Commit 87a296fa authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.1.2

parent ed939d64
Package: igraph
Version: 1.0.1
Version: 1.1.2
Title: Network Analysis and Visualization
Author: See AUTHORS file.
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Depends: methods
Imports: Matrix, magrittr, NMF, irlba
Suggests: igraphdata, stats4, rgl, tcltk, graph, ape, scales
Imports: graphics, grDevices, irlba, magrittr, Matrix, pkgconfig (>=
2.0.0), stats, utils
Suggests: ape, graph, igraphdata, NMF, rgl, scales, stats4, tcltk,
testthat
License: GPL (>= 2)
URL: http://igraph.org
SystemRequirements: gmp, libxml2
BugReports: https://github.com/igraph/igraph/issues
Encoding: UTF-8
Collate: 'adjacency.R' 'auto.R' 'assortativity.R' 'attributes.R'
'basic.R' 'bipartite.R' 'centrality.R' 'centralization.R'
'cliques.R' 'cocitation.R' 'cohesive.blocks.R' 'printr.R'
'community.R' 'components.R' 'console.R' 'conversion.R'
'data_frame.R' 'decomposition.R' 'degseq.R' 'demo.R'
'embedding.R' 'epi.R' 'fit.R' 'flow.R' 'foreign.R' 'games.R'
'glet.R' 'hrg.R' 'igraph-package.R' 'incidence.R' 'indexing.R'
'interface.R' 'iterators.R' 'layout.R' 'layout_drl.R'
'lazyeval.R' 'make.R' 'mgclust.R' 'minimum.spanning.tree.R'
'motifs.R' 'nexus.R' 'operators.R' 'other.R' 'package.R'
'palette.R' 'par.R' 'paths.R' 'plot.R' 'plot.common.R'
'plot.shapes.R' 'pp.R' 'print.R' 'random_walk.R' 'rewire.R'
'scan.R' 'scg.R' 'sgm.R' 'similarity.R' 'simple.R' 'sir.R'
'socnet.R' 'sparsedf.R' 'structural.properties.R'
'structure.info.R' 'test.R' 'tkplot.R' 'topology.R'
'triangles.R' 'utils.R' 'uuid.R' 'versions.R' 'weakref.R'
'zzz-deprecate.R'
'cliques.R' 'cocitation.R' 'cohesive.blocks.R' 'community.R'
'components.R' 'console.R' 'conversion.R' 'data_frame.R'
'decomposition.R' 'degseq.R' 'demo.R' 'embedding.R' 'epi.R'
'fit.R' 'flow.R' 'foreign.R' 'games.R' 'glet.R' 'hrg.R'
'igraph-package.R' 'incidence.R' 'indexing.R' 'interface.R'
'iterators.R' 'layout.R' 'layout_drl.R' 'lazyeval.R' 'make.R'
'mgclust.R' 'minimum.spanning.tree.R' 'motifs.R' 'nexus.R'
'operators.R' 'other.R' 'package.R' 'palette.R' 'par.R'
'paths.R' 'plot.R' 'plot.common.R' 'plot.shapes.R' 'pp.R'
'print.R' 'printr.R' 'random_walk.R' 'rewire.R' 'scan.R'
'scg.R' 'sgm.R' 'similarity.R' 'simple.R' 'sir.R' 'socnet.R'
'sparsedf.R' 'structural.properties.R' 'structure.info.R'
'test.R' 'tkplot.R' 'topology.R' 'triangles.R' 'utils.R'
'uuid.R' 'versions.R' 'weakref.R' 'zzz-deprecate.R'
NeedsCompilation: yes
Packaged: 2015-06-26 01:04:44 UTC; gaborcsardi
Packaged: 2017-07-20 21:33:52 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2015-06-26 11:13:24
Date/Publication: 2017-07-21 11:39:40 UTC
This diff is collapsed.
# Generated by roxygen2 (4.1.1): do not edit by hand
# Generated by roxygen2: do not edit by hand
S3method("$",igraph)
S3method("$",igraph.es)
......@@ -38,6 +38,9 @@ S3method(compare,membership)
S3method(difference,igraph)
S3method(difference,igraph.es)
S3method(difference,igraph.vs)
S3method(graph_id,igraph)
S3method(graph_id,igraph.es)
S3method(graph_id,igraph.vs)
S3method(groups,communities)
S3method(groups,default)
S3method(intersection,igraph)
......@@ -72,7 +75,6 @@ S3method(rglplot,igraph)
S3method(scg,Matrix)
S3method(scg,igraph)
S3method(scg,matrix)
S3method(str,igraph)
S3method(summary,cohesiveBlocks)
S3method(summary,igraph)
S3method(time_bins,sir)
......@@ -139,7 +141,6 @@ export(as_adjacency_matrix)
export(as_bipartite)
export(as_data_frame)
export(as_edgelist)
export(as_graphnel)
export(as_ids)
export(as_incidence_matrix)
export(as_long_data_frame)
......@@ -432,11 +433,11 @@ export(graph_from_atlas)
export(graph_from_data_frame)
export(graph_from_edgelist)
export(graph_from_graphdb)
export(graph_from_graphnel)
export(graph_from_incidence_matrix)
export(graph_from_isomorphism_class)
export(graph_from_lcf)
export(graph_from_literal)
export(graph_id)
export(graph_version)
export(graphlet_basis)
export(graphlet_proj)
......@@ -452,6 +453,7 @@ export(growing.random.game)
export(gsize)
export(has.multiple)
export(head_of)
export(head_print)
export(hierarchical_sbm)
export(hierarchy)
export(hrg)
......@@ -490,6 +492,7 @@ export(igraphtest)
export(in_circle)
export(incident)
export(incident_edges)
export(indent_print)
export(independence.number)
export(independent.vertex.sets)
export(induced.subgraph)
......@@ -530,6 +533,7 @@ export(is_matching)
export(is_max_matching)
export(is_min_separator)
export(is_named)
export(is_printer_callback)
export(is_separator)
export(is_simple)
export(is_subgraph_isomorphic_to)
......@@ -689,6 +693,8 @@ export(predict_edges)
export(pref)
export(preference.game)
export(print.igraph)
export(print_all)
export(printer_callback)
export(r_pal)
export(radius)
export(random.graph.game)
......@@ -852,6 +858,7 @@ export(with_fr)
export(with_gem)
export(with_graph_)
export(with_graphopt)
export(with_igraph_opt)
export(with_kk)
export(with_lgl)
export(with_mds)
......@@ -863,9 +870,53 @@ export(without_multiples)
export(write.graph)
export(write_graph)
import(methods)
importFrom(grDevices,as.raster)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.new)
importFrom(grDevices,palette)
importFrom(grDevices,rainbow)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,layout)
importFrom(graphics,layout.show)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,polygon)
importFrom(graphics,rasterImage)
importFrom(graphics,segments)
importFrom(graphics,symbols)
importFrom(graphics,text)
importFrom(graphics,xspline)
importFrom(graphics,xyinch)
importFrom(magrittr,"%>%")
importFrom(pkgconfig,get_config)
importFrom(pkgconfig,set_config)
importFrom(pkgconfig,set_config_in)
importFrom(stats,IQR)
importFrom(stats,as.dendrogram)
importFrom(stats,as.hclust)
importFrom(stats,ave)
importFrom(stats,coef)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
useDynLib(igraph)
importFrom(stats,rect.hclust)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,vcov)
importFrom(utils,URLencode)
importFrom(utils,browseURL)
importFrom(utils,capture.output)
importFrom(utils,edit)
importFrom(utils,head)
importFrom(utils,packageDescription)
importFrom(utils,packageName)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
useDynLib(igraph, .registration = TRUE, .fixes = "C_")
......@@ -50,10 +50,9 @@ graph.adjacency.dense <- function(adjmatrix, mode=c("directed", "undirected", "m
stop("not a square matrix")
}
on.exit( .Call("R_igraph_finalizer", PACKAGE="igraph") )
res <- .Call("R_igraph_weighted_adjacency", adjmatrix,
as.numeric(mode), weighted, diag,
PACKAGE="igraph")
on.exit( .Call(C_R_igraph_finalizer) )
res <- .Call(C_R_igraph_weighted_adjacency, adjmatrix,
as.numeric(mode), weighted, diag)
} else {
adjmatrix <- as.matrix(adjmatrix)
......@@ -63,9 +62,8 @@ graph.adjacency.dense <- function(adjmatrix, mode=c("directed", "undirected", "m
if (!diag) { diag(adjmatrix) <- 0 }
on.exit( .Call("R_igraph_finalizer", PACKAGE="igraph") )
res <- .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode),
PACKAGE="igraph")
on.exit( .Call(C_R_igraph_finalizer) )
res <- .Call(C_R_igraph_graph_adjacency, adjmatrix, as.numeric(mode))
}
res
......
......@@ -57,8 +57,7 @@ graph_attr <- function(graph, name) {
if (missing(name)) {
graph.attributes(graph)
} else {
base::.Call("R_igraph_mybracket2", graph, 9L, 2L,
PACKAGE="igraph")[[as.character(name)]]
.Call(C_R_igraph_mybracket2, graph, 9L, 2L)[[as.character(name)]]
}
}
......@@ -117,8 +116,7 @@ set_graph_attr <- function(graph, name, value) {
stop("Not a graph object")
}
base::.Call("R_igraph_mybracket3_set", graph, 9L, 2L, name, value,
PACKAGE="igraph")
.Call(C_R_igraph_mybracket3_set, graph, 9L, 2L, name, value)
}
#' @export
......@@ -127,8 +125,7 @@ graph.attributes <- function(graph) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
base::.Call("R_igraph_mybracket2_copy", graph, 9L, 2L,
PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_copy, graph, 9L, 2L)
}
#' @export
......@@ -142,8 +139,7 @@ graph.attributes <- function(graph) {
stop("Value must be a named list with unique names")
}
base::.Call("R_igraph_mybracket2_set", graph, 9L, 2L, value,
PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_set, graph, 9L, 2L, value)
}
......@@ -180,8 +176,8 @@ vertex_attr <- function(graph, name, index=V(graph)) {
vertex.attributes(graph, index = index)
}
} else {
myattr <- base::.Call("R_igraph_mybracket2", graph, 9L, 3L,
PACKAGE="igraph")[[as.character(name)]]
myattr <-
.Call(C_R_igraph_mybracket2, graph, 9L, 3L)[[as.character(name)]]
if (! missing(index)) {
index <- as.igraph.vs(graph, index)
myattr <- myattr[index]
......@@ -257,7 +253,7 @@ i_set_vertex_attr <- function(graph, name, index=V(graph), value,
name <- as.character(name)
vc <- vcount(graph)
vattrs <- base::.Call("R_igraph_mybracket2", graph, 9L, 3L, PACKAGE="igraph")
vattrs <- .Call(C_R_igraph_mybracket2, graph, 9L, 3L)
if (single) {
vattrs[[name]][[index]] <- value
} else {
......@@ -265,7 +261,7 @@ i_set_vertex_attr <- function(graph, name, index=V(graph), value,
}
length(vattrs[[name]]) <- vc
base::.Call("R_igraph_mybracket2_set", graph, 9L, 3L, vattrs, PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_set, graph, 9L, 3L, vattrs)
}
#' @export
......@@ -279,12 +275,12 @@ vertex.attributes <- function(graph, index = V(graph)) {
index <- as.igraph.vs(graph, index)
}
res <- base::.Call("R_igraph_mybracket2_copy", graph, 9L, 3L, PACKAGE="igraph")
res <- .Call(C_R_igraph_mybracket2_copy, graph, 9L, 3L)
if (!missing(index) &&
(length(index) != vcount(graph) || any(index != V(graph)))) {
for (i in seq_along(value)) {
value[[i]] <- value[[i]][index]
for (i in seq_along(res)) {
res[[i]] <- res[[i]][index]
}
}
res
......@@ -323,8 +319,7 @@ vertex.attributes <- function(graph, index = V(graph)) {
}
}
base::.Call("R_igraph_mybracket2_set", graph, 9L, 3L, value,
PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_set, graph, 9L, 3L, value)
}
......@@ -358,8 +353,7 @@ edge_attr <- function(graph, name, index=E(graph)) {
} else {
name <- as.character(name)
index <- as.igraph.es(graph, index)
myattr <- base::.Call("R_igraph_mybracket2", graph, 9L, 4L,
PACKAGE="igraph")[[name]]
myattr <- .Call(C_R_igraph_mybracket2, graph, 9L, 4L)[[name]]
myattr[index]
}
}
......@@ -430,7 +424,7 @@ i_set_edge_attr <- function(graph, name, index=E(graph), value,
if (!missing(index) && check) index <- as.igraph.es(graph, index)
ec <- ecount(graph)
eattrs <- base::.Call("R_igraph_mybracket2", graph, 9L, 4L, PACKAGE="igraph")
eattrs <- .Call(C_R_igraph_mybracket2, graph, 9L, 4L)
if (single) {
eattrs[[name]][[index]] <- value
} else {
......@@ -438,7 +432,7 @@ i_set_edge_attr <- function(graph, name, index=E(graph), value,
}
length(eattrs[[name]]) <- ec
base::.Call("R_igraph_mybracket2_set", graph, 9L, 4L, eattrs, PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_set, graph, 9L, 4L, eattrs)
}
#' @export
......@@ -452,12 +446,12 @@ edge.attributes <- function(graph, index = E(graph)) {
index <- as.igraph.es(graph, index)
}
res <- base::.Call("R_igraph_mybracket2_copy", graph, 9L, 4L, PACKAGE="igraph")
res <- .Call(C_R_igraph_mybracket2_copy, graph, 9L, 4L)
if (!missing(index) &&
(length(index) != ecount(graph) || any(index != E(graph)))) {
for (i in seq_along(value)) {
value[[i]] <- value[[i]][index]
for (i in seq_along(res)) {
res[[i]] <- res[[i]][index]
}
}
res
......@@ -497,8 +491,7 @@ edge.attributes <- function(graph, index = E(graph)) {
}
}
base::.Call("R_igraph_mybracket2_set", graph, 9L, 4L, value,
PACKAGE="igraph")
.Call(C_R_igraph_mybracket2_set, graph, 9L, 4L, value)
}
#' List names of graph attributes
......@@ -518,7 +511,7 @@ graph_attr_names <- function(graph) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
res <- base::.Call("R_igraph_mybracket2_names", graph, 9L, 2L, PACKAGE="igraph")
res <- .Call(C_R_igraph_mybracket2_names, graph, 9L, 2L)
if (is.null(res)) { res <- character() }
res
}
......@@ -543,7 +536,7 @@ vertex_attr_names <- function(graph) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
res <- base::.Call("R_igraph_mybracket2_names", graph, 9L, 3L, PACKAGE="igraph")
res <- .Call(C_R_igraph_mybracket2_names, graph, 9L, 3L)
if (is.null(res)) { res <- character() }
res
......@@ -568,7 +561,7 @@ edge_attr_names <- function(graph) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
res <- base::.Call("R_igraph_mybracket2_names", graph, 9L, 4L, PACKAGE="igraph")
res <- .Call(C_R_igraph_mybracket2_names, graph, 9L, 4L)
if (is.null(res)) { res <- character() }
res
}
......@@ -598,10 +591,10 @@ delete_graph_attr <- function(graph, name) {
stop("No such graph attribute: ", name)
}
gattr <- base::.Call("R_igraph_mybracket2", graph, 9L, 2L, PACKAGE="igraph")
gattr <- .Call(C_R_igraph_mybracket2, graph, 9L, 2L)
gattr[[name]] <- NULL
base::.Call