revise docs, remove c++11

kharchenkolab · Jul 3, 2023 · 087b45e · 087b45e
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commit 087b45e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,6 +13,7 @@ Imports:
     graphics,
     grDevices,
     igraph,
+    methods,
     parallel, 
     Rcpp (>= 1.0.5), 
     sccore,
@@ -21,8 +22,8 @@ Suggests:
     pbapply,
     testthat (>= 3.1.0)
 LinkingTo: Rcpp, RcppArmadillo, RcppEigen
-SystemRequirements: C++11, GNU make (optional), libxml2 (optional), glpk (>= 4.57, optional)
-RoxygenNote: 7.2.1
+SystemRequirements: GNU make (optional), libxml2 (optional), glpk (>= 4.57, optional)
+RoxygenNote: 7.2.3
 URL: https://github.com/kharchenkolab/leidenAlg
 BugReports: https://github.com/kharchenkolab/leidenAlg/issues
 NeedsCompilation: yes

diff --git a/NAMESPACE b/NAMESPACE
@@ -17,6 +17,7 @@ importFrom(igraph,V)
 importFrom(igraph,induced.subgraph)
 importFrom(igraph,membership)
 importFrom(igraph,walktrap.community)
+importFrom(methods,is)
 importFrom(stats,as.dendrogram)
 importFrom(stats,as.hclust)
 importFrom(stats,dendrapply)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,6 +1,25 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#' Refer to the R function find_partition()
+#' For notes of the graph object, refer to https://igraph.org/c/doc/igraph-Basic.html
+#'
+#' @param edgelist The graph edge list
+#' @param edgelist_length integer The length of the graph edge list
+#' @param num_vertices integer The number of vertices in the graph
+#' @param direction boolean Whether the graph is directed or undirected
+#' @param edge_weights Vector of edge weights. In weighted graphs, a real number is assigned to each (directed or undirected) edge. For an unweighted graph, this is set to 1. Refer to igraph, weighted graphs.
+#' @param resolution Integer resoluiton parameter controlling communities detected (default=1.0) Higher resolutions lead to more communities, while lower resolutions lead to fewer communities.
+#' @param niter Number of iterations that the algorithm should be run for (default=2)
+#' @return A vector of membership values
+#' @examples 
+#' library(igraph)
+#' library(leidenAlg)
+#' 
+#' g <- make_star(10)
+#' E(g)$weight <- seq(ecount(g))
+#' find_partition(g, E(g)$weight)
+#' 
 find_partition_rcpp <- function(edgelist, edgelist_length, num_vertices, direction, edge_weights, resolution = 1.0, niter = 2L) {
     .Call('_leidenAlg_find_partition_rcpp', PACKAGE = 'leidenAlg', edgelist, edgelist_length, num_vertices, direction, edge_weights, resolution, niter)
 }

diff --git a/R/communities.R b/R/communities.R
@@ -9,6 +9,7 @@
 #' @importFrom igraph membership
 #' @importFrom igraph walktrap.community
 #' @importFrom igraph induced.subgraph
+#' @importFrom methods is
 #' @import sccore
 #' @importFrom graphics par
 #' @importFrom grDevices adjustcolor
@@ -228,7 +229,7 @@ as.dendrogram.fakeCommunities <- function(object, ...) {
 
 #' Returns pre-calculated membership factor
 #'
-#' @param object fakeCommunities object
+#' @param communities fakeCommunities object
 #' @param ... further parameters for generic
 #' @return membership factor
 #' @examples 
@@ -237,8 +238,8 @@ as.dendrogram.fakeCommunities <- function(object, ...) {
 #' 
 #' @method membership fakeCommunities
 #' @export
-membership.fakeCommunities <- function(object, ...) {
-  return(object$membership)
+membership.fakeCommunities <- function(communities, ...) {
+  return(communities$membership)
 }
 
 

diff --git a/man/find_partition.Rd b/man/find_partition.Rd
diff --git a/man/find_partition_rcpp.Rd b/man/find_partition_rcpp.Rd
diff --git a/man/leiden.community.Rd b/man/leiden.community.Rd
diff --git a/man/membership.fakeCommunities.Rd b/man/membership.fakeCommunities.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -9,9 +9,7 @@ PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 
-
 PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
-CXX_STD = CXX11
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -10,7 +10,6 @@ LDFLAGS += -lpthread
 
 
 PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
-CXX_STD = CXX11
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs

diff --git a/src/leiden.cpp b/src/leiden.cpp
@@ -22,37 +22,6 @@ using namespace Rcpp;
 
 // a wrapper for the Leidgen algorithm implementation (https://github.com/vtraag/leidenalg)
 
-// REMOVED v1.1.0 with igraph (R package) v1.5.0
-//
-// int R_SEXP_to_vector(SEXP sv, igraph_vector_t *v) {
-//   v->stor_begin=REAL(sv);
-//   v->stor_end=v->stor_begin+GET_LENGTH(sv);
-//   v->end=v->stor_end;
-//   return 0;
-// }
-
-
-// int R_SEXP_to_igraph(SEXP graph, igraph_t *res) {
-// 
-//   res->n=(igraph_integer_t) REAL(VECTOR_ELT(graph, 0))[0];
-//   res->directed=LOGICAL(VECTOR_ELT(graph, 1))[0];
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 2), &res->from);
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 3), &res->to);
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 4), &res->oi);
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 5), &res->ii);
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 6), &res->os);
-//   R_SEXP_to_vector(VECTOR_ELT(graph, 7), &res->is);
-//   
-//   /* attributes */
-//   REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[0] = 1; /* R objects refcount */
-//   REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[1] = 0; /* igraph_t objects */
-//   res->attr=VECTOR_ELT(graph, 8);
-//   
-//   return 0;
-// }
-//   
-
-
 // https://stackoverflow.com/questions/10250438/using-stdvector-with-igraph
 
 void Stl_To_Igraph_vector_t(std::vector<int>& vectR, igraph_vector_t* v) {
@@ -68,8 +37,25 @@ void Stl_To_Igraph_vector_t(std::vector<int>& vectR, igraph_vector_t* v) {
 }
 
 
-// Refer to find_partition()
-// 
+//' Refer to the R function find_partition()
+//' For notes of the graph object, refer to https://igraph.org/c/doc/igraph-Basic.html
+//'
+//' @param edgelist The graph edge list
+//' @param edgelist_length integer The length of the graph edge list
+//' @param num_vertices integer The number of vertices in the graph
+//' @param direction boolean Whether the graph is directed or undirected
+//' @param edge_weights Vector of edge weights. In weighted graphs, a real number is assigned to each (directed or undirected) edge. For an unweighted graph, this is set to 1. Refer to igraph, weighted graphs.
+//' @param resolution Integer resoluiton parameter controlling communities detected (default=1.0) Higher resolutions lead to more communities, while lower resolutions lead to fewer communities.
+//' @param niter Number of iterations that the algorithm should be run for (default=2)
+//' @return A vector of membership values
+//' @examples 
+//' library(igraph)
+//' library(leidenAlg)
+//' 
+//' g <- make_star(10)
+//' E(g)$weight <- seq(ecount(g))
+//' find_partition(g, E(g)$weight)
+//' 
 // [[Rcpp::export]]
 std::vector<size_t> find_partition_rcpp(std::vector<int>& edgelist, int edgelist_length, int num_vertices, bool direction, std::vector<double>& edge_weights, double resolution=1.0, int niter=2) {
 

diff --git a/src/leidenalg/Makefile b/src/leidenalg/Makefile
@@ -1,5 +1,5 @@
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
 PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 

diff --git a/src/leidenalg/Makefile.win b/src/leidenalg/Makefile.win
@@ -1,5 +1,5 @@
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
 PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 

diff --git a/src/rigraph/Makefile b/src/rigraph/Makefile
@@ -1,12 +1,12 @@
 C ?= gcc 
-CFLAGS = -O3 -std=c11 -std=gnu11
-PKG_CFLAGS = -O3 -std=c11 -std=gnu11 -pthread -fPIC 
+CFLAGS = -O3 
+PKG_CFLAGS = -O3 -pthread -fPIC 
 PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
 PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 

diff --git a/src/rigraph/Makefile.win b/src/rigraph/Makefile.win
@@ -1,11 +1,11 @@
 C ?= gcc 
-CFLAGS = -O3 -std=c11 -std=gnu11
-PKG_CFLAGS = -O3 -std=c11 -std=gnu11 -pthread -fPIC 
+CFLAGS = -O3 
+PKG_CFLAGS = -O3  -pthread -fPIC 
 PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
 PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread