1 2# IGraph R package 3# Copyright (C) 2014 Gabor Csardi <csardi.gabor@gmail.com> 4# 334 Harvard street, Cambridge, MA 02139 USA 5# 6# This program is free software; you can redistribute it and/or modify 7# it under the terms of the GNU General Public License as published by 8# the Free Software Foundation; either version 2 of the License, or 9# (at your option) any later version. 10# 11# This program is distributed in the hope that it will be useful, 12# but WITHOUT ANY WARRANTY; without even the implied warranty of 13# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14# GNU General Public License for more details. 15# 16# You should have received a copy of the GNU General Public License 17# along with this program; if not, write to the Free Software 18# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 19# 02110-1301 USA 20# 21################################################################### 22 23#' @include attributes.R auto.R basic.R bipartite.R centrality.R 24#' @include cliques.R cocitation.R cohesive.blocks.R community.R 25#' @include components.R console.R conversion.R decomposition.R demo.R 26#' @include epi.R fit.R flow.R foreign.R games.R glet.R hrg.R indexing.R 27#' @include interface.R iterators.R layout.R minimum.spanning.tree.R 28#' @include motifs.R nexus.R operators.R other.R package.R par.R plot.R 29#' @include plot.common.R plot.shapes.R pp.R print.R scg.R socnet.R 30#' @include sparsedf.R structural.properties.R 31#' @include structure.info.R test.R tkplot.R topology.R layout_drl.R 32NULL 33 34## For the future, right now, we do not warn or even message 35 36#' @importFrom utils packageName 37 38deprecated <- function(old, new) { 39 assign(old, new, envir = asNamespace(packageName())) 40} 41 42#' @export add.edges 43deprecated("add.edges", add_edges) 44#' @export add.vertex.shape 45deprecated("add.vertex.shape", add_shape) 46#' @export add.vertices 47deprecated("add.vertices", add_vertices) 48#' @export adjacent.triangles 49deprecated("adjacent.triangles", count_triangles) 50#' @export articulation.points 51deprecated("articulation.points", articulation_points) 52#' @export aging.prefatt.game 53deprecated("aging.prefatt.game", sample_pa_age) 54#' @export aging.ba.game 55deprecated("aging.ba.game", sample_pa_age) 56#' @export aging.barabasi.game 57deprecated("aging.barabasi.game", sample_pa_age) 58#' @export alpha.centrality 59deprecated("alpha.centrality", alpha_centrality) 60#' @export are.connected 61deprecated("are.connected", are_adjacent) 62#' @export asPhylo 63deprecated("asPhylo", as_phylo) 64#' @method asPhylo communities 65deprecated("asPhylo.communities", as_phylo.communities) 66#' @method asPhylo igraphHRG 67deprecated("asPhylo.igraphHRG", as_phylo.igraphHRG) 68#' @export assortativity.degree 69deprecated("assortativity.degree", assortativity_degree) 70#' @export assortativity.nominal 71deprecated("assortativity.nominal", assortativity_nominal) 72#' @export asymmetric.preference.game 73deprecated("asymmetric.preference.game", sample_asym_pref) 74#' @export authority.score 75deprecated("authority.score", authority_score) 76#' @export autocurve.edges 77deprecated("autocurve.edges", curve_multiple) 78#' @export average.path.length 79deprecated("average.path.length", mean_distance) 80 81#' @export ba.game 82deprecated("ba.game", sample_pa) 83#' @export barabasi.game 84deprecated("barabasi.game", sample_pa) 85#' @export betweenness.estimate 86deprecated("betweenness.estimate", estimate_betweenness) 87#' @export biconnected.components 88deprecated("biconnected.components", biconnected_components) 89#' @export bipartite.mapping 90deprecated("bipartite.mapping", bipartite_mapping) 91#' @export bipartite.projection 92deprecated("bipartite.projection", bipartite_projection) 93#' @export bipartite.projection.size 94deprecated("bipartite.projection.size", bipartite_projection_size) 95#' @export bipartite.random.game 96deprecated("bipartite.random.game", sample_bipartite) 97#' @export blockGraphs 98deprecated("blockGraphs", graphs_from_cohesive_blocks) 99#' @export bonpow 100deprecated("bonpow", power_centrality) 101 102#' @export callaway.traits.game 103deprecated("callaway.traits.game", sample_traits_callaway) 104#' @export canonical.permutation 105deprecated("canonical.permutation", canonical_permutation) 106#' @export centralization.betweenness 107deprecated("centralization.betweenness", centr_betw) 108#' @export centralization.betweenness.tmax 109deprecated("centralization.betweenness.tmax", centr_betw_tmax) 110#' @export centralization.closeness 111deprecated("centralization.closeness", centr_clo) 112#' @export centralization.closeness.tmax 113deprecated("centralization.closeness.tmax", centr_clo_tmax) 114#' @export centralization.degree 115deprecated("centralization.degree", centr_degree) 116#' @export centralization.degree.tmax 117deprecated("centralization.degree.tmax", centr_degree_tmax) 118#' @export centralization.evcent 119deprecated("centralization.evcent", centr_eigen) 120#' @export centralization.evcent.tmax 121deprecated("centralization.evcent.tmax", centr_eigen_tmax) 122#' @export centralize.scores 123deprecated("centralize.scores", centralize) 124#' @export cited.type.game 125deprecated("cited.type.game", sample_cit_types) 126#' @export citing.cited.type.game 127deprecated("citing.cited.type.game", sample_cit_cit_types) 128#' @export clique.number 129deprecated("clique.number", clique_num) 130#' @export closeness.estimate 131deprecated("closeness.estimate", estimate_closeness) 132#' @export cluster.distribution 133deprecated("cluster.distribution", component_distribution) 134#' @export clusters 135deprecated("clusters", components) 136#' @export code.length 137deprecated("code.length", code_len) 138#' @export cohesive.blocks 139deprecated("cohesive.blocks", cohesive_blocks) 140#' @export connect.neighborhood 141deprecated("connect.neighborhood", connect) 142#' @export contract.vertices 143deprecated("contract.vertices", contract) 144#' @export convex.hull 145deprecated("convex.hull", convex_hull) 146#' @export count.multiple 147deprecated("count.multiple", count_multiple) 148#' @export cutat 149deprecated("cutat", cut_at) 150 151#' @export decompose.graph 152deprecated("decompose.graph", decompose) 153#' @export degree.distribution 154deprecated("degree.distribution", degree_distribution) 155#' @export degree.sequence.game 156deprecated("degree.sequence.game", sample_degseq) 157#' @export delete.edges 158deprecated("delete.edges", delete_edges) 159#' @export delete.vertices 160deprecated("delete.vertices", delete_vertices) 161#' @export dendPlot 162deprecated("dendPlot", plot_dendrogram) 163#' @method dendPlot communities 164deprecated("dendPlot.communities", plot_dendrogram.communities) 165#' @method dendPlot igraphHRG 166deprecated("dendPlot.igraphHRG", plot_dendrogram.igraphHRG) 167#' @export dominator.tree 168deprecated("dominator.tree", dominator_tree) 169#' @export dyad.census 170deprecated("dyad.census", dyad_census) 171 172#' @export ecount 173deprecated("ecount", gsize) 174#' @export edge.betweenness 175deprecated("edge.betweenness", edge_betweenness) 176#' @export edge.betweenness.community 177deprecated("edge.betweenness.community", cluster_edge_betweenness) 178#' @export edge.betweenness.estimate 179deprecated("edge.betweenness.estimate", estimate_edge_betweenness) 180#' @export edge.connectivity 181deprecated("edge.connectivity", edge_connectivity) 182#' @export edge.disjoint.paths 183deprecated("edge.disjoint.paths", edge_disjoint_paths) 184#' @export establishment.game 185deprecated("establishment.game", sample_traits) 186#' @export evcent 187deprecated("evcent", eigen_centrality) 188 189#' @export farthest.nodes 190deprecated("farthest.nodes", farthest_vertices) 191#' @export fastgreedy.community 192deprecated("fastgreedy.community", cluster_fast_greedy) 193#' @export forest.fire.game 194deprecated("forest.fire.game", sample_forestfire) 195 196#' @export get.adjedgelist 197deprecated("get.adjedgelist", as_adj_edge_list) 198#' @export get.adjlist 199deprecated("get.adjlist", as_adj_list) 200#' @export get.adjacency 201deprecated("get.adjacency", as_adjacency_matrix) 202#' @export get.data.frame 203deprecated("get.data.frame", as_data_frame) 204#' @export get.edge.attribute 205deprecated("get.edge.attribute", edge_attr) 206#' @export get.edgelist 207deprecated("get.edgelist", as_edgelist) 208#' @export get.graph.attribute 209deprecated("get.graph.attribute", graph_attr) 210#' @export get.incidence 211deprecated("get.incidence", as_incidence_matrix) 212#' @export get.stochastic 213deprecated("get.stochastic", stochastic_matrix) 214#' @export get.vertex.attribute 215deprecated("get.vertex.attribute", vertex_attr) 216#' @export graph.adhesion 217deprecated("graph.adhesion", adhesion) 218#' @export graph.adjacency 219deprecated("graph.adjacency", graph_from_adjacency_matrix) 220#' @export graph.adjlist 221deprecated("graph.adjlist", graph_from_adj_list) 222#' @export graph.atlas 223deprecated("graph.atlas", graph_from_atlas) 224#' @export graph.automorphisms 225deprecated("graph.automorphisms", automorphisms) 226#' @export graph.bfs 227deprecated("graph.bfs", bfs) 228#' @export graph.bipartite 229deprecated("graph.bipartite", make_bipartite_graph) 230#' @export graph.cohesion 231deprecated("graph.cohesion", cohesion) 232#' @export graph.complementer 233deprecated("graph.complementer", complementer) 234#' @export graph.compose 235deprecated("graph.compose", compose) 236#' @export graph.coreness 237deprecated("graph.coreness", coreness) 238#' @export graph.data.frame 239deprecated("graph.data.frame", graph_from_data_frame) 240#' @export graph.de.bruijn 241deprecated("graph.de.bruijn", make_de_bruijn_graph) 242#' @export graph.density 243deprecated("graph.density", edge_density) 244#' @export graph.disjoint.union 245deprecated("graph.disjoint.union", disjoint_union) 246#' @export graph.dfs 247deprecated("graph.dfs", dfs) 248#' @export graph.difference 249deprecated("graph.difference", difference) 250#' @export graph.diversity 251deprecated("graph.diversity", diversity) 252#' @export graph.edgelist 253deprecated("graph.edgelist", graph_from_edgelist) 254#' @export graph.eigen 255deprecated("graph.eigen", spectrum) 256#' @export graph.empty 257deprecated("graph.empty", make_empty_graph) 258#' @export graph.extended.chordal.ring 259deprecated("graph.extended.chordal.ring", make_chordal_ring) 260#' @export graph.formula 261deprecated("graph.formula", graph_from_literal) 262#' @export graph.full 263deprecated("graph.full", make_full_graph) 264#' @export graph.full.bipartite 265deprecated("graph.full.bipartite", make_full_bipartite_graph) 266#' @export graph.full.citation 267deprecated("graph.full.citation", make_full_citation_graph) 268#' @export graph.graphdb 269deprecated("graph.graphdb", graph_from_graphdb) 270#' @export graph.incidence 271deprecated("graph.incidence", graph_from_incidence_matrix) 272#' @export graph.isocreate 273deprecated("graph.isocreate", graph_from_isomorphism_class) 274#' @export graph.kautz 275deprecated("graph.kautz", make_kautz_graph) 276#' @export graph.knn 277deprecated("graph.knn", knn) 278#' @export graph.laplacian 279deprecated("graph.laplacian", laplacian_matrix) 280#' @export graph.lattice 281deprecated("graph.lattice", make_lattice) 282#' @export graph.lcf 283deprecated("graph.lcf", graph_from_lcf) 284#' @export graph.maxflow 285deprecated("graph.maxflow", max_flow) 286#' @export graph.mincut 287deprecated("graph.mincut", min_cut) 288#' @export graph.motifs 289deprecated("graph.motifs", motifs) 290#' @export graph.motifs.est 291deprecated("graph.motifs.est", sample_motifs) 292#' @export graph.motifs.no 293deprecated("graph.motifs.no", count_motifs) 294#' @export graph.neighborhood 295deprecated("graph.neighborhood", make_ego_graph) 296#' @export graph.star 297deprecated("graph.star", make_star) 298#' @export graph.strength 299deprecated("graph.strength", strength) 300#' @export graph.tree 301deprecated("graph.tree", make_tree) 302#' @export graph.union 303deprecated("graph.union", union.igraph) 304#' @export graph.ring 305deprecated("graph.ring", make_ring) 306#' @export graphlets.candidate.basis 307deprecated("graphlets.candidate.basis", graphlet_basis) 308#' @export graphlets.project 309deprecated("graphlets.project", graphlet_proj) 310#' @export growing.random.game 311deprecated("growing.random.game", sample_growing) 312#' @export grg.game 313deprecated("grg.game", sample_grg) 314 315#' @export has.multiple 316deprecated("has.multiple", any_multiple) 317#' @export hrg.consensus 318deprecated("hrg.consensus", consensus_tree) 319#' @export hrg.create 320deprecated("hrg.create", hrg) 321#' @export hrg.dendrogram 322deprecated("hrg.dendrogram", hrg_tree) 323#' @export hrg.game 324deprecated("hrg.game", sample_hrg) 325#' @export hrg.fit 326deprecated("hrg.fit", fit_hrg) 327#' @export hrg.predict 328deprecated("hrg.predict", predict_edges) 329#' @export hub.score 330deprecated("hub.score", hub_score) 331 332#' @export igraph.arpack.default 333deprecated("igraph.arpack.default", arpack_defaults) 334#' @export igraph.console 335deprecated("igraph.console", console) 336#' @export igraph.eigen.default 337deprecated("igraph.eigen.default", eigen_defaults) 338#' @export igraph.sample 339deprecated("igraph.sample", sample_seq) 340#' @export igraph.version 341deprecated("igraph.version", igraph_version) 342#' @export igraphdemo 343deprecated("igraphdemo", igraph_demo) 344#' @export igraphtest 345deprecated("igraphtest", igraph_test) 346#' @export independence.number 347deprecated("independence.number", ivs_size) 348#' @export independent.vertex.sets 349deprecated("independent.vertex.sets", ivs) 350#' @export infomap.community 351deprecated("infomap.community", cluster_infomap) 352#' @export induced.subgraph 353deprecated("induced.subgraph", induced_subgraph) 354#' @export interconnected.islands.game 355deprecated("interconnected.islands.game", sample_islands) 356#' @export is.bipartite 357deprecated("is.bipartite", is_bipartite) 358#' @export is.chordal 359deprecated("is.chordal", is_chordal) 360#' @export is.connected 361deprecated("is.connected", is_connected) 362#' @export is.dag 363deprecated("is.dag", is_dag) 364#' @export is.degree.sequence 365deprecated("is.degree.sequence", is_degseq) 366#' @export is.directed 367deprecated("is.directed", is_directed) 368#' @export is.graphical.degree.sequence 369deprecated("is.graphical.degree.sequence", is_graphical) 370#' @export is.hierarchical 371deprecated("is.hierarchical", is_hierarchical) 372#' @export is.igraph 373deprecated("is.igraph", is_igraph) 374#' @export is.loop 375deprecated("is.loop", which_loop) 376#' @export is.matching 377deprecated("is.matching", is_matching) 378#' @export is.maximal.matching 379deprecated("is.maximal.matching", is_max_matching) 380#' @export is.minimal.separator 381deprecated("is.minimal.separator", is_min_separator) 382#' @export is.multiple 383deprecated("is.multiple", which_multiple) 384#' @export is.mutual 385deprecated("is.mutual", which_mutual) 386#' @export is.named 387deprecated("is.named", is_named) 388#' @export is.separator 389deprecated("is.separator", is_separator) 390#' @export is.simple 391deprecated("is.simple", is_simple) 392#' @export is.weighted 393deprecated("is.weighted", is_weighted) 394 395#' @export k.regular.game 396deprecated("k.regular.game", sample_k_regular) 397 398#' @export label.propagation.community 399deprecated("label.propagation.community", cluster_label_prop) 400#' @export largest.cliques 401deprecated("largest.cliques", largest_cliques) 402#' @export largest.independent.vertex.sets 403deprecated("largest.independent.vertex.sets", largest_ivs) 404#' @export lastcit.game 405deprecated("lastcit.game", sample_last_cit) 406#' @export layout.auto 407deprecated("layout.auto", layout_nicely) 408#' @export layout.bipartite 409deprecated("layout.bipartite", layout_as_bipartite) 410#' @export layout.davidson.harel 411deprecated("layout.davidson.harel", layout_with_dh) 412#' @export layout.drl 413deprecated("layout.drl", layout_with_drl) 414#' @export layout.gem 415deprecated("layout.gem", layout_with_gem) 416#' @export layout.graphopt 417deprecated("layout.graphopt", layout_with_graphopt) 418#' @export layout.grid 419deprecated("layout.grid", layout_on_grid) 420#' @export layout.mds 421deprecated("layout.mds", layout_with_mds) 422#' @export layout.merge 423deprecated("layout.merge", merge_coords) 424#' @export layout.norm 425deprecated("layout.norm", norm_coords) 426#' @export layout.star 427deprecated("layout.star", layout_as_star) 428#' @export layout.sugiyama 429deprecated("layout.sugiyama", layout_with_sugiyama) 430#' @export leading.eigenvector.community 431deprecated("leading.eigenvector.community", cluster_leading_eigen) 432#' @export line.graph 433deprecated("line.graph", make_line_graph) 434#' @export list.edge.attributes 435deprecated("list.edge.attributes", edge_attr_names) 436#' @export list.graph.attributes 437deprecated("list.graph.attributes", graph_attr_names) 438#' @export list.vertex.attributes 439deprecated("list.vertex.attributes", vertex_attr_names) 440 441#' @export maxcohesion 442deprecated("maxcohesion", max_cohesion) 443#' @export maximal.cliques 444deprecated("maximal.cliques", max_cliques) 445#' @export maximal.cliques.count 446deprecated("maximal.cliques.count", count_max_cliques) 447#' @export maximal.independent.vertex.sets 448deprecated("maximal.independent.vertex.sets", maximal_ivs) 449#' @export minimal.st.separators 450deprecated("minimal.st.separators", min_st_separators) 451#' @export maximum.bipartite.matching 452deprecated("maximum.bipartite.matching", max_bipartite_match) 453#' @export maximum.cardinality.search 454deprecated("maximum.cardinality.search", max_cardinality) 455#' @export minimum.size.separators 456deprecated("minimum.size.separators", min_separators) 457#' @export minimum.spanning.tree 458deprecated("minimum.spanning.tree", mst) 459#' @export mod.matrix 460deprecated("mod.matrix", modularity_matrix) 461#' @export multilevel.community 462deprecated("multilevel.community", cluster_louvain) 463 464#' @export neighborhood 465deprecated("neighborhood", ego) 466#' @export neighborhood.size 467deprecated("neighborhood.size", ego_size) 468#' @export nexus.get 469deprecated("nexus.get", nexus_get) 470#' @export nexus.info 471deprecated("nexus.info", nexus_info) 472#' @export nexus.list 473deprecated("nexus.list", nexus_list) 474#' @export nexus.search 475deprecated("nexus.search", nexus_search) 476#' @export no.clusters 477deprecated("no.clusters", count_components) 478 479#' @export optimal.community 480deprecated("optimal.community", cluster_optimal) 481 482#' @export page.rank 483deprecated("page.rank", page_rank) 484#' @export page.rank.old 485deprecated("page.rank.old", page_rank_old) 486#' @export path.length.hist 487deprecated("path.length.hist", distance_table) 488#' @export permute.vertices 489deprecated("permute.vertices", permute) 490#' @export piecewise.layout 491deprecated("piecewise.layout", layout_components) 492#' @export plotHierarchy 493deprecated("plotHierarchy", plot_hierarchy) 494#' @export power.law.fit 495deprecated("power.law.fit", fit_power_law) 496#' @export preference.game 497deprecated("preference.game", sample_pref) 498 499#' @export read.graph 500deprecated("read.graph", read_graph) 501#' @export remove.edge.attribute 502deprecated("remove.edge.attribute", delete_edge_attr) 503#' @export remove.graph.attribute 504deprecated("remove.graph.attribute", delete_graph_attr) 505#' @export remove.vertex.attribute 506deprecated("remove.vertex.attribute", delete_vertex_attr) 507#' @export running.mean 508deprecated("running.mean", running_mean) 509 510#' @export sbm.game 511deprecated("sbm.game", sample_sbm) 512#' @export scgGrouping 513deprecated("scgGrouping", scg_group) 514#' @export scgNormEps 515deprecated("scgNormEps", scg_eps) 516#' @export scgSemiProjectors 517deprecated("scgSemiProjectors", scg_semi_proj) 518#' @export set.edge.attribute 519deprecated("set.edge.attribute", set_edge_attr) 520#' @export set.graph.attribute 521deprecated("set.graph.attribute", set_graph_attr) 522#' @export set.vertex.attribute 523deprecated("set.vertex.attribute", set_vertex_attr) 524#' @export shortest.paths 525deprecated("shortest.paths", distances) 526#' @export showtrace 527deprecated("showtrace", show_trace) 528#' @export spinglass.community 529deprecated("spinglass.community", cluster_spinglass) 530#' @export stCuts 531deprecated("stCuts", st_cuts) 532#' @export stMincuts 533deprecated("stMincuts", st_min_cuts) 534#' @export static.fitness.game 535deprecated("static.fitness.game", sample_fitness) 536#' @export static.power.law.game 537deprecated("static.power.law.game", sample_fitness_pl) 538#' @export subgraph.centrality 539deprecated("subgraph.centrality", subgraph_centrality) 540 541#' @export tkplot.canvas 542deprecated("tkplot.canvas", tk_canvas) 543#' @export tkplot.center 544deprecated("tkplot.center", tk_center) 545#' @export tkplot.close 546deprecated("tkplot.close", tk_close) 547#' @export tkplot.export.postscript 548deprecated("tkplot.export.postscript", tk_postscript) 549#' @export tkplot.fit.to.screen 550deprecated("tkplot.fit.to.screen", tk_fit) 551#' @export tkplot.getcoords 552deprecated("tkplot.getcoords", tk_coords) 553#' @export tkplot.off 554deprecated("tkplot.off", tk_off) 555#' @export tkplot.reshape 556deprecated("tkplot.reshape", tk_reshape) 557#' @export tkplot.rotate 558deprecated("tkplot.rotate", tk_rotate) 559#' @export tkplot.setcoords 560deprecated("tkplot.setcoords", tk_set_coords) 561 562#' @export topological.sort 563deprecated("topological.sort", topo_sort) 564#' @export triad.census 565deprecated("triad.census", triad_census) 566 567#' @export unfold.tree 568deprecated("unfold.tree", unfold_tree) 569 570#' @export vcount 571deprecated("vcount", gorder) 572#' @export vertex.connectivity 573deprecated("vertex.connectivity", vertex_connectivity) 574#' @export vertex.disjoint.paths 575deprecated("vertex.disjoint.paths", vertex_disjoint_paths) 576 577#' @export walktrap.community 578deprecated("walktrap.community", cluster_walktrap) 579#' @export watts.strogatz.game 580deprecated("watts.strogatz.game", sample_smallworld) 581#' @export write.graph 582deprecated("write.graph", write_graph) 583#' @export graph.famous 584deprecated("graph.famous", make_famous_graph) 585#' @export igraph.from.graphNEL 586deprecated("igraph.from.graphNEL", graph_from_graphnel) 587#' @export igraph.to.graphNEL 588deprecated("igraph.to.graphNEL", as_graphnel) 589#' @export getIgraphOpt 590deprecated("getIgraphOpt", igraph_opt) 591#' @export igraph.options 592deprecated("igraph.options", igraph_options) 593#' @export graph.intersection 594deprecated("graph.intersection", intersection) 595#' @export exportPajek 596deprecated("exportPajek", export_pajek) 597#' @export get.diameter 598deprecated("get.diameter", get_diameter) 599#' @export get.all.shortest.paths 600deprecated("get.all.shortest.paths", all_shortest_paths) 601#' @export get.shortest.paths 602deprecated("get.shortest.paths", shortest_paths) 603#' @export graph 604deprecated("graph", make_graph) 605#' @export vertex.shapes 606deprecated("vertex.shapes", shapes) 607#' @export igraph.shape.noclip 608deprecated("igraph.shape.noclip", shape_noclip) 609#' @export igraph.shape.noplot 610deprecated("igraph.shape.noplot", shape_noplot) 611#' @export create.communities 612deprecated("create.communities", make_clusters) 613