100644 --- a/man/as_membership.Rd +++ b/man/as_membership.Rd @@ -27,7 +27,7 @@ compare(correct, fc) compare(correct, membership(fc)) } \seealso{ -Community detection +Other community: \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/authority_score.Rd b/man/authority_score.Rd index b7c7c9add6..48faa728fd 100644 --- a/man/authority_score.Rd +++ b/man/authority_score.Rd @@ -66,7 +66,7 @@ eigenvector centrality, \code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for the underlining machinery of the computation. -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{closeness}()}, diff --git a/man/betweenness.Rd b/man/betweenness.Rd index cc5ab996a2..b1dcac5456 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -133,7 +133,7 @@ of Mathematical Sociology} 25(2):163-177, 2001. \seealso{ \code{\link[=closeness]{closeness()}}, \code{\link[=degree]{degree()}}, \code{\link[=harmonic_centrality]{harmonic_centrality()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, @@ -148,7 +148,7 @@ Centrality measures \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, @@ -163,7 +163,7 @@ Centrality measures \code{\link{strength}()}, \code{\link{subgraph_centrality}()} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/biconnected_components.Rd b/man/biconnected_components.Rd index 3fe8dd3016..cf73788922 100644 --- a/man/biconnected_components.Rd +++ b/man/biconnected_components.Rd @@ -46,7 +46,7 @@ bc <- biconnected_components(g) \code{\link[=articulation_points]{articulation_points()}}, \code{\link[=components]{components()}}, \code{\link[=is_connected]{is_connected()}}, \code{\link[=vertex_connectivity]{vertex_connectivity()}} -Connected components +Other components: \code{\link{articulation_points}()}, \code{\link{component_distribution}()}, \code{\link{decompose}()} diff --git a/man/bipartite_mapping.Rd b/man/bipartite_mapping.Rd index d5a3f0c599..20f1b8e7fd 100644 --- a/man/bipartite_mapping.Rd +++ b/man/bipartite_mapping.Rd @@ -52,7 +52,7 @@ g3 <- add_edges(g3, c(1, 3)) bipartite_mapping(g3) } \seealso{ -Bipartite graphs +Other bipartite: \code{\link{bipartite_projection}()}, \code{\link{is_bipartite}()} } diff --git a/man/bipartite_projection.Rd b/man/bipartite_projection.Rd index dc009fb2f9..56cc5c84a0 100644 --- a/man/bipartite_projection.Rd +++ b/man/bipartite_projection.Rd @@ -90,7 +90,7 @@ print(proj2[[2]], g = TRUE, e = TRUE) } \seealso{ -Bipartite graphs +Other bipartite: \code{\link{bipartite_mapping}()}, \code{\link{is_bipartite}()} } diff --git a/man/closeness.Rd b/man/closeness.Rd index b7587d2da0..f59039a83b 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -88,7 +88,7 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239. \seealso{ \code{\link[=betweenness]{betweenness()}}, \code{\link[=degree]{degree()}}, \code{\link[=harmonic_centrality]{harmonic_centrality()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/cluster_edge_betweenness.Rd b/man/cluster_edge_betweenness.Rd index 0829b4b459..840cc7c526 100644 --- a/man/cluster_edge_betweenness.Rd +++ b/man/cluster_edge_betweenness.Rd @@ -110,7 +110,7 @@ methods. See \code{\link[=communities]{communities()}} for extracting the results of the community detection. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_fast_greedy}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/cluster_fast_greedy.Rd b/man/cluster_fast_greedy.Rd index 96ba6c2461..5d17e46a11 100644 --- a/man/cluster_fast_greedy.Rd +++ b/man/cluster_fast_greedy.Rd @@ -69,7 +69,7 @@ See also \code{\link[=cluster_walktrap]{cluster_walktrap()}}, \code{\link[=cluster_edge_betweenness]{cluster_edge_betweenness()}}, \code{\link[=cluster_louvain]{cluster_louvain()}} \code{\link[=cluster_leiden]{cluster_leiden()}} for other methods. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fluid_communities}()}, diff --git a/man/cluster_fluid_communities.Rd b/man/cluster_fluid_communities.Rd index 84369a92ae..cbe3eb9bda 100644 --- a/man/cluster_fluid_communities.Rd +++ b/man/cluster_fluid_communities.Rd @@ -48,7 +48,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_louvain]{cluster_louvain()}}, \code{\link[=cluster_leiden]{cluster_leiden()}} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_infomap.Rd b/man/cluster_infomap.Rd index c6686d9877..5841c4fe1d 100644 --- a/man/cluster_infomap.Rd +++ b/man/cluster_infomap.Rd @@ -68,7 +68,7 @@ equation, \emph{Eur. Phys. J. Special Topics} 178, 13 (2009). \seealso{ Other community finding methods and \code{\link[=communities]{communities()}}. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_label_prop.Rd b/man/cluster_label_prop.Rd index 9921b49129..68f3f887bd 100644 --- a/man/cluster_label_prop.Rd +++ b/man/cluster_label_prop.Rd @@ -70,7 +70,7 @@ Rev E} 76, 036106. (2007) \code{\link[=cluster_spinglass]{cluster_spinglass()}}, \code{\link[=cluster_louvain]{cluster_louvain()}} and \code{\link[=cluster_leiden]{cluster_leiden()}} for other community detection methods. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_leading_eigen.Rd b/man/cluster_leading_eigen.Rd index 9797582c90..568d18a692 100644 --- a/man/cluster_leading_eigen.Rd +++ b/man/cluster_leading_eigen.Rd @@ -122,7 +122,7 @@ of matrices, Physical Review E 74 036104, 2006. \code{\link[=cluster_edge_betweenness]{cluster_edge_betweenness()}}, \code{\link[=cluster_fast_greedy]{cluster_fast_greedy()}}, \code{\link[=as.dendrogram]{as.dendrogram()}} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_leiden.Rd b/man/cluster_leiden.Rd index dc97b8b91a..b78653fe63 100644 --- a/man/cluster_leiden.Rd +++ b/man/cluster_leiden.Rd @@ -130,7 +130,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_optimal]{cluster_optimal()}} \code{\link[=cluster_walktrap]{cluster_walktrap()}} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_louvain.Rd b/man/cluster_louvain.Rd index 8a746e3dce..9cf4e4be44 100644 --- a/man/cluster_louvain.Rd +++ b/man/cluster_louvain.Rd @@ -76,7 +76,7 @@ Other community detection algorithms: \code{\link[=cluster_walktrap]{cluster_wal \code{\link[=cluster_label_prop]{cluster_label_prop()}} \code{\link[=cluster_leiden]{cluster_leiden()}} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_optimal.Rd b/man/cluster_optimal.Rd index a5b9e5cb37..13d230858d 100644 --- a/man/cluster_optimal.Rd +++ b/man/cluster_optimal.Rd @@ -75,7 +75,7 @@ Martin Hoefer, Zoran Nikoloski, Dorothea Wagner: On Modularity Clustering, \code{\link[=modularity]{modularity()}}. See also \code{\link[=cluster_fast_greedy]{cluster_fast_greedy()}} for a fast greedy optimizer. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_spinglass.Rd b/man/cluster_spinglass.Rd index 70d28a27dd..c25af27998 100644 --- a/man/cluster_spinglass.Rd +++ b/man/cluster_spinglass.Rd @@ -146,7 +146,7 @@ positive and negative links, \url{https://arxiv.org/abs/0811.2329} (2008). \seealso{ \code{\link[=communities]{communities()}}, \code{\link[=components]{components()}} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/cluster_walktrap.Rd b/man/cluster_walktrap.Rd index 99d51a045f..4dc45fd02a 100644 --- a/man/cluster_walktrap.Rd +++ b/man/cluster_walktrap.Rd @@ -75,7 +75,7 @@ vector, merge matrix, modularity score, etc. and \code{\link[=cluster_leiden]{cluster_leiden()}} for other community detection methods. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/communities.Rd b/man/communities.Rd index 81aa4af09d..1094a04f1d 100644 --- a/man/communities.Rd +++ b/man/communities.Rd @@ -275,7 +275,7 @@ The different methods for finding communities, they all return a \code{\link[=cluster_optimal]{cluster_optimal()}}, \code{\link[=cluster_spinglass]{cluster_spinglass()}}, \code{\link[=cluster_walktrap]{cluster_walktrap()}}. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -295,7 +295,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -315,7 +315,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -335,7 +335,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -355,7 +355,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -375,7 +375,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -395,7 +395,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -415,7 +415,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -435,7 +435,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -455,7 +455,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -475,7 +475,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -495,7 +495,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -515,7 +515,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -535,7 +535,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -555,7 +555,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -575,7 +575,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -595,7 +595,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/compare.Rd b/man/compare.Rd index 8eef71fc43..5677c33a71 100644 --- a/man/compare.Rd +++ b/man/compare.Rd @@ -76,7 +76,7 @@ See \code{\link[=cluster_walktrap]{cluster_walktrap()}}, \code{\link[=cluster_leiden]{cluster_leiden()}} for various community detection methods. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/components.Rd b/man/components.Rd index 264977ca37..2252a2747d 100644 --- a/man/components.Rd +++ b/man/components.Rd @@ -80,7 +80,7 @@ groups(clu) \seealso{ \code{\link[=decompose]{decompose()}}, \code{\link[=subcomponent]{subcomponent()}}, \code{\link[=groups]{groups()}} -Connected components +Other components: \code{\link{articulation_points}()}, \code{\link{biconnected_components}()}, \code{\link{decompose}()} diff --git a/man/decompose.Rd b/man/decompose.Rd index 4bf6567e71..25be6adfea 100644 --- a/man/decompose.Rd +++ b/man/decompose.Rd @@ -42,7 +42,7 @@ sapply(components, diameter) \code{\link[=is_connected]{is_connected()}} to decide whether a graph is connected, \code{\link[=components]{components()}} to calculate the connected components of a graph. -Connected components +Other components: \code{\link{articulation_points}()}, \code{\link{biconnected_components}()}, \code{\link{component_distribution}()} diff --git a/man/delete_edge_attr.Rd b/man/delete_edge_attr.Rd index 933d737cd9..83ffaf4b2f 100644 --- a/man/delete_edge_attr.Rd +++ b/man/delete_edge_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_edge_attr(g, "name") edge_attr_names(g2) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, diff --git a/man/delete_graph_attr.Rd b/man/delete_graph_attr.Rd index cb185a78dd..c3bf6be7cf 100644 --- a/man/delete_graph_attr.Rd +++ b/man/delete_graph_attr.Rd @@ -25,7 +25,7 @@ g2 <- delete_graph_attr(g, "name") graph_attr_names(g2) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, diff --git a/man/delete_vertex_attr.Rd b/man/delete_vertex_attr.Rd index 3852e56e99..40c64cd693 100644 --- a/man/delete_vertex_attr.Rd +++ b/man/delete_vertex_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_vertex_attr(g, "name") vertex_attr_names(g2) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{edge_attr<-}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index 1be804a923..ffcbe42644 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -53,7 +53,7 @@ Nathan Eagle, Michael Macy and Rob Claxton: Network Diversity and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010. } \seealso{ -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/edge_attr-set.Rd b/man/edge_attr-set.Rd index 7b14870552..430ae2a112 100644 --- a/man/edge_attr-set.Rd +++ b/man/edge_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/edge_attr.Rd b/man/edge_attr.Rd index 3782d28951..8eb9e2e951 100644 --- a/man/edge_attr.Rd +++ b/man/edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g, edge.width = E(g)$weight) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/edge_attr_names.Rd b/man/edge_attr_names.Rd index c51a641cb8..112a326ad7 100644 --- a/man/edge_attr_names.Rd +++ b/man/edge_attr_names.Rd @@ -23,7 +23,7 @@ edge_attr_names(g) plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index df989a0679..a3df9eaeef 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -103,7 +103,7 @@ Bonacich, P. (1987). Power and Centrality: A Family of Measures. \emph{American Journal of Sociology}, 92, 1170-1182. } \seealso{ -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 16a0b7918a..6b61a6fe83 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -67,7 +67,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_pa]{sample_pa()}} -Random graph models (games) +Other games: \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_correlated_gnp}()}, diff --git a/man/graph_attr-set.Rd b/man/graph_attr-set.Rd index 8f0e6d340c..6884d17af2 100644 --- a/man/graph_attr-set.Rd +++ b/man/graph_attr-set.Rd @@ -34,7 +34,7 @@ graph_attr(g) <- list( plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/graph_attr.Rd b/man/graph_attr.Rd index 24da90ff98..90bbad9a89 100644 --- a/man/graph_attr.Rd +++ b/man/graph_attr.Rd @@ -26,7 +26,7 @@ graph_attr(g) graph_attr(g, "name") } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/graph_attr_names.Rd b/man/graph_attr_names.Rd index 8a91c0b3b1..a6ced3f0f2 100644 --- a/man/graph_attr_names.Rd +++ b/man/graph_attr_names.Rd @@ -22,7 +22,7 @@ g <- make_ring(10) graph_attr_names(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/graph_from_graphdb.Rd b/man/graph_from_graphdb.Rd index 77824ec73e..77414d3dc0 100644 --- a/man/graph_from_graphdb.Rd +++ b/man/graph_from_graphdb.Rd @@ -95,7 +95,7 @@ of graphs and its use for benchmarking graph isomorphism algorithms, \seealso{ \code{\link[=read_graph]{read_graph()}}, \code{\link[=graph.isomorphic.vf2]{graph.isomorphic.vf2()}} -Foreign format readers +Other foreign: \code{\link{read_graph}()}, \code{\link{write_graph}()} } diff --git a/man/groups.Rd b/man/groups.Rd index a72ac54bb8..99e67389db 100644 --- a/man/groups.Rd +++ b/man/groups.Rd @@ -40,7 +40,7 @@ groups(components(g2)) \code{\link[=components]{components()}} and the various community finding functions. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index bc2249e8f8..2918a4f731 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -69,7 +69,7 @@ M. Marchiori and V. Latora, Harmony in the small-world, \seealso{ \code{\link[=betweenness]{betweenness()}}, \code{\link[=closeness]{closeness()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/hub_score.Rd b/man/hub_score.Rd index 69e993d124..7fc8e9aa3c 100644 --- a/man/hub_score.Rd +++ b/man/hub_score.Rd @@ -64,7 +64,7 @@ as IBM Research Report RJ 10076, May 1997. \code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for the underlining machinery of the computation. -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/igraph-attribute-combination.Rd b/man/igraph-attribute-combination.Rd index 2afea5b1b7..51ed51885c 100644 --- a/man/igraph-attribute-combination.Rd +++ b/man/igraph-attribute-combination.Rd @@ -106,7 +106,7 @@ simplify(g, edge.attr.comb = list( \code{\link[=edge_attr]{edge_attr()}} on how to use graph/vertex/edge attributes in general. \code{\link[=igraph_options]{igraph_options()}} on igraph parameters. -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/igraph-dollar.Rd b/man/igraph-dollar.Rd index 141eb013e5..7b274b7d8f 100644 --- a/man/igraph-dollar.Rd +++ b/man/igraph-dollar.Rd @@ -29,7 +29,7 @@ g$name <- "10-ring" g$name } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/igraph-vs-attributes.Rd b/man/igraph-vs-attributes.Rd index bbc9f5e79f..fa52ecc3e2 100644 --- a/man/igraph-vs-attributes.Rd +++ b/man/igraph-vs-attributes.Rd @@ -88,7 +88,7 @@ Other vertex and edge sequences: \code{\link{print.igraph.es}()}, \code{\link{print.igraph.vs}()} -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/make_bipartite_graph.Rd b/man/make_bipartite_graph.Rd index c431c006b8..f5826e93ca 100644 --- a/man/make_bipartite_graph.Rd +++ b/man/make_bipartite_graph.Rd @@ -67,7 +67,7 @@ print(g, v = TRUE) \seealso{ \code{\link[=graph]{graph()}} to create one-mode networks -Bipartite graphs +Other bipartite: \code{\link{bipartite_mapping}()}, \code{\link{bipartite_projection}()} } diff --git a/man/make_clusters.Rd b/man/make_clusters.Rd index 2d43b04272..cce710a005 100644 --- a/man/make_clusters.Rd +++ b/man/make_clusters.Rd @@ -38,7 +38,7 @@ This is useful to integrate the results of community finding algorithms that are not included in igraph. } \seealso{ -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/modularity.igraph.Rd b/man/modularity.igraph.Rd index be8a1d40be..d3df27171a 100644 --- a/man/modularity.igraph.Rd +++ b/man/modularity.igraph.Rd @@ -104,7 +104,7 @@ structure in very large networks, \emph{Physical Review E} 2004, 70, 066111 \code{\link[=cluster_louvain]{cluster_louvain()}} and \code{\link[=cluster_leiden]{cluster_leiden()}} for various community detection methods. -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -124,7 +124,7 @@ Community detection \code{\link{plot_dendrogram}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/page_rank.Rd b/man/page_rank.Rd index c3e8ea81e5..636624f37c 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -109,7 +109,7 @@ Conference, Brisbane, Australia, April 1998. Other centrality scores: \code{\link[=closeness]{closeness()}}, \code{\link[=betweenness]{betweenness()}}, \code{\link[=degree]{degree()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/plot.sir.Rd b/man/plot.sir.Rd index f8d69ada43..12e9eb7418 100644 --- a/man/plot.sir.Rd +++ b/man/plot.sir.Rd @@ -85,7 +85,7 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=sir]{sir()}} for running the actual simulation. -Processes on graphs +Other processes: \code{\link{time_bins.sir}()} } \author{ diff --git a/man/plot_dendrogram.communities.Rd b/man/plot_dendrogram.communities.Rd index 4646891908..a0bd71492e 100644 --- a/man/plot_dendrogram.communities.Rd +++ b/man/plot_dendrogram.communities.Rd @@ -101,7 +101,7 @@ plot_dendrogram(fc) } \seealso{ -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, @@ -121,7 +121,7 @@ Community detection \code{\link{modularity.igraph}()}, \code{\link{split_join_distance}()} -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index e06107d313..c3f222eac3 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -135,7 +135,7 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.'' \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=alpha_centrality]{alpha_centrality()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/read_graph.Rd b/man/read_graph.Rd index 3b69485609..189cafa9a8 100644 --- a/man/read_graph.Rd +++ b/man/read_graph.Rd @@ -59,7 +59,7 @@ default value is \code{TRUE}.} } \seealso{ \code{\link[=write_graph]{write_graph()}} -Foreign format readers +Other foreign: \code{\link{graph_from_graphdb}()}, \code{\link{write_graph}()} } diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R deleted file mode 100644 index 6faddc1d86..0000000000 --- a/man/roxygen/meta.R +++ /dev/null @@ -1,17 +0,0 @@ -list( - rd_family_title = list( - adjacency = "Adjacency matrices", - attributes = "Vertex, edge and graph attributes", - bipartite = "Bipartite graphs", - centrality = "Centrality measures", - coloring = "Graph coloring", - community = "Community detection", - components = "Connected components", - processes = "Processes on graphs", - cycles = "Graph cycles", - foreign = "Foreign format readers", - games = "Random graph models (games)", - scg = "Spectral Coarse Graining", - sgm = "Graph matching" - ) -) diff --git a/man/sample_.Rd b/man/sample_.Rd index 67173bc2b9..13f0754e03 100644 --- a/man/sample_.Rd +++ b/man/sample_.Rd @@ -30,7 +30,7 @@ blocky3 <- pref_matrix \%>\% sample_(sbm(), n = 20, block.sizes = c(10, 10)) } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index c0cf409ffa..1e4c2fc5f2 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -76,7 +76,7 @@ sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} and \code{\link[=sample_gnm]{sample_gnm()}} for the unipartite version. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_correlated_gnp}()}, @@ -102,7 +102,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_correlated_gnp}()}, diff --git a/man/sample_correlated_gnp.Rd b/man/sample_correlated_gnp.Rd index de47064bc4..9d0d4b1887 100644 --- a/man/sample_correlated_gnp.Rd +++ b/man/sample_correlated_gnp.Rd @@ -58,7 +58,7 @@ graph matching for correlated Erdos-Renyi graphs. \code{\link[=sample_correlated_gnp_pair]{sample_correlated_gnp_pair()}}, \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index 5ca3163aaa..f298b9230b 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -51,7 +51,7 @@ graph matching for correlated Erdos-Renyi graphs. \code{\link[=sample_correlated_gnp]{sample_correlated_gnp()}}, \code{\link[=sample_gnp]{sample_gnp()}}. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp}()}, diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index 5bc1857403..cccaf32d71 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -108,7 +108,7 @@ all(degree(g5) == degs) \code{\link[=simplify]{simplify()}} to get rid of the multiple and/or loops edges, \code{\link[=realize_degseq]{realize_degseq()}} for a deterministic variant. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -134,7 +134,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index 40f6368f9c..88b4d39de7 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -56,7 +56,7 @@ for social networks. Dissertation, Johns Hopkins University, Maryland, USA, \code{\link[=sample_dirichlet]{sample_dirichlet()}}, \code{\link[=sample_sphere_surface]{sample_sphere_surface()}} and \code{\link[=sample_sphere_volume]{sample_sphere_volume()}} for sampling position vectors. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -82,7 +82,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index 408b230ce7..355451dc9f 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -79,7 +79,7 @@ distribution in scale-free networks. \emph{Phys Rev Lett} 87(27):278701, 2001. } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index 8d7957e574..b132ec52c2 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -88,7 +88,7 @@ scale-free networks under the Achlioptas process. \emph{Phys Rev Lett} 103:135702, 2009. } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index db2a553406..189a275fb6 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -72,7 +72,7 @@ conference on Knowledge discovery in data mining}, 177--187, 2005. \code{\link[=barabasi.game]{barabasi.game()}} for the basic preferential attachment model. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 6a1b076510..0f6fd2515e 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -46,7 +46,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_pa]{sample_pa()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -72,7 +72,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index b0ce3e6939..72eec4f2b5 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -45,7 +45,7 @@ Mathematicae} 6, 290--297 (1959). \seealso{ \code{\link[=sample_gnm]{sample_gnm()}}, \code{\link[=sample_pa]{sample_pa()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -71,7 +71,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 58253883ef..3f7684edb1 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -47,7 +47,7 @@ g2 <- sample_grg(1000, 0.05, torus = TRUE) \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -73,7 +73,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index bb3b7014b2..ffacc79df7 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -44,7 +44,7 @@ g2 <- sample_growing(500, citation = TRUE) \seealso{ \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -70,7 +70,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index 74de881742..18fcf81b63 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -58,7 +58,7 @@ if (require(Matrix)) { \seealso{ \code{\link[=sbm.game]{sbm.game()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -84,7 +84,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 04dcf2d1f1..a9155243c0 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -36,7 +36,7 @@ oc \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 6808ab72f4..36d0842f0c 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -48,7 +48,7 @@ sapply(k10, plot, vertex.label = NA) \code{\link[=sample_degseq]{sample_degseq()}} for a generator with prescribed degree sequence. -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index ec1259857a..650447753e 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -82,7 +82,7 @@ but the probability of an edge depends on the (potentially) cited vertex only. } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -108,7 +108,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -134,7 +134,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -160,7 +160,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -186,7 +186,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -212,7 +212,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index 1cc3d63a4e..19ccbcb05a 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -130,7 +130,7 @@ de Solla Price, D. J. 1965. Networks of Scientific Papers \emph{Science}, \seealso{ \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -156,7 +156,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index cd940e879d..261ec49221 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -140,7 +140,7 @@ max(degree(g3)) \seealso{ \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -166,7 +166,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index cf50ad99b1..7d04d5b26d 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -101,7 +101,7 @@ tkplot(g, layout = layout_in_circle) \code{\link[=sample_traits]{sample_traits()}}. \code{\link[=sample_traits_callaway]{sample_traits_callaway()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -127,7 +127,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -153,7 +153,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -179,7 +179,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index 3f7cf092f7..0383639adf 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -55,7 +55,7 @@ and evaluation. \emph{Social Networks}, 14, 5--61. \seealso{ \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_gnm]{sample_gnm()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -81,7 +81,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 2106f3c476..70206f6b19 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -56,7 +56,7 @@ Duncan J Watts and Steven H Strogatz: Collective dynamics of \seealso{ \code{\link[=make_lattice]{make_lattice()}}, \code{\link[=rewire]{rewire()}} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -82,7 +82,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index 9546a9b46c..84d86d411e 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -80,7 +80,7 @@ g1 <- sample_traits_callaway(1000, 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2)) } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -106,7 +106,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -132,7 +132,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, @@ -158,7 +158,7 @@ Random graph models (games) \code{\link{sample_tree}()}, \code{\link{sample_}()} -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_tree.Rd b/man/sample_tree.Rd index 2cada8d411..f310e68e73 100644 --- a/man/sample_tree.Rd +++ b/man/sample_tree.Rd @@ -36,7 +36,7 @@ g <- sample_tree(100, method = "lerw") } \seealso{ -Random graph models (games) +Other games: \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/scg-method.Rd b/man/scg-method.Rd index 00b2cbc4e3..ae9d4e98d0 100644 --- a/man/scg-method.Rd +++ b/man/scg-method.Rd @@ -46,7 +46,7 @@ Networks, \emph{Physical Review Letters}, \strong{99}(3), 2007. \url{https://arxiv.org/abs/0706.0812} } \seealso{ -Spectral Coarse Graining +Other scg: \code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, diff --git a/man/scg.Rd b/man/scg.Rd index fa77e9bd11..2a831910cf 100644 --- a/man/scg.Rd +++ b/man/scg.Rd @@ -240,7 +240,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for an introduction. \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} and \code{\link[=scg_semi_proj]{scg_semi_proj()}}. -Spectral Coarse Graining +Other scg: \code{\link{scg-method}}, \code{\link{scg_eps}()}, \code{\link{scg_group}()}, diff --git a/man/scg_eps.Rd b/man/scg_eps.Rd index d317f1fb1c..9c3fb53412 100644 --- a/man/scg_eps.Rd +++ b/man/scg_eps.Rd @@ -58,7 +58,7 @@ Matrix Analysis and Applications}, 2008. \seealso{ \link{scg-method} and \code{\link[=scg]{scg()}}. -Spectral Coarse Graining +Other scg: \code{\link{scg-method}}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, diff --git a/man/scg_group.Rd b/man/scg_group.Rd index 24aa1fada7..a3ebe96f8a 100644 --- a/man/scg_group.Rd +++ b/man/scg_group.Rd @@ -135,7 +135,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for a detailed introduction. \code{\link[=scg]{scg()}}, \code{\link[=scg_eps]{scg_eps()}} -Spectral Coarse Graining +Other scg: \code{\link{scg-method}}, \code{\link{scg_eps}()}, \code{\link{scg_semi_proj}()}, diff --git a/man/scg_semi_proj.Rd b/man/scg_semi_proj.Rd index 8df8cb9f99..3a0d6cd44e 100644 --- a/man/scg_semi_proj.Rd +++ b/man/scg_semi_proj.Rd @@ -100,7 +100,7 @@ Matrix Analysis and Applications}, 2008. \link{scg-method} for a detailed introduction. \code{\link[=scg]{scg()}}, \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} -Spectral Coarse Graining +Other scg: \code{\link{scg-method}}, \code{\link{scg_eps}()}, \code{\link{scg_group}()}, diff --git a/man/set_edge_attr.Rd b/man/set_edge_attr.Rd index d188cdc00b..1209d6dc92 100644 --- a/man/set_edge_attr.Rd +++ b/man/set_edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/set_graph_attr.Rd b/man/set_graph_attr.Rd index 0675b57342..433303b7f2 100644 --- a/man/set_graph_attr.Rd +++ b/man/set_graph_attr.Rd @@ -27,7 +27,7 @@ g plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/set_vertex_attr.Rd b/man/set_vertex_attr.Rd index 3c0ef7f9fd..2ba306beca 100644 --- a/man/set_vertex_attr.Rd +++ b/man/set_vertex_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/sir.Rd b/man/sir.Rd index 8e62895a78..0d37f7b67a 100644 --- a/man/sir.Rd +++ b/man/sir.Rd @@ -106,13 +106,13 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=plot.sir]{plot.sir()}} to conveniently plot the results -Processes on graphs +Other processes: \code{\link{plot.sir}()} -Processes on graphs +Other processes: \code{\link{plot.sir}()} -Processes on graphs +Other processes: \code{\link{plot.sir}()} } \author{ diff --git a/man/spectrum.Rd b/man/spectrum.Rd index b5ee09d396..d69ed862cb 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -78,7 +78,7 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values \seealso{ \code{\link[=as_adj]{as_adj()}} to create a (sparse) adjacency matrix. -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/split_join_distance.Rd b/man/split_join_distance.Rd index 241059882b..8e926d1384 100644 --- a/man/split_join_distance.Rd +++ b/man/split_join_distance.Rd @@ -42,7 +42,7 @@ Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. } \seealso{ -Community detection +Other community: \code{\link{as_membership}()}, \code{\link{cluster_edge_betweenness}()}, \code{\link{cluster_fast_greedy}()}, diff --git a/man/stochastic_matrix.Rd b/man/stochastic_matrix.Rd index 74bd73bb93..22822eb2d8 100644 --- a/man/stochastic_matrix.Rd +++ b/man/stochastic_matrix.Rd @@ -53,7 +53,7 @@ max(abs(rowSums(W)) - 1) \seealso{ \code{\link[=as_adj]{as_adj()}} -Spectral Coarse Graining +Other scg: \code{\link{scg-method}}, \code{\link{scg_eps}()}, \code{\link{scg_group}()}, diff --git a/man/strength.Rd b/man/strength.Rd index 86fd457bc9..7c0052f671 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -55,7 +55,7 @@ Natl. Acad. Sci. USA 101, 3747 (2004) \seealso{ \code{\link[=degree]{degree()}} for the unweighted version. -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index cb5128c0bd..de600ec292 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -45,7 +45,7 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005). \seealso{ \code{\link[=eigen_centrality]{eigen_centrality()}}, \code{\link[=page_rank]{page_rank()}} -Centrality measures +Other centrality: \code{\link{alpha_centrality}()}, \code{\link{arpack_defaults}}, \code{\link{authority_score}()}, diff --git a/man/vertex_attr-set.Rd b/man/vertex_attr-set.Rd index 90469b00ba..e28f740070 100644 --- a/man/vertex_attr-set.Rd +++ b/man/vertex_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/vertex_attr.Rd b/man/vertex_attr.Rd index 04b04357df..960c0e2d7e 100644 --- a/man/vertex_attr.Rd +++ b/man/vertex_attr.Rd @@ -33,7 +33,7 @@ vertex_attr(g) plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/vertex_attr_names.Rd b/man/vertex_attr_names.Rd index d62dcfd92e..36111f8747 100644 --- a/man/vertex_attr_names.Rd +++ b/man/vertex_attr_names.Rd @@ -24,7 +24,7 @@ vertex_attr_names(g) plot(g) } \seealso{ -Vertex, edge and graph attributes +Other attributes: \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, diff --git a/man/write_graph.Rd b/man/write_graph.Rd index f5c9882970..3be2c656c5 100644 --- a/man/write_graph.Rd +++ b/man/write_graph.Rd @@ -58,7 +58,7 @@ networks. \emph{J Mol Biol.