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refactor: adapt to cut.prob's new handling of NULL in the C core (sim… #1574

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refactor: adapt to cut.prob's new handling of NULL in the C core (sim… #1574

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70 changes: 46 additions & 24 deletions R/motifs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ triad.census <- function(graph) { # nocov start
#' @inheritParams count_motifs
#' @keywords internal
#' @export
graph.motifs.no <- function(graph, size = 3, cut.prob = rep(0, size)) { # nocov start
graph.motifs.no <- function(graph, size = 3, cut.prob = NULL) { # nocov start
lifecycle::deprecate_soft("2.0.0", "graph.motifs.no()", "count_motifs()")
count_motifs(graph = graph, size = size, cut.prob = cut.prob)
} # nocov end
Expand All @@ -39,7 +39,7 @@ graph.motifs.no <- function(graph, size = 3, cut.prob = rep(0, size)) { # nocov
#' @inheritParams sample_motifs
#' @keywords internal
#' @export
graph.motifs.est <- function(graph, size = 3, cut.prob = rep(0, size), sample.size = vcount(graph) / 10, sample = NULL) { # nocov start
graph.motifs.est <- function(graph, size = 3, cut.prob = NULL, sample.size = vcount(graph) / 10, sample = NULL) { # nocov start
lifecycle::deprecate_soft("2.0.0", "graph.motifs.est()", "sample_motifs()")
sample_motifs(graph = graph, size = size, cut.prob = cut.prob, sample.size = sample.size, sample = sample)
} # nocov end
Expand All @@ -54,7 +54,7 @@ graph.motifs.est <- function(graph, size = 3, cut.prob = rep(0, size), sample.si
#' @inheritParams motifs
#' @keywords internal
#' @export
graph.motifs <- function(graph, size = 3, cut.prob = rep(0, size)) { # nocov start
graph.motifs <- function(graph, size = 3, cut.prob = NULL) { # nocov start
lifecycle::deprecate_soft("2.0.0", "graph.motifs()", "motifs()")
motifs(graph = graph, size = size, cut.prob = cut.prob)
} # nocov end
Expand Down Expand Up @@ -110,7 +110,7 @@ dyad.census <- function(graph) { # nocov start
#' directed graphs and sizes 3-6 in undirected graphs.
#' @param cut.prob Numeric vector giving the probabilities that the search
#' graph is cut at a certain level. Its length should be the same as the size
#' of the motif (the `size` argument). By default no cuts are made.
#' of the motif (the `size` argument). If `NULL`, the default, no cuts are made.
#' @return `motifs()` returns a numeric vector, the number of occurrences of
#' each motif in the graph. The motifs are ordered by their isomorphism
#' classes. Note that for unconnected subgraphs, which are not considered to be
Expand All @@ -125,21 +125,28 @@ dyad.census <- function(graph) { # nocov start
#' motifs(g, 3)
#' count_motifs(g, 3)
#' sample_motifs(g, 3)
motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
motifs <- function(graph, size = 3, cut.prob = NULL) {
ensure_igraph(graph)
if (!is.null(cut.prob) && length(cut.prob) != size) {
cut.prob <- as.numeric(cut.prob)
if (length(cut.prob) != size) {
cut.prob <- c(
cut.prob[-length(cut.prob)],
rep(cut.prob[-length(cut.prob)], length(cut.prob) - 1)
)
}

on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_motifs_randesu, graph, as.numeric(size),
as.numeric(cut.prob)
)
if (is.null(cut.prob)) {
res <- .Call(
R_igraph_motifs_randesu, graph, as.numeric(size),
NULL
)
} else {
res <- .Call(
R_igraph_motifs_randesu, graph, as.numeric(size),
as.numeric(cut.prob)
)
}
res[is.nan(res)] <- NA
res
}
Expand All @@ -156,7 +163,7 @@ motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
#' @param size The size of the motif.
#' @param cut.prob Numeric vector giving the probabilities that the search
#' graph is cut at a certain level. Its length should be the same as the size
#' of the motif (the `size` argument). By default no cuts are made.
#' of the motif (the `size` argument). If `NULL`, the default, no cuts are made.
#' @return `count_motifs()` returns a numeric scalar.
#' @seealso [isomorphism_class()]
#'
Expand All @@ -168,21 +175,28 @@ motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
#' motifs(g, 3)
#' count_motifs(g, 3)
#' sample_motifs(g, 3)
count_motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
count_motifs <- function(graph, size = 3, cut.prob = NULL) {
ensure_igraph(graph)
if (!is.null(cut.prob) && length(cut.prob) != size) {
cut.prob <- as.numeric(cut.prob)
if (length(cut.prob) != size) {
cut.prob <- c(
cut.prob[-length(cut.prob)],
rep(cut.prob[-length(cut.prob)], length(cut.prob) - 1)
)
}

on.exit(.Call(R_igraph_finalizer))
.Call(
R_igraph_motifs_randesu_no, graph, as.numeric(size),
as.numeric(cut.prob)
)
if (is.null(cut.prob)) {
.Call(
R_igraph_motifs_randesu_no, graph, as.numeric(size),
NULL
)
} else {
.Call(
R_igraph_motifs_randesu_no, graph, as.numeric(size),
as.numeric(cut.prob)
)
}
}

#' Graph motifs
Expand All @@ -198,7 +212,7 @@ count_motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
#' in directed graphs and sizes 3-6 in undirected graphs.
#' @param cut.prob Numeric vector giving the probabilities that the search
#' graph is cut at a certain level. Its length should be the same as the size
#' of the motif (the `size` argument). By default no cuts are made.
#' of the motif (the `size` argument). If `NULL`, the default, no cuts are made.
#' @param sample.size The number of vertices to use as a starting point for
#' finding motifs. Only used if the `sample` argument is `NULL`.
#' @param sample If not `NULL` then it specifies the vertices to use as a
Expand All @@ -215,22 +229,30 @@ count_motifs <- function(graph, size = 3, cut.prob = rep(0, size)) {
#' motifs(g, 3)
#' count_motifs(g, 3)
#' sample_motifs(g, 3)
sample_motifs <- function(graph, size = 3, cut.prob = rep(0, size),
sample_motifs <- function(graph, size = 3, cut.prob = NULL,
sample.size = vcount(graph) / 10, sample = NULL) {
ensure_igraph(graph)
if (!is.null(cut.prob) && length(cut.prob) != size) {
cut.prob <- as.numeric(cut.prob)
if (length(cut.prob) != size) {
cut.prob <- c(
cut.prob[-length(cut.prob)],
rep(cut.prob[-length(cut.prob)], length(cut.prob) - 1)
)
}

on.exit(.Call(R_igraph_finalizer))
.Call(
R_igraph_motifs_randesu_estimate, graph, as.numeric(size),
as.numeric(cut.prob), as.numeric(sample.size), as.numeric(sample)
)
if (is.null(cut.prob)) {
.Call(
R_igraph_motifs_randesu_estimate, graph, as.numeric(size),
cut.prob, as.numeric(sample.size), as.numeric(sample)
)
} else {
.Call(
R_igraph_motifs_randesu_estimate, graph, as.numeric(size),
as.numeric(cut.prob), as.numeric(sample.size), as.numeric(sample)
)

}
Comment on lines +244 to +255
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Instead of putting the call in a conditional, update the value of cut.prob in a conditional, and keep a single call to the C function.

}


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4 changes: 2 additions & 2 deletions man/count_motifs.Rd
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4 changes: 2 additions & 2 deletions man/graph.motifs.Rd
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4 changes: 2 additions & 2 deletions man/graph.motifs.est.Rd
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4 changes: 2 additions & 2 deletions man/graph.motifs.no.Rd
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4 changes: 2 additions & 2 deletions man/motifs.Rd
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4 changes: 2 additions & 2 deletions man/sample_motifs.Rd
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