Squashed merge of major changes

.Rbuildignore

@@ -19,3 +19,9 @@
 \.sh$
 \.tar\.gz$
 \.txt$
+
+^temp\.
+\.temp$
+^vignettes/memoise
+
+^data-raw$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: graphicalExtremes
 Title: Statistical Methodology for Graphical Extreme Value Models
-Version: 0.2.0
+Version: 0.3.0
 Maintainer: Sebastian Engelke <[email protected]>
 Authors@R: 
     c(

NAMESPACE

@@ -1,12 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Gamma2Gamma)
 export(Gamma2Sigma)
 export(Gamma2Theta)
 export(Gamma2chi)
 export(Gamma2graph)
 export(Sigma2Gamma)
+export(Sigma2Sigma)
+export(Sigma2Theta)
+export(Sigma2graph)
 export(Theta2Gamma)
+export(Theta2Sigma)
+export(Theta2Theta)
 export(Theta2graph)
+export(checkGamma)
+export(checkMatrix)
+export(checkSigma)
+export(checkSigmaTheta)
+export(checkTheta)
 export(chi2Gamma)
 export(complete_Gamma)
 export(complete_Gamma_decomposable)
@@ -22,19 +33,39 @@ export(emp_vario)
 export(emp_vario_pairwise)
 export(emst)
 export(emtp2)
+export(ensure_matrix_symmetry)
+export(ensure_matrix_symmetry_and_truncate_zeros)
+export(fit_graph_to_Theta)
 export(flightCountMatrixToConnectionList)
+export(fmpareto_HR_MLE)
 export(fmpareto_graph_HR)
 export(generate_random_Gamma)
 export(generate_random_cactus)
+export(generate_random_chordal_graph)
+export(generate_random_connected_graph)
+export(generate_random_graphical_Gamma)
 export(generate_random_integer_Gamma)
 export(generate_random_model)
+export(generate_random_spd_matrix)
+export(generate_random_tree)
+export(getDanubeFlowGraph)
+export(getFlightDelayData)
+export(get_alert_function)
 export(get_large_tol)
 export(get_mc_cores)
 export(get_small_tol)
+export(is_valid_Gamma)
+export(is_valid_Sigma)
+export(is_valid_Theta)
 export(loglik_HR)
+export(matrix2matrix)
+export(partialMatrixToGraph)
+export(plotDanube)
+export(plotDanubeIGraph)
 export(plotFlights)
 export(rmpareto)
 export(rmpareto_tree)
 export(rmstable)
 export(rmstable_tree)
+export(truncate_zeros)
 importFrom(Rdpack,reprompt)

R/data.R

@@ -1,3 +1,31 @@
+
+#' Get package data
+#' 
+#' Get private data sets from `inst/extdata`.
+#' 
+#' @param filename Base name of the file. E.g. `"FILENAME"` for a file `inst/extdata/FILENAME`.
+#' @param isRDS Whether the file is an `.RDS` file.
+#' 
+#' @return
+#' If `isRDS=TRUE` an R object.
+#' If `isRDS=FALSE` an environment, containing the R objects from the file.
+#' 
+#' @keywords internal
+getPackageData <- function(filename, isRDS=TRUE){
+  # Path of data file
+  fpath <- system.file('extdata', filename, package='graphicalExtremes')
+
+  # RDS files contain a single object which is returned
+  if(isRDS){
+    return(readRDS(fpath))
+  }
+
+  # RDA files contain one/multiple R object(s) which are returned in a new environment
+  env <- new.env(parent = emptyenv())
+  load(fpath, envir = env)
+  return(env)
+}
+
 #' Upper Danube basin dataset
 #'
 #' A dataset containing river discharge data for tributaries of the Danube.
@@ -8,8 +36,8 @@
 #'  \item{`data_raw`}{A numeric matrix, containing daily (raw) discharge data for each gauging station}
 #'  \item{`info`}{A data frame, containing information about each gauging station}
 #'  \item{`flow_edges`}{
-#'    A two-column numeric matrix. Each row contains the indices (in `info`)
-#'    of a pair of gauging stations that are directly connected by a river.
+#'  A two-column numeric matrix. Each row contains the indices (in `info`)
+#'  of a pair of gauging stations that are directly connected by a river.
 #'  }
 #' }
 #' 
@@ -32,7 +60,7 @@
 #'  \item{`Area`}{Area of the catchment corresponding to the gauging station}
 #'  \item{`Slope`}{Mean slope of the catchment}
 #'  \item{`PlotCoordX`, `PlotCoordY`}{
-#'    X-Y-coordinates which can be used to arrange the gauging stations when plotting a flow graph.
+#'  X-Y-coordinates which can be used to arrange the gauging stations when plotting a flow graph.
 #'  }
 #' }
 #' 
@@ -41,13 +69,13 @@
 #' loc <- as.matrix(danube$info[,c('PlotCoordX', 'PlotCoordY')])
 #' plot(g, layout = loc)
 #' 
-#' @seealso [`flights`], `vignette('graphicalExtremes')`
+#' @family danubeData
+#' @family datasets
 #' 
 #' @references
 #' \insertAllCited{}
 #'
 #' @source Bavarian Environmental Agency <https://www.gkd.bayern.de>.
-#'
 "danube"
 
 
@@ -59,14 +87,14 @@
 #' and pre-processed as described in
 #' \insertCite{hen2022;textual}{graphicalExtremes}.
 #' *Note: The CRAN version of this package contains only data from 2010-2013.*
-#' *The full dataset is available in the Github version of this package.*
+#' *The full dataset is available in the GitHub version of this package.*
 #' 
 #' @format A named `list` with three entries:
 #' \describe{
 #'  \item{`airports`}{A `data.frame`, containing information about US airports}
 #'  \item{`delays`}{A numeric matrix, containing daily aggregated delays at the airports in the dataset}
 #'  \item{`flightCounts`}{
-#'    A numeric array, containing yearly flight numbers between airports in the dataset
+#'  A numeric array, containing yearly flight numbers between airports in the dataset
 #'  }
 #' }
 #' 
@@ -122,7 +150,8 @@
 #' totalDelays <- apply(flights$delays, c(1,2), sum)
 #' }
 #' 
-#' @seealso [`danube`], [`flightCountMatrixToConnectionList`], [`plotFlights`]
+#' @family flightData
+#' @family datasets
 #' 
 #' @source
 #' Raw delays data:
@@ -134,6 +163,5 @@
 #' - <https://esubmit.rita.dot.gov/On-Time-Form3A.aspx>
 #' 
 #' Airports (includes license information):
-#' - <https://openflights.org/data.html>
-#' 
+#' - <https://openflights.org/data>
 "flights"