} 2004 Jun 25;340(1):179-90. \seealso{ \code{\link[=read_graph]{read_graph()}} -Foreign format readers +Other foreign: \code{\link{graph_from_graphdb}()}, \code{\link{read_graph}()} } diff --git a/src/Makevars b/src/Makevars index d9535e9849..fc864eb796 100644 --- a/src/Makevars +++ b/src/Makevars @@ -5,10 +5,10 @@ PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT \ + -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ -DINTERNAL_ARPACK \ -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) all: $(SHLIB) From 973b5afb784ab6da5d3f24a54ad96eadc585614c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:21:47 +0100 Subject: [PATCH 39/54] reorganization as explained in https://github.com/igraph/rigraph/pull/662#issuecomment-1419447295 --- _pkgdown.yml | 60 +++++++++++++++++++++++++--------------------------- 1 file changed, 29 insertions(+), 31 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index b66b343850..db664a600e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -43,6 +43,7 @@ reference: - subtitle: Graph coloring - contents: - has_concept("coloring") +# The following are mostly about programming rather than analysis - title: Functions for manipulating graph structure - contents: - has_concept("functions for manipulating graph structure") @@ -53,6 +54,13 @@ reference: - subtitle: Rewiring functions - contents: - has_concept("rewiring functions") +- title: Vertex, edge and graph attributes +- contents: + - has_concept("attributes") +- title: Vertex and edge sequences +- contents: + - has_concept("vertex and edge sequences") + - has_concept("vertex and edge sequence operations") - title: Utilities - subtitle: Utilities - subtitle: Graph ID, comparison, name, weight @@ -82,6 +90,7 @@ reference: - running_mean - sample_seq - fit_power_law +# [[[ network analysis start - title: Structural properties - contents: - has_concept("structural.properties") @@ -145,23 +154,33 @@ reference: - title: Graph cycles - contents: - has_concept("cycles") -- title: Processes on graphs +- title: Connected components - contents: - - has_concept("processes") - - has_concept("random_walk") -- title: Vertex, edge and graph attributes + - has_concept("components") +- title: Scan statistics - contents: - - has_concept("attributes") -- title: Cliques + - has_concept("scan statistics") +- title: Spectral Coarse Graining - contents: - - has_concept("cliques") - - has_concept("glet") -- title: Connected components + - has_concept("scg") +- title: Embedding - contents: - - has_concept("components") + - has_concept("embedding") + - embed_laplacian_matrix +- title: Hierarchical random graph functions +- contents: + - has_concept("hierarchical random graph functions") +# network analysis end, we keep these sections together ]]] +# the following two are also "scientific functions" (not "programming functions"), +# but they do not compute a result for a graph, like in the previous sections - title: Graphical degree sequences - contents: - has_concept("graphical degree sequences") +- title: Processes on graphs +- contents: + - has_concept("processes") + - has_concept("random_walk") +# ----- - title: Demo - contents: - has_concept("demo") @@ -171,27 +190,6 @@ reference: - title: I/O Read/Write Files - contents: - has_concept("foreign") -- title: Hierarchical random graph functions -- contents: - - has_concept("hierarchical random graph functions") -- title: Vertex and edge sequences -- contents: - - has_concept("vertex and edge sequences") - - has_concept("vertex and edge sequence operations") -- title: Functions for manipulating graph structure -- contents: - - has_concept("functions for manipulating graph structure") - -- title: Scan statistics -- contents: - - has_concept("scan statistics") -- title: Spectral Coarse Graining -- contents: - - has_concept("scg") -- title: Embedding -- contents: - - has_concept("embedding") - - embed_laplacian_matrix - title: Interactive functions - contents: - has_concept("socnet") From 6e0a059650191a65c2937d4f8a163d6c3554a575 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:28:54 +0100 Subject: [PATCH 40/54] place games directly after deterministic constructors --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index db664a600e..1b8b24d527 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -13,6 +13,9 @@ reference: - starts_with("make_") - realize_degseq - has_concept("deterministic constructors") +- subtitle: "Stochastic constructors -- Random graph models (games)" +- contents: + - has_concept("games") - subtitle: Constructor modifiers - contents: - has_concept("constructor modifiers") @@ -21,9 +24,6 @@ reference: - as.igraph - graph_from_lcf - graph_ -- subtitle: "Random graph models (games)" -- contents: - - has_concept("games") - subtitle: Adjacency matrices - contents: - has_concept("adjacency") From 5896cd4602f800f1eb27475e7e3c5b6cc68d79ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:29:22 +0100 Subject: [PATCH 41/54] keep capitalization consistent --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 1b8b24d527..74b562251b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -187,7 +187,7 @@ reference: - title: Latent position vector samplers - contents: - has_concept("latent position vector samplers") -- title: I/O Read/Write Files +- title: I/O read/write files - contents: - has_concept("foreign") - title: Interactive functions From 091f3747a34c162f08cec9c529ef0357ac603a10 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:35:29 +0100 Subject: [PATCH 42/54] rename section --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 74b562251b..7c3e8e03e2 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -44,7 +44,7 @@ reference: - contents: - has_concept("coloring") # The following are mostly about programming rather than analysis -- title: Functions for manipulating graph structure +- title: Functions for manipulating graphs - contents: - has_concept("functions for manipulating graph structure") - permute From 82aa2a3403a74260da2f2f2040f94181cdcd3fd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:45:57 +0100 Subject: [PATCH 43/54] abc order + srand --- R/community.R | 1 + R/games.R | 1 + R/other.R | 1 + R/simple.R | 4 +- R/topology.R | 1 + _pkgdown.yml | 4 -- man/add_edges.Rd | 4 ++ man/add_vertices.Rd | 4 ++ man/complementer.Rd | 4 ++ man/compose.Rd | 4 ++ man/contract.Rd | 27 ++++++++++++++ man/delete_edges.Rd | 4 ++ man/delete_vertices.Rd | 4 ++ man/difference.Rd | 4 ++ man/difference.igraph.Rd | 4 ++ man/disjoint_union.Rd | 4 ++ man/edge.Rd | 8 ++++ man/ego.Rd | 26 +++++++++++++ man/igraph-minus.Rd | 4 ++ man/intersection.Rd | 4 ++ man/intersection.igraph.Rd | 4 ++ man/path.Rd | 4 ++ man/permute.Rd | 26 +++++++++++++ man/plus-.igraph.Rd | 4 ++ man/rep.igraph.Rd | 8 ++++ man/reverse_edges.Rd | 8 ++++ man/simplify.Rd | 76 ++++++++++++++++++++++++++++++++++++++ man/srand.Rd | 1 + man/union.Rd | 4 ++ man/union.igraph.Rd | 4 ++ man/vertex.Rd | 8 ++++ 31 files changed, 259 insertions(+), 5 deletions(-) diff --git a/R/community.R b/R/community.R index 6318d2fffa..113c568edd 100644 --- a/R/community.R +++ b/R/community.R @@ -2549,4 +2549,5 @@ communities <- groups.communities #' print(g2, g = TRUE, v = TRUE, e = TRUE) #' #' @export +#' @family functions for manipulating graph structure contract <- contract diff --git a/R/games.R b/R/games.R index d6a3d95b0e..6ce3acc8b0 100644 --- a/R/games.R +++ b/R/games.R @@ -1070,6 +1070,7 @@ asym_pref <- function(...) constructor_spec(sample_asym_pref, ...) #' @rdname ego #' @export +#' @family functions for manipulating graph structure connect <- function(graph, order, mode = c("all", "out", "in", "total")) { if (!is_igraph(graph)) { stop("Not a graph object") diff --git a/R/other.R b/R/other.R index 267aa7282f..ac759bdc36 100644 --- a/R/other.R +++ b/R/other.R @@ -162,6 +162,7 @@ igraph.i.spMatrix <- function(M) { #' @param seed Ignored. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @family other +#' @keywords internal #' @export srand <- function(seed) { warning( diff --git a/R/simple.R b/R/simple.R index 25af6fd2ef..9e812959f5 100644 --- a/R/simple.R +++ b/R/simple.R @@ -70,17 +70,19 @@ #' is_simple(simplify(g, remove.multiple = FALSE)) #' is_simple(simplify(g)) #' @family simple +#' @family functions for manipulating graph structure #' @export simplify <- simplify #' @family simple +#' @family functions for manipulating graph structure #' @export #' @rdname simplify is_simple <- is_simple #' @family isomorphism #' @family simple -#' @family isomorphism +#' @family functions for manipulating graph structure #' @export #' @rdname simplify simplify_and_colorize <- function(graph) { diff --git a/R/topology.R b/R/topology.R index 0a39ea1f1b..d7bb403438 100644 --- a/R/topology.R +++ b/R/topology.R @@ -821,6 +821,7 @@ canonical_permutation <- canonical_permutation #' E(g2)$weight #' all(sort(E(g2)$weight) == sort(E(g)$weight)) #' @export +#' @family functions for manipulating graph structure permute <- permute diff --git a/_pkgdown.yml b/_pkgdown.yml index 7c3e8e03e2..9cb8121321 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -47,10 +47,6 @@ reference: - title: Functions for manipulating graphs - contents: - has_concept("functions for manipulating graph structure") - - permute - - contract - - connect - - has_concept("simple") - subtitle: Rewiring functions - contents: - has_concept("rewiring functions") diff --git a/man/add_edges.Rd b/man/add_edges.Rd index 94b57d37cb..7e05d7483a 100644 --- a/man/add_edges.Rd +++ b/man/add_edges.Rd @@ -53,6 +53,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -63,8 +65,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/add_vertices.Rd b/man/add_vertices.Rd index de2979130e..d0911fac5d 100644 --- a/man/add_vertices.Rd +++ b/man/add_vertices.Rd @@ -48,6 +48,8 @@ Other functions for manipulating graph structure: \code{\link{add_edges}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -58,8 +60,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/complementer.Rd b/man/complementer.Rd index ac8f7b6a31..2d28bf6c9d 100644 --- a/man/complementer.Rd +++ b/man/complementer.Rd @@ -47,6 +47,8 @@ Other functions for manipulating graph structure: \code{\link{add_edges}()}, \code{\link{add_vertices}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -57,8 +59,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/compose.Rd b/man/compose.Rd index 15bd33bba9..5ee0634c6c 100644 --- a/man/compose.Rd +++ b/man/compose.Rd @@ -77,6 +77,8 @@ Other functions for manipulating graph structure: \code{\link{add_edges}()}, \code{\link{add_vertices}()}, \code{\link{complementer}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -87,8 +89,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/contract.Rd b/man/contract.Rd index 1bf4e2ab7f..91c22c2af7 100644 --- a/man/contract.Rd +++ b/man/contract.Rd @@ -44,8 +44,35 @@ g2 <- contract(g, rep(1:5, each = 2), ## combined using the 'toString' function. print(g2, g = TRUE, v = TRUE, e = TRUE) +} +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/delete_edges.Rd b/man/delete_edges.Rd index b35fa9b6c6..448acc4573 100644 --- a/man/delete_edges.Rd +++ b/man/delete_edges.Rd @@ -41,6 +41,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, \code{\link{difference}()}, @@ -50,8 +52,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/delete_vertices.Rd b/man/delete_vertices.Rd index ecd16181f4..ff96924401 100644 --- a/man/delete_vertices.Rd +++ b/man/delete_vertices.Rd @@ -36,6 +36,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{difference.igraph}()}, \code{\link{difference}()}, @@ -45,8 +47,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/difference.Rd b/man/difference.Rd index aa2ffc2512..30e241b234 100644 --- a/man/difference.Rd +++ b/man/difference.Rd @@ -28,6 +28,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -37,8 +39,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/difference.igraph.Rd b/man/difference.igraph.Rd index a84560564d..34a5e3e2f2 100644 --- a/man/difference.igraph.Rd +++ b/man/difference.igraph.Rd @@ -67,6 +67,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference}()}, @@ -76,8 +78,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/disjoint_union.Rd b/man/disjoint_union.Rd index f16f7bf875..3e16c99628 100644 --- a/man/disjoint_union.Rd +++ b/man/disjoint_union.Rd @@ -58,6 +58,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -67,8 +69,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/edge.Rd b/man/edge.Rd index a015be3489..cc4985cd90 100644 --- a/man/edge.Rd +++ b/man/edge.Rd @@ -57,6 +57,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -66,8 +68,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} @@ -78,6 +82,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -87,8 +93,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/ego.Rd b/man/ego.Rd index b5f9b94e89..309e6da8ec 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -108,6 +108,31 @@ g <- connect(g, 2) } \seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + Other structural.properties: \code{\link{bfs}()}, \code{\link{component_distribution}()}, @@ -184,5 +209,6 @@ Other structural.properties: Gabor Csardi \email{csardi.gabor@gmail.com}, the first version was done by Vincent Matossian } +\concept{functions for manipulating graph structure} \concept{structural.properties} \keyword{graphs} diff --git a/man/igraph-minus.Rd b/man/igraph-minus.Rd index 115f53b3de..f226b68c81 100644 --- a/man/igraph-minus.Rd +++ b/man/igraph-minus.Rd @@ -63,6 +63,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -72,8 +74,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/intersection.Rd b/man/intersection.Rd index b85da21edf..a81426e2f7 100644 --- a/man/intersection.Rd +++ b/man/intersection.Rd @@ -28,6 +28,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -37,8 +39,10 @@ Other functions for manipulating graph structure: \code{\link{igraph-minus}}, \code{\link{intersection.igraph}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/intersection.igraph.Rd b/man/intersection.igraph.Rd index 1219bcaf31..dc9c688975 100644 --- a/man/intersection.igraph.Rd +++ b/man/intersection.igraph.Rd @@ -65,6 +65,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -74,8 +76,10 @@ Other functions for manipulating graph structure: \code{\link{igraph-minus}}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/path.Rd b/man/path.Rd index 8a9de91239..4268ff5ba8 100644 --- a/man/path.Rd +++ b/man/path.Rd @@ -51,6 +51,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -60,8 +62,10 @@ Other functions for manipulating graph structure: \code{\link{igraph-minus}}, \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/permute.Rd b/man/permute.Rd index 20d2d18444..55ab931dba 100644 --- a/man/permute.Rd +++ b/man/permute.Rd @@ -48,8 +48,34 @@ all(sort(E(g2)$weight) == sort(E(g)$weight)) } \seealso{ \code{\link[=canonical_permutation]{canonical_permutation()}} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/plus-.igraph.Rd b/man/plus-.igraph.Rd index abfae59451..def387d876 100644 --- a/man/plus-.igraph.Rd +++ b/man/plus-.igraph.Rd @@ -107,6 +107,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -117,8 +119,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/rep.igraph.Rd b/man/rep.igraph.Rd index 1fa3c6e3d5..249bf87610 100644 --- a/man/rep.igraph.Rd +++ b/man/rep.igraph.Rd @@ -35,6 +35,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -45,7 +47,9 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} @@ -56,6 +60,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -66,7 +72,9 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/reverse_edges.Rd b/man/reverse_edges.Rd index ad949f2850..ea72fea1fa 100644 --- a/man/reverse_edges.Rd +++ b/man/reverse_edges.Rd @@ -38,6 +38,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -48,7 +50,9 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} @@ -59,6 +63,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -69,7 +75,9 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()}, \code{\link{vertex}()} diff --git a/man/simplify.Rd b/man/simplify.Rd index 055f33c730..cdf3ea03c2 100644 --- a/man/simplify.Rd +++ b/man/simplify.Rd @@ -71,10 +71,86 @@ is_simple(simplify(g)) \code{\link[=which_loop]{which_loop()}}, \code{\link[=which_multiple]{which_multiple()}} and \code{\link[=count_multiple]{count_multiple()}}, \code{\link[=delete_edges]{delete_edges()}}, \code{\link[=delete_vertices]{delete_vertices()}} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \concept{isomorphism} \concept{simple} \keyword{graphs} diff --git a/man/srand.Rd b/man/srand.Rd index bc6bda18b9..9c3fad06c8 100644 --- a/man/srand.Rd +++ b/man/srand.Rd @@ -22,3 +22,4 @@ Other other: Gabor Csardi \email{csardi.gabor@gmail.com} } \concept{other} +\keyword{internal} diff --git a/man/union.Rd b/man/union.Rd index b0de5cf2d1..c162971553 100644 --- a/man/union.Rd +++ b/man/union.Rd @@ -28,6 +28,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -38,8 +40,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{vertex}()} } diff --git a/man/union.igraph.Rd b/man/union.igraph.Rd index a9ea1b0eb8..60fb4d413d 100644 --- a/man/union.igraph.Rd +++ b/man/union.igraph.Rd @@ -62,6 +62,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -72,8 +74,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union}()}, \code{\link{vertex}()} } diff --git a/man/vertex.Rd b/man/vertex.Rd index 5467d790cd..375fe1e0d2 100644 --- a/man/vertex.Rd +++ b/man/vertex.Rd @@ -44,6 +44,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -54,8 +56,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()} @@ -65,6 +69,8 @@ Other functions for manipulating graph structure: \code{\link{add_vertices}()}, \code{\link{complementer}()}, \code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, \code{\link{difference.igraph}()}, @@ -75,8 +81,10 @@ Other functions for manipulating graph structure: \code{\link{intersection.igraph}()}, \code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, \code{\link{rep.igraph}()}, \code{\link{reverse_edges}()}, +\code{\link{simplify}()}, \code{\link{union.igraph}()}, \code{\link{union}()} } From a071a8abaa8a1c87fc49dd8c08f34f238fd671f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:49:37 +0100 Subject: [PATCH 44/54] more reorg --- R/games.R | 1 + _pkgdown.yml | 5 +++-- man/erdos.renyi.game.Rd | 1 + 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/R/games.R b/R/games.R index 6ce3acc8b0..c569ba78ea 100644 --- a/R/games.R +++ b/R/games.R @@ -355,6 +355,7 @@ gnm <- function(...) constructor_spec(sample_gnm, ...) #' @family games #' @export #' @keywords graphs +#' @keywords internal #' @examples #' #' g <- erdos.renyi.game(1000, 1 / 1000) diff --git a/_pkgdown.yml b/_pkgdown.yml index 9cb8121321..49ccb20c30 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -13,6 +13,8 @@ reference: - starts_with("make_") - realize_degseq - has_concept("deterministic constructors") + - graph_ + - graph_from_lcf - subtitle: "Stochastic constructors -- Random graph models (games)" - contents: - has_concept("games") @@ -22,8 +24,6 @@ reference: - subtitle: Convert to igraph - contents: - as.igraph - - graph_from_lcf - - graph_ - subtitle: Adjacency matrices - contents: - has_concept("adjacency") @@ -134,6 +134,7 @@ reference: - has_concept("graph isomorphism") - simplify_and_colorize - has_concept("graph automorphism") + - permute - subtitle: Graph matching - contents: - has_concept("sgm") diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 6b61a6fe83..cfcbb04ac2 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -98,3 +98,4 @@ Gabor Csardi \email{csardi.gabor@gmail.com} } \concept{games} \keyword{graphs} +\keyword{internal} From ae1ab98963133d8866a11593e670532acac6be25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:51:30 +0100 Subject: [PATCH 45/54] more reorg --- _pkgdown.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 49ccb20c30..af8e500c3b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -58,7 +58,6 @@ reference: - has_concept("vertex and edge sequences") - has_concept("vertex and edge sequence operations") - title: Utilities -- subtitle: Utilities - subtitle: Graph ID, comparison, name, weight - contents: - graph_id @@ -80,7 +79,10 @@ reference: - printr - has_concept("print") - has_concept("printer callbacks") -- subtitle: Misc +- subtitle: Latent position vector samplers +- contents: + - has_concept("latent position vector samplers") +- subtitle: Miscellaneous - contents: - convex_hull - running_mean @@ -135,7 +137,7 @@ reference: - simplify_and_colorize - has_concept("graph automorphism") - permute -- subtitle: Graph matching +- title: Graph matching - contents: - has_concept("sgm") - title: Maximum flow and connectivity @@ -181,9 +183,6 @@ reference: - title: Demo - contents: - has_concept("demo") -- title: Latent position vector samplers -- contents: - - has_concept("latent position vector samplers") - title: I/O read/write files - contents: - has_concept("foreign") From 92ba5477bed874e70598aa1b75336205144a26cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 16 Feb 2023 15:52:17 +0100 Subject: [PATCH 46/54] more reorg --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index af8e500c3b..8c4d6c0849 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -124,7 +124,7 @@ reference: - subtitle: Centrality measures - contents: - has_concept("centrality") -- title: Centralization related +- subtitle: Centralization - contents: - has_concept("centralization related") - title: Graph motifs and subgraphs From 699ce44abc6abe35ebb70672c8deba41ae95e0b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 20 Feb 2023 10:49:37 +0100 Subject: [PATCH 47/54] console() is fixed --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 8c4d6c0849..4589fde9f0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -190,6 +190,7 @@ reference: - contents: - has_concept("socnet") - has_concept("tkplot") + - has_concept("console") - title: Versions - contents: - has_concept("versions") @@ -204,4 +205,3 @@ reference: - layout.svd - srand - "%>%" - - has_concept("console") From b252ebec5d62b3f0cb0ffe645abfd0bacfa469b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 20 Feb 2023 11:00:25 +0100 Subject: [PATCH 48/54] make internal actually internal :facepalm: --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 4589fde9f0..6a075d654d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -195,7 +195,7 @@ reference: - contents: - has_concept("versions") - title: internal -- contents: + contents: - igraph-package - has_concept("nexus") - has_concept("test") From e69fcf6daa0abaa6c267b1b261f623f20cf8563e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 20 Feb 2023 11:07:01 +0100 Subject: [PATCH 49/54] make layout.grid.3d internal --- R/layout.R | 1 + man/layout_on_grid.Rd | 1 + 2 files changed, 2 insertions(+) diff --git a/R/layout.R b/R/layout.R index 44047003e0..9ff7baf2b6 100644 --- a/R/layout.R +++ b/R/layout.R @@ -696,6 +696,7 @@ on_grid <- function(...) layout_spec(layout_on_grid, ...) #' @rdname layout_on_grid #' @export +#' @keywords internal layout.grid.3d <- function(graph, width = 0, height = 0) { .Deprecated("layout_on_grid", msg = paste0( "layout.grid.3d is deprecated from\n", diff --git a/man/layout_on_grid.Rd b/man/layout_on_grid.Rd index 43cd3145bc..6f14eb395b 100644 --- a/man/layout_on_grid.Rd +++ b/man/layout_on_grid.Rd @@ -85,3 +85,4 @@ Tamas Nepusz \email{ntamas@gmail.com} } \concept{graph layouts} \keyword{graphs} +\keyword{internal} From ea2e9e2a4522d9d3c07e707591889831b816df52 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 20 Feb 2023 11:08:06 +0100 Subject: [PATCH 50/54] Scan statistics as subsection of structural properties --- _pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 6a075d654d..d1ef6be584 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -127,6 +127,9 @@ reference: - subtitle: Centralization - contents: - has_concept("centralization related") +- subtitle: Scan statistics +- contents: + - has_concept("scan statistics") - title: Graph motifs and subgraphs - contents: - has_concept("graph motifs") @@ -156,9 +159,6 @@ reference: - title: Connected components - contents: - has_concept("components") -- title: Scan statistics -- contents: - - has_concept("scan statistics") - title: Spectral Coarse Graining - contents: - has_concept("scg") From 5a69c3bc018f47cce3e1768ed36644b907173e8c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 6 Mar 2023 15:39:47 +0100 Subject: [PATCH 51/54] edit --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index d1ef6be584..7b987bb7e8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -15,7 +15,7 @@ reference: - has_concept("deterministic constructors") - graph_ - graph_from_lcf -- subtitle: "Stochastic constructors -- Random graph models (games)" +- subtitle: "Stochastic constructors (random graph models)" - contents: - has_concept("games") - subtitle: Constructor modifiers From 5c2bf0dc07480912e07f648cdd440daaabf7d3df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 7 Mar 2023 07:16:21 +0100 Subject: [PATCH 52/54] last tweaks? :-) --- R/centrality.R | 5 ++--- R/decomposition.R | 2 +- R/paths.R | 5 +++-- R/structural.properties.R | 4 +++- _pkgdown.yml | 13 ++++++++++--- man/all_simple_paths.Rd | 3 +-- man/alpha_centrality.Rd | 2 -- man/arpack.Rd | 32 +------------------------------- man/authority_score.Rd | 2 -- man/betweenness.Rd | 6 ------ man/bfs.Rd | 2 +- man/closeness.Rd | 2 -- man/components.Rd | 2 +- man/constraint.Rd | 2 +- man/coreness.Rd | 2 +- man/degree.Rd | 4 ++-- man/dfs.Rd | 2 +- man/diameter.Rd | 28 +++++----------------------- man/distances.Rd | 11 +++++------ man/diversity.Rd | 2 -- man/eccentricity.Rd | 3 +-- man/edge_density.Rd | 2 +- man/ego.Rd | 6 +++--- man/eigen_centrality.Rd | 2 -- man/feedback_arc_set.Rd | 2 +- man/girth.Rd | 2 +- man/harmonic_centrality.Rd | 2 -- man/has_eulerian_path.Rd | 13 +++++++++++++ man/hub_score.Rd | 2 -- man/is_chordal.Rd | 5 ++++- man/is_dag.Rd | 33 +++++++++++++++++++++++++++------ man/knn.Rd | 2 +- man/laplacian_matrix.Rd | 2 +- man/matching.Rd | 6 +++--- man/max_cardinality.Rd | 10 +++------- man/page_rank.Rd | 2 -- man/power_centrality.Rd | 2 -- man/radius.Rd | 5 ++--- man/reciprocity.Rd | 2 +- man/spectrum.Rd | 16 ---------------- man/strength.Rd | 2 -- man/subcomponent.Rd | 2 +- man/subgraph.Rd | 6 +++--- man/subgraph_centrality.Rd | 2 -- man/topo_sort.Rd | 2 +- man/transitivity.Rd | 2 +- man/unfold_tree.Rd | 2 +- man/which_multiple.Rd | 2 +- man/which_mutual.Rd | 2 +- 49 files changed, 109 insertions(+), 163 deletions(-) diff --git a/R/centrality.R b/R/centrality.R index d1ee482c51..341798abc5 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -303,7 +303,7 @@ estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "al } #' @rdname arpack -#' @family centrality +#' @family arpack #' @export arpack_defaults <- list( bmat = "I", n = 0, which = "XX", nev = 1, tol = 0.0, @@ -497,7 +497,7 @@ arpack_defaults <- list( #' which = "LM", maxiter = 2000 #' )) #' } -#' @family centrality +#' @family arpack #' @export arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults, env = parent.frame(), complex = !sym) { @@ -677,7 +677,6 @@ subgraph_centrality <- function(graph, diag = FALSE) { #' ## Smallest eigenvalues #' spectrum(kite, which = list(pos = "SM", howmany = 2))$values #' -#' @family centrality #' @export spectrum <- spectrum diff --git a/R/decomposition.R b/R/decomposition.R index e0503bb409..6215653a04 100644 --- a/R/decomposition.R +++ b/R/decomposition.R @@ -63,7 +63,7 @@ #' linear-time algorithms to test chordality of graphs, test acyclicity of #' hypergraphs, and selectively reduce acyclic hypergraphs. *SIAM Journal #' of Computation* 13, 566--579. -#' @family decomposition +#' @family chordal #' @export #' @keywords graphs #' @examples diff --git a/R/paths.R b/R/paths.R index a6c28c7f6d..dc9fbf7a21 100644 --- a/R/paths.R +++ b/R/paths.R @@ -106,7 +106,8 @@ all_simple_paths <- function(graph, from, to = V(graph), #' is_dag(g) #' g2 <- g + edge(5, 1) #' is_dag(g2) -#' @family paths +#' @family cycles +#' @family structural.properties #' @export is_dag <- is_dag @@ -157,7 +158,7 @@ is_dag <- is_dag #' ) #' max_cardinality(g2) #' is_chordal(g2, fillin = TRUE) -#' @family paths +#' @family chordal max_cardinality <- max_cardinality diff --git a/R/structural.properties.R b/R/structural.properties.R index 3110feac8c..3669fd36c9 100644 --- a/R/structural.properties.R +++ b/R/structural.properties.R @@ -58,7 +58,7 @@ #' } #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @seealso [distances()] -#' @family structural.properties +#' @family paths #' @export #' @keywords graphs #' @examples @@ -1414,6 +1414,7 @@ topo_sort <- function(graph, mode = c("out", "all", "in")) { #' 47:6, pp. 319-323, 1993 #' @keywords graphs #' @family structural.properties +#' @family cycles #' @export #' @examples #' @@ -1446,6 +1447,7 @@ feedback_arc_set <- feedback_arc_set #' graph *Proceedings of the ninth annual ACM symposium on Theory of #' computing*, 1-10, 1977 #' @family structural.properties +#' @family cycles #' @export #' @keywords graphs #' @examples diff --git a/_pkgdown.yml b/_pkgdown.yml index 7b987bb7e8..a2c72e3d9e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -96,6 +96,10 @@ reference: - has_concept("cohesive.blocks") - has_concept("triangles") - starts_with("assortativity") + - spectrum +- subtitle: Chordal graphs +- contents: + - has_concept("chordal") - subtitle: Triangles and transitivity - contents: - matches("triangles") @@ -121,6 +125,9 @@ reference: - subtitle: Structural queries - contents: - has_concept("structural queries") +- subtitle: ARPACK eigenvector calculation +- contents: + - has_concept("arpack") - subtitle: Centrality measures - contents: - has_concept("centrality") @@ -159,14 +166,14 @@ reference: - title: Connected components - contents: - has_concept("components") -- title: Spectral Coarse Graining +- title: Spectral coarse graining - contents: - has_concept("scg") -- title: Embedding +- title: Spectral embedding - contents: - has_concept("embedding") - embed_laplacian_matrix -- title: Hierarchical random graph functions +- title: Hierarchical random graphs - contents: - has_concept("hierarchical random graph functions") # network analysis end, we keep these sections together ]]] diff --git a/man/all_simple_paths.Rd b/man/all_simple_paths.Rd index 2a4f3a0d3c..f0cf3b4468 100644 --- a/man/all_simple_paths.Rd +++ b/man/all_simple_paths.Rd @@ -54,10 +54,9 @@ all_simple_paths(g, 1, c(3, 5)) } \seealso{ Other paths: +\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{eccentricity}()}, -\code{\link{is_dag}()}, -\code{\link{max_cardinality}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 4ffb8d007a..bac475a3cc 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -94,7 +94,6 @@ measures of centrality for asymmetric relations'' \emph{Social Networks}, \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=power_centrality]{power_centrality()}} Other centrality: -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -104,7 +103,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/arpack.Rd b/man/arpack.Rd index 97536eb852..b03d3d7647 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -217,41 +217,11 @@ Matrices. \emph{Linear Algebra and its Applications}, vol 88/89, pp 575-595, \code{\link[=eigen_centrality]{eigen_centrality()}}, \code{\link[=page_rank]{page_rank()}}, \code{\link[=hub_score]{hub_score()}}, \code{\link[=cluster_leading_eigen]{cluster_leading_eigen()}} are some of the functions in igraph that use ARPACK. - -Other centrality: -\code{\link{alpha_centrality}()}, -\code{\link{authority_score}()}, -\code{\link{closeness}()}, -\code{\link{diversity}()}, -\code{\link{eigen_centrality}()}, -\code{\link{estimate_betweenness}()}, -\code{\link{harmonic_centrality}()}, -\code{\link{hub_score}()}, -\code{\link{page_rank}()}, -\code{\link{power_centrality}()}, -\code{\link{spectrum}()}, -\code{\link{strength}()}, -\code{\link{subgraph_centrality}()} - -Other centrality: -\code{\link{alpha_centrality}()}, -\code{\link{authority_score}()}, -\code{\link{closeness}()}, -\code{\link{diversity}()}, -\code{\link{eigen_centrality}()}, -\code{\link{estimate_betweenness}()}, -\code{\link{harmonic_centrality}()}, -\code{\link{hub_score}()}, -\code{\link{page_rank}()}, -\code{\link{power_centrality}()}, -\code{\link{spectrum}()}, -\code{\link{strength}()}, -\code{\link{subgraph_centrality}()} } \author{ Rich Lehoucq, Kristi Maschhoff, Danny Sorensen, Chao Yang for ARPACK, Gabor Csardi \email{csardi.gabor@gmail.com} for the R interface. } -\concept{centrality} +\concept{arpack} \keyword{datasets} \keyword{graphs} diff --git a/man/authority_score.Rd b/man/authority_score.Rd index 48faa728fd..148c3ff1f4 100644 --- a/man/authority_score.Rd +++ b/man/authority_score.Rd @@ -68,7 +68,6 @@ computation. Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, @@ -77,7 +76,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/betweenness.Rd b/man/betweenness.Rd index b1dcac5456..5fed1e55d6 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -135,7 +135,6 @@ of Mathematical Sociology} 25(2):163-177, 2001. Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -144,13 +143,11 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -159,13 +156,11 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -174,7 +169,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/bfs.Rd b/man/bfs.Rd index 5360ec0832..e60f3ca951 100644 --- a/man/bfs.Rd +++ b/man/bfs.Rd @@ -140,11 +140,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/closeness.Rd b/man/closeness.Rd index f59039a83b..b6210b19ca 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -90,7 +90,6 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239. Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, @@ -99,7 +98,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/components.Rd b/man/components.Rd index 2252a2747d..1a6ab80d7f 100644 --- a/man/components.Rd +++ b/man/components.Rd @@ -92,11 +92,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/constraint.Rd b/man/constraint.Rd index a4766730b9..fb48088192 100644 --- a/man/constraint.Rd +++ b/man/constraint.Rd @@ -59,11 +59,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/coreness.Rd b/man/coreness.Rd index 3d29621ac2..1a38d3e189 100644 --- a/man/coreness.Rd +++ b/man/coreness.Rd @@ -55,11 +55,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/degree.Rd b/man/degree.Rd index a981dc5f51..f2d15a3432 100644 --- a/man/degree.Rd +++ b/man/degree.Rd @@ -65,11 +65,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -89,11 +89,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/dfs.Rd b/man/dfs.Rd index f18fe174db..b413626c0a 100644 --- a/man/dfs.Rd +++ b/man/dfs.Rd @@ -132,11 +132,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{degree}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/diameter.Rd b/man/diameter.Rd index 25e9d7f040..7f3df2bf17 100644 --- a/man/diameter.Rd +++ b/man/diameter.Rd @@ -67,32 +67,14 @@ get_diameter(g, weights = NA) \seealso{ \code{\link[=distances]{distances()}} -Other structural.properties: -\code{\link{bfs}()}, -\code{\link{component_distribution}()}, -\code{\link{connect}()}, -\code{\link{constraint}()}, -\code{\link{coreness}()}, -\code{\link{degree}()}, -\code{\link{dfs}()}, +Other paths: +\code{\link{all_simple_paths}()}, \code{\link{distance_table}()}, -\code{\link{edge_density}()}, -\code{\link{feedback_arc_set}()}, -\code{\link{girth}()}, -\code{\link{is_matching}()}, -\code{\link{knn}()}, -\code{\link{laplacian_matrix}()}, -\code{\link{reciprocity}()}, -\code{\link{subcomponent}()}, -\code{\link{subgraph}()}, -\code{\link{topo_sort}()}, -\code{\link{transitivity}()}, -\code{\link{unfold_tree}()}, -\code{\link{which_multiple}()}, -\code{\link{which_mutual}()} +\code{\link{eccentricity}()}, +\code{\link{radius}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{structural.properties} +\concept{paths} \keyword{graphs} diff --git a/man/distances.Rd b/man/distances.Rd index 2d5e278300..b58a796336 100644 --- a/man/distances.Rd +++ b/man/distances.Rd @@ -261,9 +261,8 @@ Saddle River, N.J.: Prentice Hall. \seealso{ Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{eccentricity}()}, -\code{\link{is_dag}()}, -\code{\link{max_cardinality}()}, \code{\link{radius}()} Other structural.properties: @@ -274,10 +273,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -298,10 +297,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -322,10 +321,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -346,10 +345,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index ffcbe42644..4f2e740bc5 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -55,7 +55,6 @@ and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010. \seealso{ Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{eigen_centrality}()}, @@ -64,7 +63,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/eccentricity.Rd b/man/eccentricity.Rd index ed00536c23..33480743d9 100644 --- a/man/eccentricity.Rd +++ b/man/eccentricity.Rd @@ -48,9 +48,8 @@ Harary, F. Graph Theory. Reading, MA: Addison-Wesley, p. 35, Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{distance_table}()}, -\code{\link{is_dag}()}, -\code{\link{max_cardinality}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/edge_density.Rd b/man/edge_density.Rd index de181a8307..fcf573dfb6 100644 --- a/man/edge_density.Rd +++ b/man/edge_density.Rd @@ -58,10 +58,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/ego.Rd b/man/ego.Rd index 309e6da8ec..8d41e757cd 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -140,11 +140,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -164,11 +164,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -188,11 +188,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index a3df9eaeef..3be30cee2a 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -105,7 +105,6 @@ Measures. \emph{American Journal of Sociology}, 92, 1170-1182. \seealso{ Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -114,7 +113,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/feedback_arc_set.Rd b/man/feedback_arc_set.Rd index cbbfef93be..08630ed9fc 100644 --- a/man/feedback_arc_set.Rd +++ b/man/feedback_arc_set.Rd @@ -58,10 +58,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/girth.Rd b/man/girth.Rd index fc1b719a70..4098256efd 100644 --- a/man/girth.Rd +++ b/man/girth.Rd @@ -59,10 +59,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index 2918a4f731..1ae917e066 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -71,7 +71,6 @@ M. Marchiori and V. Latora, Harmony in the small-world, Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -80,7 +79,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/has_eulerian_path.Rd b/man/has_eulerian_path.Rd index d5e041fdb8..f0c98b3f77 100644 --- a/man/has_eulerian_path.Rd +++ b/man/has_eulerian_path.Rd @@ -55,6 +55,19 @@ eulerian_path(g) has_eulerian_cycle(g) try(eulerian_cycle(g)) +} +\seealso{ +Other cycles: +\code{\link{is_dag}()} + +Other cycles: +\code{\link{is_dag}()} + +Other cycles: +\code{\link{is_dag}()} + +Other cycles: +\code{\link{is_dag}()} } \concept{cycles} \keyword{graphs} diff --git a/man/hub_score.Rd b/man/hub_score.Rd index 7fc8e9aa3c..4f941b253d 100644 --- a/man/hub_score.Rd +++ b/man/hub_score.Rd @@ -66,7 +66,6 @@ the underlining machinery of the computation. Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -75,7 +74,6 @@ Other centrality: \code{\link{harmonic_centrality}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/is_chordal.Rd b/man/is_chordal.Rd index 38fa341097..576094a3de 100644 --- a/man/is_chordal.Rd +++ b/man/is_chordal.Rd @@ -80,9 +80,12 @@ of Computation} 13, 566--579. } \seealso{ \code{\link[=max_cardinality]{max_cardinality()}} + +Other chordal: +\code{\link{max_cardinality}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{decomposition} +\concept{chordal} \keyword{graphs} diff --git a/man/is_dag.Rd b/man/is_dag.Rd index cd5eec83c6..226b078c02 100644 --- a/man/is_dag.Rd +++ b/man/is_dag.Rd @@ -30,16 +30,37 @@ g2 <- g + edge(5, 1) is_dag(g2) } \seealso{ -Other paths: -\code{\link{all_simple_paths}()}, +Other cycles: +\code{\link{has_eulerian_path}()} + +Other structural.properties: +\code{\link{bfs}()}, +\code{\link{component_distribution}()}, +\code{\link{connect}()}, +\code{\link{constraint}()}, +\code{\link{coreness}()}, +\code{\link{degree}()}, +\code{\link{dfs}()}, \code{\link{distance_table}()}, -\code{\link{eccentricity}()}, -\code{\link{max_cardinality}()}, -\code{\link{radius}()} +\code{\link{edge_density}()}, +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_matching}()}, +\code{\link{knn}()}, +\code{\link{laplacian_matrix}()}, +\code{\link{reciprocity}()}, +\code{\link{subcomponent}()}, +\code{\link{subgraph}()}, +\code{\link{topo_sort}()}, +\code{\link{transitivity}()}, +\code{\link{unfold_tree}()}, +\code{\link{which_multiple}()}, +\code{\link{which_mutual}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} for the C code, Gabor Csardi \email{csardi.gabor@gmail.com} for the R interface. } -\concept{paths} +\concept{cycles} +\concept{structural.properties} \keyword{graphs} diff --git a/man/knn.Rd b/man/knn.Rd index 3d1ff264c7..a04f009b39 100644 --- a/man/knn.Rd +++ b/man/knn.Rd @@ -98,11 +98,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, diff --git a/man/laplacian_matrix.Rd b/man/laplacian_matrix.Rd index f95386f592..eaf2808b73 100644 --- a/man/laplacian_matrix.Rd +++ b/man/laplacian_matrix.Rd @@ -66,11 +66,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{reciprocity}()}, diff --git a/man/matching.Rd b/man/matching.Rd index 5920e564b4..ee1e61fb38 100644 --- a/man/matching.Rd +++ b/man/matching.Rd @@ -122,11 +122,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, @@ -146,11 +146,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, @@ -170,11 +170,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, diff --git a/man/max_cardinality.Rd b/man/max_cardinality.Rd index a78cdc0e19..970e29c606 100644 --- a/man/max_cardinality.Rd +++ b/man/max_cardinality.Rd @@ -59,15 +59,11 @@ of Computation} 13, 566--579. \seealso{ \code{\link[=is_chordal]{is_chordal()}} -Other paths: -\code{\link{all_simple_paths}()}, -\code{\link{distance_table}()}, -\code{\link{eccentricity}()}, -\code{\link{is_dag}()}, -\code{\link{radius}()} +Other chordal: +\code{\link{is_chordal}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{paths} +\concept{chordal} \keyword{graphs} diff --git a/man/page_rank.Rd b/man/page_rank.Rd index 636624f37c..c8160de41e 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -111,7 +111,6 @@ Other centrality scores: \code{\link[=closeness]{closeness()}}, Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -120,7 +119,6 @@ Other centrality: \code{\link{harmonic_centrality}()}, \code{\link{hub_score}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index c3f222eac3..6a49836754 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -137,7 +137,6 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.'' Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -146,7 +145,6 @@ Other centrality: \code{\link{harmonic_centrality}()}, \code{\link{hub_score}()}, \code{\link{page_rank}()}, -\code{\link{spectrum}()}, \code{\link{strength}()}, \code{\link{subgraph_centrality}()} } diff --git a/man/radius.Rd b/man/radius.Rd index aadd142ab6..874aea51bb 100644 --- a/man/radius.Rd +++ b/man/radius.Rd @@ -48,9 +48,8 @@ calculations. Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{distance_table}()}, -\code{\link{eccentricity}()}, -\code{\link{is_dag}()}, -\code{\link{max_cardinality}()} +\code{\link{eccentricity}()} } \concept{paths} diff --git a/man/reciprocity.Rd b/man/reciprocity.Rd index f81e2b4a3d..2bf970cded 100644 --- a/man/reciprocity.Rd +++ b/man/reciprocity.Rd @@ -51,11 +51,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/spectrum.Rd b/man/spectrum.Rd index d69ed862cb..861dabdbc6 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -77,24 +77,8 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values } \seealso{ \code{\link[=as_adj]{as_adj()}} to create a (sparse) adjacency matrix. - -Other centrality: -\code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, -\code{\link{authority_score}()}, -\code{\link{closeness}()}, -\code{\link{diversity}()}, -\code{\link{eigen_centrality}()}, -\code{\link{estimate_betweenness}()}, -\code{\link{harmonic_centrality}()}, -\code{\link{hub_score}()}, -\code{\link{page_rank}()}, -\code{\link{power_centrality}()}, -\code{\link{strength}()}, -\code{\link{subgraph_centrality}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{centrality} \keyword{graphs} diff --git a/man/strength.Rd b/man/strength.Rd index 7c0052f671..b5de8d9095 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -57,7 +57,6 @@ Natl. Acad. Sci. USA 101, 3747 (2004) Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -67,7 +66,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{subgraph_centrality}()} } \author{ diff --git a/man/subcomponent.Rd b/man/subcomponent.Rd index d47b97251c..ebaabd50e7 100644 --- a/man/subcomponent.Rd +++ b/man/subcomponent.Rd @@ -46,11 +46,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/subgraph.Rd b/man/subgraph.Rd index 1362344b9a..33846981d6 100644 --- a/man/subgraph.Rd +++ b/man/subgraph.Rd @@ -74,11 +74,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -98,11 +98,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -122,11 +122,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index de600ec292..eb0867bd23 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -47,7 +47,6 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005). Other centrality: \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{authority_score}()}, \code{\link{closeness}()}, \code{\link{diversity}()}, @@ -57,7 +56,6 @@ Other centrality: \code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, -\code{\link{spectrum}()}, \code{\link{strength}()} } \author{ diff --git a/man/topo_sort.Rd b/man/topo_sort.Rd index 77dc7fb76a..84a34bc411 100644 --- a/man/topo_sort.Rd +++ b/man/topo_sort.Rd @@ -46,11 +46,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/transitivity.Rd b/man/transitivity.Rd index f80ce04fd7..ea7127ff4a 100644 --- a/man/transitivity.Rd +++ b/man/transitivity.Rd @@ -123,11 +123,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/unfold_tree.Rd b/man/unfold_tree.Rd index 72af710a16..597f2478fb 100644 --- a/man/unfold_tree.Rd +++ b/man/unfold_tree.Rd @@ -53,11 +53,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/which_multiple.Rd b/man/which_multiple.Rd index 451ae52a89..6cc2bc5bcf 100644 --- a/man/which_multiple.Rd +++ b/man/which_multiple.Rd @@ -89,11 +89,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/which_mutual.Rd b/man/which_mutual.Rd index 2cbdd06f72..06597d1766 100644 --- a/man/which_mutual.Rd +++ b/man/which_mutual.Rd @@ -49,11 +49,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, From c0dd82547f589b44e096eac53a85157df4b7fefe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 7 Mar 2023 07:18:06 +0100 Subject: [PATCH 53/54] gitignored on main --- src/Makevars | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 src/Makevars diff --git a/src/Makevars b/src/Makevars deleted file mode 100644 index fc864eb796..0000000000 --- a/src/Makevars +++ /dev/null @@ -1,15 +0,0 @@ -CXX_STD=CXX11 - -PKG_CFLAGS=$(C_VISIBILITY) -PKG_CXXFLAGS=$(CXX_VISIBILITY) -PKG_FFLAGS=$(F_VISIBILITY) - -PKG_CPPFLAGS=-DUSING_R -I. -Icore -Iinclude -Ivendor \ - -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT \ - -DINTERNAL_ARPACK \ - -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -PKG_LIBS=-lxml2 -lgmp -lglpk $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) - -all: $(SHLIB) - -OBJECTS=core/centrality/betweenness.o core/centrality/centrality_other.o core/centrality/centralization.o core/centrality/closeness.o core/centrality/coreness.o core/centrality/prpack.o core/centrality/prpack/prpack_base_graph.o core/centrality/prpack/prpack_igraph_graph.o core/centrality/prpack/prpack_preprocessed_ge_graph.o core/centrality/prpack/prpack_preprocessed_gs_graph.o core/centrality/prpack/prpack_preprocessed_scc_graph.o core/centrality/prpack/prpack_preprocessed_schur_graph.o core/centrality/prpack/prpack_result.o core/centrality/prpack/prpack_solver.o core/centrality/prpack/prpack_utils.o core/cliques/cliquer/cliquer.o core/cliques/cliquer/cliquer_graph.o core/cliques/cliquer/reorder.o core/cliques/cliquer_wrapper.o core/cliques/cliques.o core/cliques/glet.o core/cliques/maximal_cliques.o core/community/community_misc.o core/community/edge_betweenness.o core/community/fast_modularity.o core/community/fluid.o core/community/infomap/infomap.o core/community/infomap/infomap_FlowGraph.o core/community/infomap/infomap_Greedy.o core/community/infomap/infomap_Node.o core/community/label_propagation.o core/community/leading_eigenvector.o core/community/leiden.o 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core/isomorphism/bliss.o core/isomorphism/bliss/defs.o core/isomorphism/bliss/graph.o core/isomorphism/bliss/heap.o core/isomorphism/bliss/orbit.o core/isomorphism/bliss/partition.o core/isomorphism/bliss/uintseqhash.o core/isomorphism/bliss/utils.o core/isomorphism/isoclasses.o core/isomorphism/isomorphism_misc.o core/isomorphism/lad.o core/isomorphism/queries.o core/isomorphism/vf2.o core/layout/circular.o core/layout/davidson_harel.o core/layout/drl/DensityGrid.o core/layout/drl/DensityGrid_3d.o core/layout/drl/drl_graph.o core/layout/drl/drl_graph_3d.o core/layout/drl/drl_layout.o core/layout/drl/drl_layout_3d.o core/layout/drl/drl_parse.o core/layout/fruchterman_reingold.o core/layout/gem.o core/layout/graphopt.o core/layout/kamada_kawai.o core/layout/large_graph.o core/layout/layout_bipartite.o core/layout/layout_grid.o core/layout/layout_random.o core/layout/mds.o core/layout/merge_dla.o core/layout/merge_grid.o core/layout/reingold_tilford.o core/layout/sugiyama.o core/linalg/arpack.o core/linalg/blas.o core/linalg/eigen.o core/linalg/lapack.o core/math/bfgs.o core/math/complex.o core/math/utils.o core/misc/bipartite.o core/misc/chordality.o core/misc/cocitation.o core/misc/coloring.o core/misc/conversion.o core/misc/degree_sequence.o core/misc/embedding.o core/misc/feedback_arc_set.o core/misc/graphicality.o core/misc/matching.o core/misc/microscopic_update.o core/misc/mixing.o core/misc/motifs.o core/misc/other.o core/misc/scan.o core/misc/sir.o core/misc/spanning_trees.o core/operators/add_edge.o core/operators/complementer.o core/operators/compose.o core/operators/connect_neighborhood.o core/operators/contract.o core/operators/difference.o core/operators/disjoint_union.o core/operators/intersection.o core/operators/misc_internal.o core/operators/permute.o core/operators/reverse.o core/operators/rewire.o core/operators/rewire_edges.o core/operators/simplify.o core/operators/subgraph.o core/operators/union.o core/paths/all_shortest_paths.o core/paths/bellman_ford.o core/paths/dijkstra.o core/paths/distances.o core/paths/eulerian.o core/paths/histogram.o core/paths/johnson.o core/paths/random_walk.o core/paths/shortest_paths.o core/paths/simple_paths.o core/paths/unweighted.o core/properties/basic_properties.o core/properties/constraint.o core/properties/convergence_degree.o core/properties/dag.o core/properties/degrees.o core/properties/girth.o core/properties/loops.o core/properties/multiplicity.o core/properties/neighborhood.o core/properties/spectral.o core/properties/trees.o core/properties/triangles.o core/random/random.o core/scg/scg.o core/scg/scg_approximate_methods.o core/scg/scg_exact_scg.o core/scg/scg_kmeans.o core/scg/scg_optimal_method.o core/scg/scg_utils.o core/version.o vendor/cs/cs_add.o vendor/cs/cs_amd.o vendor/cs/cs_chol.o vendor/cs/cs_cholsol.o vendor/cs/cs_compress.o vendor/cs/cs_counts.o vendor/cs/cs_cumsum.o vendor/cs/cs_dfs.o vendor/cs/cs_dmperm.o vendor/cs/cs_droptol.o vendor/cs/cs_dropzeros.o vendor/cs/cs_dupl.o vendor/cs/cs_entry.o vendor/cs/cs_ereach.o vendor/cs/cs_etree.o vendor/cs/cs_fkeep.o vendor/cs/cs_gaxpy.o vendor/cs/cs_happly.o vendor/cs/cs_house.o vendor/cs/cs_ipvec.o vendor/cs/cs_leaf.o vendor/cs/cs_load.o vendor/cs/cs_lsolve.o vendor/cs/cs_ltsolve.o vendor/cs/cs_lu.o vendor/cs/cs_lusol.o vendor/cs/cs_malloc.o vendor/cs/cs_maxtrans.o vendor/cs/cs_multiply.o vendor/cs/cs_norm.o vendor/cs/cs_permute.o vendor/cs/cs_pinv.o vendor/cs/cs_post.o vendor/cs/cs_print.o vendor/cs/cs_pvec.o vendor/cs/cs_qr.o vendor/cs/cs_qrsol.o vendor/cs/cs_randperm.o vendor/cs/cs_reach.o vendor/cs/cs_scatter.o vendor/cs/cs_scc.o vendor/cs/cs_schol.o vendor/cs/cs_spsolve.o vendor/cs/cs_sqr.o vendor/cs/cs_symperm.o vendor/cs/cs_tdfs.o vendor/cs/cs_transpose.o vendor/cs/cs_updown.o vendor/cs/cs_usolve.o vendor/cs/cs_util.o vendor/cs/cs_utsolve.o vendor/mini-gmp/mini-gmp.o vendor/plfit/gss.o vendor/plfit/hzeta.o vendor/plfit/kolmogorov.o vendor/plfit/lbfgs.o vendor/plfit/mt.o vendor/plfit/options.o vendor/plfit/platform.o vendor/plfit/plfit.o vendor/plfit/plfit_error.o vendor/plfit/rbinom.o vendor/plfit/sampling.o vendor/arpack/dgetv0.o vendor/arpack/dlaqrb.o vendor/arpack/dmout.o vendor/arpack/dnaitr.o vendor/arpack/dnapps.o vendor/arpack/dnaup2.o vendor/arpack/dnaupd.o vendor/arpack/dnconv.o vendor/arpack/dneigh.o vendor/arpack/dneupd.o vendor/arpack/dngets.o vendor/arpack/dsaitr.o vendor/arpack/dsapps.o vendor/arpack/dsaup2.o vendor/arpack/dsaupd.o vendor/arpack/dsconv.o vendor/arpack/dseigt.o vendor/arpack/dsesrt.o vendor/arpack/dseupd.o vendor/arpack/dsgets.o vendor/arpack/dsortc.o vendor/arpack/dsortr.o vendor/arpack/dstatn.o vendor/arpack/dstats.o vendor/arpack/dstqrb.o vendor/arpack/dvout.o vendor/arpack/ivout.o vendor/arpack/second.o vendor/arpack/wrap.o vendor/simpleraytracer/Color.o vendor/simpleraytracer/Light.o vendor/simpleraytracer/Point.o vendor/simpleraytracer/RIgraphRay.o vendor/simpleraytracer/Ray.o vendor/simpleraytracer/RayTracer.o vendor/simpleraytracer/RayVector.o vendor/simpleraytracer/Shape.o vendor/simpleraytracer/Sphere.o vendor/simpleraytracer/Triangle.o vendor/simpleraytracer/unit_limiter.o vendor/uuid/R.o vendor/uuid/clear.o vendor/uuid/compare.o vendor/uuid/copy.o vendor/uuid/gen_uuid.o vendor/uuid/isnull.o vendor/uuid/pack.o vendor/uuid/parse.o vendor/uuid/unpack.o vendor/uuid/unparse.o rinterface.o rinterface_extra.o rrandom.o lazyeval.o From 48e88da3bf689a341a05106a3c1676d5c2371304 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 13 Mar 2023 13:42:18 +0100 Subject: [PATCH 54/54] rm pr hack :-) --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 8c9d1bf5d0..087f0b05fc 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -2,7 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, reference-reorg] + branches: [main, master] pull_request: branches: [main, master] release: