diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 4fc3be5a2f9..087f0b05fc6 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -2,7 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, config-draft] + branches: [main, master] pull_request: branches: [main, master] release: diff --git a/R/aaa-auto.R b/R/aaa-auto.R index 287beb96fab..f7bce518e9d 100644 --- a/R/aaa-auto.R +++ b/R/aaa-auto.R @@ -1518,6 +1518,8 @@ count_triangles <- function(graph, vids=V(graph)) { res } +#' @family triangles +#' @rdname count_triangles #' @export triangles <- function(graph) { # Argument checks @@ -2143,6 +2145,7 @@ embed_adjacency_matrix <- function(graph, no, weights=NULL, which=c("lm", "la", res } +#' @family embedding #' @export embed_laplacian_matrix <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), type=c("default", "D-A", "DAD", "I-DAD", "OAP"), scaled=TRUE, options=igraph.arpack.default) { # Argument checks diff --git a/R/attributes.R b/R/attributes.R index 1c0c7f7722e..24e4af01bbc 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -43,7 +43,7 @@ #' @return A list of graph attributes, or a single graph attribute. #' #' @aliases get.graph.attribute graph.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -72,7 +72,7 @@ graph_attr <- function(graph, name) { #' @return The graph, with the attribute(s) added. #' #' @aliases graph.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -102,7 +102,7 @@ graph_attr <- function(graph, name) { #' @param value New value of the attribute. #' @return The graph with the new graph attribute added or set. #' -#' @family graph attributes +#' @family attributes #' @aliases set.graph.attribute #' #' @export @@ -152,7 +152,7 @@ graph.attributes <- function(graph) { #' all vertex attributes, if `name` is missing. #' #' @aliases get.vertex.attribute vertex.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -197,7 +197,7 @@ vertex_attr <- function(graph, name, index = V(graph)) { #' @return The graph, with the vertex attribute(s) added or set. #' #' @aliases vertex.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -229,7 +229,7 @@ vertex_attr <- function(graph, name, index = V(graph)) { #' @return The graph, with the vertex attribute added or set. #' #' @aliases set.vertex.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -363,7 +363,7 @@ vertex.attributes <- function(graph, index = V(graph)) { #' edge attributes if `name` is missing. #' #' @aliases get.edge.attribute edge.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -407,7 +407,7 @@ edge_attr <- function(graph, name, index = E(graph)) { #' @return The graph, with the edge attribute(s) added or set. #' #' @aliases edge.attributes<- -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -439,7 +439,7 @@ edge_attr <- function(graph, name, index = E(graph)) { #' @return The graph, with the edge attribute added or set. #' #' @aliases set.edge.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -567,7 +567,7 @@ edge.attributes <- function(graph, index = E(graph)) { #' @return Character vector, the names of the graph attributes. #' #' @aliases list.graph.attributes attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -590,7 +590,7 @@ graph_attr_names <- function(graph) { #' @return Character vector, the names of the vertex attributes. #' #' @aliases list.vertex.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -617,7 +617,7 @@ vertex_attr_names <- function(graph) { #' @return Character vector, the names of the edge attributes. #' #' @aliases list.edge.attributes -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -643,7 +643,7 @@ edge_attr_names <- function(graph) { #' @return The graph, with the specified attribute removed. #' #' @aliases remove.graph.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -673,7 +673,7 @@ delete_graph_attr <- function(graph, name) { #' @return The graph, with the specified vertex attribute removed. #' #' @aliases remove.vertex.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -704,7 +704,7 @@ delete_vertex_attr <- function(graph, name) { #' @return The graph, with the specified edge attribute removed. #' #' @aliases remove.edge.attribute -#' @family graph attributes +#' @family attributes #' #' @export #' @examples @@ -809,6 +809,7 @@ is_weighted <- function(graph) { } #' @rdname make_bipartite_graph +#' @family bipartite #' @export is_bipartite <- function(graph) { if (!is_igraph(graph)) { @@ -895,6 +896,7 @@ igraph.i.attribute.combination <- function(comb) { #' new edge should be sum of the weights of the corresponding edges in the old #' graph; and that the rest of the attributes should be ignored (=dropped). #' +#' @family attributes #' @name igraph-attribute-combination #' @aliases attribute.combination #' @section Predefined combination functions: The following combination @@ -971,7 +973,7 @@ NULL #' @method $ igraph #' @name igraph-dollar #' @export -#' @family graph attributes +#' @family attributes #' @examples #' g <- make_ring(10) #' g$name diff --git a/R/centrality.R b/R/centrality.R index 4006095bd22..df4a1e830ae 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -303,7 +303,7 @@ estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "al } #' @rdname arpack -#' @family centrality +#' @family arpack #' @export arpack_defaults <- list( bmat = "I", n = 0, which = "XX", nev = 1, tol = 0.0, @@ -497,7 +497,7 @@ arpack_defaults <- list( #' which = "LM", maxiter = 2000 #' )) #' } -#' @family centrality +#' @family arpack #' @export arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults, env = parent.frame(), complex = !sym) { @@ -909,6 +909,7 @@ diversity <- diversity #' g2 <- make_ring(10) #' hub_score(g2)$vector #' authority_score(g2)$vector +#' @family centrality hub_score <- hub_score diff --git a/R/community.R b/R/community.R index 16325a84804..5b2b444e437 100644 --- a/R/community.R +++ b/R/community.R @@ -2548,6 +2548,6 @@ communities <- groups.communities #' ## combined using the 'toString' function. #' print(g2, g = TRUE, v = TRUE, e = TRUE) #' -#' @family community #' @export +#' @family functions for manipulating graph structure contract <- contract diff --git a/R/decomposition.R b/R/decomposition.R index e0503bb4094..6215653a045 100644 --- a/R/decomposition.R +++ b/R/decomposition.R @@ -63,7 +63,7 @@ #' linear-time algorithms to test chordality of graphs, test acyclicity of #' hypergraphs, and selectively reduce acyclic hypergraphs. *SIAM Journal #' of Computation* 13, 566--579. -#' @family decomposition +#' @family chordal #' @export #' @keywords graphs #' @examples diff --git a/R/embedding.R b/R/embedding.R index deb923e2968..96a6d4b7ba4 100644 --- a/R/embedding.R +++ b/R/embedding.R @@ -88,6 +88,7 @@ #' }) #' RDP <- sample_dot_product(lpvs) #' embed <- embed_adjacency_matrix(RDP, 5) +#' @family embedding #' @export embed_adjacency_matrix <- embed_adjacency_matrix @@ -148,6 +149,7 @@ embed_adjacency_matrix <- embed_adjacency_matrix #' RDP.graph.3 <- sample_dot_product(lpvs.sph) #' dim_select(embed_adjacency_matrix(RDP.graph.3, 10)$D) #' +#' @family embedding #' @export dim_select <- dim_select diff --git a/R/epi.R b/R/epi.R index b60c2a59136..dbfbaa4cbaa 100644 --- a/R/epi.R +++ b/R/epi.R @@ -19,7 +19,7 @@ # ################################################################### -#' @family epi +#' @family processes #' @export time_bins <- function(x, middle = TRUE) { UseMethod("time_bins") @@ -27,7 +27,7 @@ time_bins <- function(x, middle = TRUE) { #' @method time_bins sir #' @rdname sir -#' @family epi +#' @family processes #' @export #' @importFrom stats IQR time_bins.sir <- function(x, middle = TRUE) { @@ -52,7 +52,7 @@ time_bins.sir <- function(x, middle = TRUE) { #' @importFrom stats median #' @method median sir #' @rdname sir -#' @family epi +#' @family processes #' @export median.sir <- function(x, na.rm = FALSE, ...) { sir <- x @@ -73,7 +73,7 @@ median.sir <- function(x, na.rm = FALSE, ...) { #' @importFrom stats quantile #' @method quantile sir #' @rdname sir -#' @family epi +#' @family processes #' @export quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) { sir <- x @@ -144,7 +144,7 @@ quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) { #' @references Bailey, Norman T. J. (1975). The mathematical theory of #' infectious diseases and its applications (2nd ed.). London: Griffin. #' @method plot sir -#' @family epi +#' @family processes #' @export #' @importFrom graphics plot lines #' @keywords graphs diff --git a/R/eulerian.R b/R/eulerian.R index 1a5f26f8c86..d92657672e2 100644 --- a/R/eulerian.R +++ b/R/eulerian.R @@ -59,21 +59,21 @@ #' has_eulerian_cycle(g) #' try(eulerian_cycle(g)) #' -#' @family eulerian +#' @family cycles #' @export has_eulerian_path <- function(graph) is_eulerian(graph)$has_path #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export has_eulerian_cycle <- function(graph) is_eulerian(graph)$has_cycle #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export eulerian_path <- eulerian_path #' @rdname has_eulerian_path -#' @family eulerian +#' @family cycles #' @export eulerian_cycle <- eulerian_cycle diff --git a/R/flow.R b/R/flow.R index b6d263ca8ca..42039189776 100644 --- a/R/flow.R +++ b/R/flow.R @@ -614,6 +614,7 @@ dominator_tree <- function(graph, root, mode = c("out", "in", "all", "total")) { #' #' chvatal <- make_graph("chvatal") #' min_st_separators(chvatal) +#' @family flow min_st_separators <- min_st_separators diff --git a/R/games.R b/R/games.R index 4eb30c2bc86..b1fe3c4122f 100644 --- a/R/games.R +++ b/R/games.R @@ -355,6 +355,7 @@ gnm <- function(...) constructor_spec(sample_gnm, ...) #' @family games #' @export #' @keywords graphs +#' @keywords internal #' @examples #' #' g <- erdos.renyi.game(1000, 1 / 1000) @@ -1069,8 +1070,8 @@ asym_pref <- function(...) constructor_spec(sample_asym_pref, ...) #' @rdname ego -#' @family games #' @export +#' @family functions for manipulating graph structure connect <- function(graph, order, mode = c("all", "out", "in", "total")) { if (!is_igraph(graph)) { stop("Not a graph object") @@ -1661,6 +1662,7 @@ sample_k_regular <- sample_k_regular #' distribution in scale-free networks. *Phys Rev Lett* 87(27):278701, #' 2001. #' @keywords graphs +#' @family games #' @examples #' #' N <- 10000 @@ -1727,6 +1729,7 @@ sample_fitness <- sample_fitness #' Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation transitions in #' scale-free networks under the Achlioptas process. *Phys Rev Lett* #' 103:135702, 2009. +#' @family games #' @keywords graphs #' @examples #' @@ -1780,6 +1783,7 @@ sample_fitness_pl <- sample_fitness_pl #' time: densification laws, shrinking diameters and possible explanations. #' *KDD '05: Proceeding of the eleventh ACM SIGKDD international #' conference on Knowledge discovery in data mining*, 177--187, 2005. +#' @family games #' @keywords graphs #' @examples #' @@ -1821,6 +1825,7 @@ sample_forestfire <- sample_forestfire #' @references Lyzinski, V., Fishkind, D. E., Priebe, C. E. (2013). Seeded #' graph matching for correlated Erdos-Renyi graphs. #' +#' @family games #' @examples #' g <- sample_gnp(1000, .1) #' g2 <- sample_correlated_gnp(g, corr = 0.5) @@ -1857,6 +1862,7 @@ sample_correlated_gnp <- sample_correlated_gnp #' graph matching for correlated Erdos-Renyi graphs. #' #' @keywords graphs +#' @family games #' @examples #' gg <- sample_correlated_gnp_pair( #' n = 10, corr = .8, p = .5, diff --git a/R/iterators.R b/R/iterators.R index c5cae425fec..ae6d548b401 100644 --- a/R/iterators.R +++ b/R/iterators.R @@ -1063,7 +1063,7 @@ simple_es_index <- function(x, i, na_ok = FALSE) { #' #' @export #' @family vertex and edge sequences -#' @family graph attributes +#' @family attributes #' @examples #' g <- make_( #' ring(10), @@ -1789,6 +1789,7 @@ rev.igraph.es <- rev.igraph.vs #' V(g)$name <- letters[1:10] #' as_ids(V(g)) #' as_ids(E(g)) +#' @family vertex and edge sequences as_ids <- function(seq) { UseMethod("as_ids") } diff --git a/R/layout.R b/R/layout.R index 0bc78d2140e..0aa213fead8 100644 --- a/R/layout.R +++ b/R/layout.R @@ -696,6 +696,7 @@ on_grid <- function(...) layout_spec(layout_on_grid, ...) #' @rdname layout_on_grid #' @export +#' @keywords internal layout.grid.3d <- function(graph, width = 0, height = 0) { .Deprecated("layout_on_grid", msg = paste0( "layout.grid.3d is deprecated from\n", diff --git a/R/make.R b/R/make.R index 17dc2808e78..db017c1d06d 100644 --- a/R/make.R +++ b/R/make.R @@ -34,6 +34,7 @@ #' @param .variant Constructor variant; must be one of \sQuote{make}, #' \sQuote{graph} or \sQuote{sample}. Used in cases when the same constructor #' specification has deterministic and random variants. +#' @family constructor modifiers #' @return A named list with three items: \sQuote{cons} for the constructor #' function, \sQuote{mods} for the modifiers and \sQuote{args} for the #' remaining, unparsed arguments. @@ -84,6 +85,7 @@ #' #' @param graph The graph to apply the modifiers to #' @param mods The modifiers to apply +#' @family constructor modifiers #' @return The modified graph #' @noRd .apply_modifiers <- function(graph, mods) { @@ -204,6 +206,7 @@ make_ <- function(...) { #' ## Arguments are passed on from sample_ to sample_sbm #' blocky3 <- pref_matrix %>% #' sample_(sbm(), n = 20, block.sizes = c(10, 10)) +#' @family games sample_ <- function(...) { me <- attr(sys.function(), "name") %||% "construct" extracted <- .extract_constructor_and_modifiers(..., .operation = me, .variant = "sample") @@ -1207,6 +1210,7 @@ make_tree <- function(n, children = 2, mode = c("out", "in", "undirected")) { #' Prüfer sequences does not support directed trees at the moment. #' @return A graph object. #' +#' @family games #' @keywords graphs #' @examples #' @@ -1243,7 +1247,7 @@ tree <- function(...) constructor_spec(list(make = make_tree, sample = sample_tr #' #' g <- make_tree(13, 3) #' to_prufer(g) -#' +#' @family trees #' @export make_from_prufer <- make_from_prufer diff --git a/R/motifs.R b/R/motifs.R index c817f9c28fe..477bba0370b 100644 --- a/R/motifs.R +++ b/R/motifs.R @@ -195,6 +195,7 @@ sample_motifs <- function(graph, size = 3, cut.prob = rep(0, size), #' #' g <- sample_pa(100) #' dyad_census(g) +#' @family graph motifs #' @export dyad_census <- dyad_census @@ -236,5 +237,6 @@ dyad_census <- dyad_census #' #' g <- sample_gnm(15, 45, directed = TRUE) #' triad_census(g) +#' @family motifs #' @export triad_census <- triad_census diff --git a/R/operators.R b/R/operators.R index 2a36c14f17e..0bc808f5e35 100644 --- a/R/operators.R +++ b/R/operators.R @@ -177,6 +177,7 @@ disjoint_union <- function(...) { #' @export #' @rdname disjoint_union +#' @family functions for manipulating graph structure "%du%" <- function(x, y) { disjoint_union(x, y) } @@ -297,12 +298,14 @@ disjoint_union <- function(...) { #' the function that implements `union()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export union <- function(...) { UseMethod("union") } #' @method union default +#' @family functions for manipulating graph structure #' @export union.default <- function(...) { base::union(...) @@ -343,6 +346,7 @@ union.default <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method union igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -361,6 +365,7 @@ union.igraph <- function(..., byname = "auto") { ) } +#' @family functions for manipulating graph structure #' @export "%u%" <- function(x, y) { union(x, y) @@ -379,6 +384,7 @@ union.igraph <- function(..., byname = "auto") { #' the function that implements `intersection()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export intersection <- function(...) { UseMethod("intersection") @@ -421,6 +427,7 @@ intersection <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method intersection igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -440,6 +447,7 @@ intersection.igraph <- function(..., byname = "auto", ) } +#' @family functions for manipulating graph structure #' @export "%s%" <- function(x, y) { intersection(x, y) @@ -458,6 +466,7 @@ intersection.igraph <- function(..., byname = "auto", #' the function that implements `difference()`. #' @return Depends on the function that implements this method. #' +#' @family functions for manipulating graph structure #' @export difference <- function(...) { UseMethod("difference") @@ -496,6 +505,7 @@ difference <- function(...) { #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @method difference igraph +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -552,6 +562,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) { } } +#' @family functions for manipulating graph structure #' @export "%m%" <- function(x, y) { difference(x, y) @@ -576,6 +587,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) { #' @param loops Logical constant, whether to generate loop edges. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -651,6 +663,7 @@ complementer <- function(graph, loops = FALSE) { #' but not both graphs are named. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} +#' @family functions for manipulating graph structure #' @export #' @keywords graphs #' @examples @@ -727,6 +740,7 @@ compose <- function(g1, g2, byname = "auto") { res } +#' @family functions for manipulating graph structure #' @export "%c%" <- function(x, y) { compose(x, y) @@ -777,6 +791,7 @@ edge <- function(...) { structure(list(...), class = "igraph.edge") } +#' @family functions for manipulating graph structure #' @export #' @rdname edge edges <- edge @@ -813,6 +828,7 @@ vertex <- function(...) { structure(list(...), class = "igraph.vertex") } +#' @family functions for manipulating graph structure #' @export #' @rdname vertex vertices <- vertex @@ -1123,6 +1139,7 @@ path <- function(...) { #' currently ignored. #' #' @method rep igraph +#' @family functions for manipulating graph structure #' @export #' #' @examples @@ -1142,6 +1159,7 @@ rep.igraph <- function(x, n, mark = TRUE, ...) { #' @rdname rep.igraph #' @method * igraph +#' @family functions for manipulating graph structure #' @export `*.igraph` <- function(x, n) { if (!is_igraph(x) && is_igraph(n)) { @@ -1173,11 +1191,13 @@ rep.igraph <- function(x, n, mark = TRUE, ...) { #' #' g <- make_graph(~ 1 -+ 2, 2 -+ 3, 3 -+ 4) #' reverse_edges(g, 2) +#' @family functions for manipulating graph structure #' @export reverse_edges <- reverse_edges #' @rdname reverse_edges #' @param x The input graph. #' @method t igraph +#' @family functions for manipulating graph structure #' @export t.igraph <- function(x) reverse_edges(x) diff --git a/R/other.R b/R/other.R index fb3fc4fec47..9d918ef45b9 100644 --- a/R/other.R +++ b/R/other.R @@ -162,6 +162,7 @@ igraph.i.spMatrix <- function(M) { #' @param seed Ignored. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @family other +#' @keywords internal #' @export srand <- function(seed) { warning( diff --git a/R/paths.R b/R/paths.R index 8f725439c0d..259996526d6 100644 --- a/R/paths.R +++ b/R/paths.R @@ -106,7 +106,8 @@ all_simple_paths <- function(graph, from, to = V(graph), #' is_dag(g) #' g2 <- g + edge(5, 1) #' is_dag(g2) -#' @family paths +#' @family cycles +#' @family structural.properties #' @export is_dag <- is_dag @@ -157,6 +158,7 @@ is_dag <- is_dag #' ) #' max_cardinality(g2) #' is_chordal(g2, fillin = TRUE) +#' @family chordal max_cardinality <- max_cardinality diff --git a/R/scg.R b/R/scg.R index 1a3d958a916..7441c8cb0f9 100644 --- a/R/scg.R +++ b/R/scg.R @@ -26,6 +26,7 @@ #' graphs. #' #' @name scg-method +#' @family scg #' @section Introduction: The SCG functions provide a framework, called #' Spectral Coarse Graining (SCG), for reducing large graphs while preserving #' their *spectral-related features*, that is features closely related @@ -843,4 +844,5 @@ myscg <- function(graph, matrix, sparsemat, ev, nt, groups = NULL, #' km <- kmeans(v, 5) #' sum(km$withinss) #' scg_eps(cbind(v), km$cluster)^2 +#' @family scg scg_eps <- scg_eps diff --git a/R/simple.R b/R/simple.R index 7619abd7157..9e812959f5e 100644 --- a/R/simple.R +++ b/R/simple.R @@ -70,16 +70,19 @@ #' is_simple(simplify(g, remove.multiple = FALSE)) #' is_simple(simplify(g)) #' @family simple +#' @family functions for manipulating graph structure #' @export simplify <- simplify #' @family simple +#' @family functions for manipulating graph structure #' @export #' @rdname simplify is_simple <- is_simple #' @family isomorphism #' @family simple +#' @family functions for manipulating graph structure #' @export #' @rdname simplify simplify_and_colorize <- function(graph) { diff --git a/R/structural.properties.R b/R/structural.properties.R index 069536d26e9..20cd556d346 100644 --- a/R/structural.properties.R +++ b/R/structural.properties.R @@ -58,7 +58,7 @@ #' } #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @seealso [distances()] -#' @family structural.properties +#' @family paths #' @export #' @keywords graphs #' @examples @@ -1418,6 +1418,7 @@ topo_sort <- function(graph, mode = c("out", "all", "in")) { #' 47:6, pp. 319-323, 1993 #' @keywords graphs #' @family structural.properties +#' @family cycles #' @export #' @examples #' @@ -1450,6 +1451,7 @@ feedback_arc_set <- feedback_arc_set #' graph *Proceedings of the ninth annual ACM symposium on Theory of #' computing*, 1-10, 1977 #' @family structural.properties +#' @family cycles #' @export #' @keywords graphs #' @examples diff --git a/R/topology.R b/R/topology.R index af564f4f910..d7bb4034386 100644 --- a/R/topology.R +++ b/R/topology.R @@ -778,6 +778,7 @@ graph_from_isomorphism_class <- graph_from_isomorphism_class #' el1 <- el1[order(el1[, 1], el1[, 2]), ] #' el2 <- el2[order(el2[, 1], el2[, 2]), ] #' all(el1 == el2) +#' @family graph isomorphism #' @export canonical_permutation <- canonical_permutation @@ -820,6 +821,7 @@ canonical_permutation <- canonical_permutation #' E(g2)$weight #' all(sort(E(g2)$weight) == sort(E(g)$weight)) #' @export +#' @family functions for manipulating graph structure permute <- permute @@ -881,6 +883,7 @@ permute <- permute #' ## matching by colors, leading to only 4 automorphisms #' g <- make_full_graph(4) #' count_automorphisms(g, colors = c(1, 2, 1, 2)) +#' @family graph automorphism #' @export count_automorphisms <- count_automorphisms @@ -939,5 +942,6 @@ count_automorphisms <- count_automorphisms #' ## "turns" the ring by one vertex to the left or right #' g <- make_ring(10) #' automorphism_group(g) +#' @family graph automorphism #' @export automorphism_group <- automorphism_group diff --git a/_pkgdown.yml b/_pkgdown.yml index d7279719f2a..931a83c1a9c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -3,8 +3,6 @@ url: ~ template: bootstrap: 5 -authors: - after: "See the [AUTHORS file](/AUTHORS-list.html) for other contributors." navbar: structure: @@ -31,217 +29,212 @@ navbar: - text: "All articles" href: articles/index.html + reference: -- title: Adjacency -- contents: - - has_concept("adjacency") -- title: Graph attributes +- title: igraph options - contents: - - has_concept("graph attributes") -- title: Structural queries -- contents: - - has_concept("structural queries") -- title: Bipartite + - has_concept("igraph options") +- title: Construction +- subtitle: Deterministic constructors - contents: - - has_concept("bipartite") -- title: Centrality + - starts_with("make_") + - realize_degseq + - has_concept("deterministic constructors") + - graph_ + - graph_from_lcf +- subtitle: "Stochastic constructors (random graph models)" - contents: - - has_concept("centrality") -- title: Centralization related + - has_concept("games") +- subtitle: Constructor modifiers - contents: - - has_concept("centralization related") -- title: Cliques + - has_concept("constructor modifiers") +- subtitle: Convert to igraph - contents: - - has_concept("cliques") -- title: Cocitation + - as.igraph +- subtitle: Adjacency matrices - contents: - - has_concept("cocitation") -- title: Cohesive blocks + - has_concept("adjacency") +- title: Visualization - contents: - - has_concept("cohesive.blocks") -- title: Coloring + - has_concept("graph layouts") + - has_concept("layout modifiers") + - has_concept("layout_drl") + - has_concept("palettes") + - has_concept("plot") + - igraph.plotting + - plot_dendrogram.igraphHRG + - plot_dendrogram + - has_concept("plot.common") + - has_concept("plot.shapes") + - vertex.shape.pie +- subtitle: Graph coloring - contents: - has_concept("coloring") -- title: Community -- contents: - - has_concept("community") -- title: Components +# The following are mostly about programming rather than analysis +- title: Functions for manipulating graphs - contents: - - has_concept("components") -- title: Console -- contents: - - has_concept("console") -- title: Conversion -- contents: - - has_concept("conversion") -- title: Deterministic constructors -- contents: - - has_concept("deterministic constructors") -- title: Decomposition + - has_concept("functions for manipulating graph structure") +- subtitle: Rewiring functions - contents: - - has_concept("decomposition") -- title: Graphical degree sequences + - has_concept("rewiring functions") +- title: Vertex, edge and graph attributes - contents: - - has_concept("graphical degree sequences") -- title: Demo + - has_concept("attributes") +- title: Vertex and edge sequences - contents: - - has_concept("demo") -- title: Efficiency + - has_concept("vertex and edge sequences") + - has_concept("vertex and edge sequence operations") +- title: Utilities +- subtitle: Graph ID, comparison, name, weight - contents: - - has_concept("efficiency") -- title: Latent position vector samplers + - graph_id + - identical_graphs + - is_igraph + - is_named + - is_weighted + - is_chordal +- subtitle: Conversion - contents: - - has_concept("latent position vector samplers") -- title: Env and data + - has_concept("conversion") +- subtitle: Env and data - contents: - has_concept("env-and-data") -- title: Epi -- contents: - - has_concept("epi") -- title: Eulerian +- subtitle: Printing - contents: - - has_concept("eulerian") -- title: Fit + - head_print + - indent_print + - printr + - has_concept("print") + - has_concept("printer callbacks") +- subtitle: Latent position vector samplers - contents: - - has_concept("fit") -- title: Flow + - has_concept("latent position vector samplers") +- subtitle: Miscellaneous - contents: - - has_concept("flow") -- title: Foreign + - convex_hull + - running_mean + - sample_seq + - fit_power_law +# [[[ network analysis start +- title: Structural properties - contents: - - has_concept("foreign") -- title: Games + - has_concept("structural.properties") + - has_concept("cocitation") + - has_concept("cohesive.blocks") + - has_concept("triangles") + - starts_with("assortativity") + - spectrum +- subtitle: Chordal graphs - contents: - - has_concept("games") -- title: Glet + - has_concept("chordal") +- subtitle: Triangles and transitivity - contents: - - has_concept("glet") -- title: Hierarchical random graph functions + - matches("triangles") + - matches("transitivity") +- subtitle: Paths - contents: - - has_concept("hierarchical random graph functions") -- title: Incidence + - has_concept("paths") +- subtitle: Bipartite graphs - contents: + - has_concept("bipartite") - has_concept("incidence") -- title: Structural queries +- subtitle: Efficiency - contents: - - has_concept("structural queries") -- title: Functions for manipulating graph structure + - has_concept("efficiency") +- subtitle: Similarity - contents: - - has_concept("functions for manipulating graph structure") -- title: Functions for manipulating graph structure + - has_concept("similarity") +- subtitle: Trees - contents: - - has_concept("functions for manipulating graph structure") -- title: Structural queries + - has_concept("trees") + - make_from_prufer + - has_concept("minimum.spanning.tree") +- subtitle: Structural queries - contents: - has_concept("structural queries") -- title: Vertex and edge sequences +- subtitle: ARPACK eigenvector calculation - contents: - - has_concept("vertex and edge sequences") -- title: Vertex and edge sequence operations -- contents: - - has_concept("vertex and edge sequence operations") -- title: Graph attributes -- contents: - - has_concept("graph attributes") -- title: Graph layouts -- contents: - - has_concept("graph layouts") -- title: Layout modifiers -- contents: - - has_concept("layout modifiers") -- title: Layout drl -- contents: - - has_concept("layout_drl") -- title: Constructor modifiers + - has_concept("arpack") +- subtitle: Centrality measures - contents: - - has_concept("constructor modifiers") -- title: Deterministic constructors + - has_concept("centrality") +- subtitle: Centralization - contents: - - has_concept("deterministic constructors") -- title: Minimum spanning tree + - has_concept("centralization related") +- subtitle: Scan statistics - contents: - - has_concept("minimum.spanning.tree") -- title: Graph motifs + - has_concept("scan statistics") +- title: Graph motifs and subgraphs - contents: - has_concept("graph motifs") -- title: Functions for manipulating graph structure -- contents: - - has_concept("functions for manipulating graph structure") -- title: Other -- contents: - - has_concept("other") -- title: Palettes -- contents: - - has_concept("palettes") -- title: Igraph options -- contents: - - has_concept("igraph options") -- title: Paths -- contents: - - has_concept("paths") -- title: Plot -- contents: - - has_concept("plot") -- title: Plot common + - triad_census +- title: Graph isomorphism - contents: - - has_concept("plot.common") -- title: Plot shapes + - has_concept("graph isomorphism") + - simplify_and_colorize + - has_concept("graph automorphism") + - permute +- title: Graph matching - contents: - - has_concept("plot.shapes") -- title: Print + - has_concept("sgm") +- title: Maximum flow and connectivity - contents: - - has_concept("print") -- title: Printer callbacks + - has_concept("flow") +- title: Cliques - contents: - - has_concept("printer callbacks") -- title: Random walk + - has_concept("cliques") + - has_concept("glet") +- title: Community detection - contents: - - has_concept("random_walk") -- title: Rewiring functions + - has_concept("community") +- title: Graph cycles - contents: - - has_concept("rewiring functions") -- title: Scan statistics + - has_concept("cycles") +- title: Connected components - contents: - - has_concept("scan statistics") -- title: Scg + - has_concept("components") +- title: Spectral coarse graining - contents: - has_concept("scg") -- title: Sgm +- title: Spectral embedding - contents: - - has_concept("sgm") -- title: Similarity + - has_concept("embedding") + - embed_laplacian_matrix +- title: Hierarchical random graphs - contents: - - has_concept("similarity") -- title: Simple -- contents: - - has_concept("simple") -- title: Socnet + - has_concept("hierarchical random graph functions") +# network analysis end, we keep these sections together ]]] +# the following two are also "scientific functions" (not "programming functions"), +# but they do not compute a result for a graph, like in the previous sections +- title: Graphical degree sequences - contents: - - has_concept("socnet") -- title: Structural properties + - has_concept("graphical degree sequences") +- title: Processes on graphs - contents: - - has_concept("structural.properties") -- title: Structural queries + - has_concept("processes") + - has_concept("random_walk") +# ----- +- title: Demo - contents: - - has_concept("structural queries") -- title: Test + - has_concept("demo") +- title: I/O read/write files - contents: - - has_concept("test") -- title: Tkplot + - has_concept("foreign") +- title: Interactive functions - contents: + - has_concept("socnet") - has_concept("tkplot") -- title: Graph isomorphism -- contents: - - has_concept("graph isomorphism") -- title: Trees -- contents: - - has_concept("trees") -- title: Triangles -- contents: - - has_concept("triangles") + - has_concept("console") - title: Versions - contents: - has_concept("versions") -- title: Others -- contents: - - lacks_concepts(c("adjacency", "graph attributes", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions")) +- title: internal + contents: + - igraph-package + - has_concept("test") + - layout.reingold.tilford + - layout.fruchterman.reingold.grid + - layout.spring + - layout.svd + - srand + - "%>%" diff --git a/man/E.Rd b/man/E.Rd index 716a8ec0298..51ebe64ad31 100644 --- a/man/E.Rd +++ b/man/E.Rd @@ -71,6 +71,7 @@ E(g2) \seealso{ Other vertex and edge sequences: \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/V.Rd b/man/V.Rd index 4d1e49048b5..ef1cd750cc7 100644 --- a/man/V.Rd +++ b/man/V.Rd @@ -64,6 +64,7 @@ V(g2) \seealso{ Other vertex and edge sequences: \code{\link{E}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/add_edges.Rd b/man/add_edges.Rd index 804028b90e0..7e05d7483a2 100644 --- a/man/add_edges.Rd +++ b/man/add_edges.Rd @@ -51,11 +51,26 @@ plot(g) Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/add_vertices.Rd b/man/add_vertices.Rd index d692626e80e..d0911fac5d9 100644 --- a/man/add_vertices.Rd +++ b/man/add_vertices.Rd @@ -46,11 +46,26 @@ plot(g) Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/all_simple_paths.Rd b/man/all_simple_paths.Rd index 273b5a5eec3..0bba46fb2cb 100644 --- a/man/all_simple_paths.Rd +++ b/man/all_simple_paths.Rd @@ -54,9 +54,9 @@ all_simple_paths(g, 1, c(3, 5)) } \seealso{ Other paths: +\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{eccentricity}()}, -\code{\link{is_dag}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 6f980120ecb..4c3af0083fd 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -94,12 +94,12 @@ measures of centrality for asymmetric relations'' \emph{Social Networks}, \code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=power_centrality]{power_centrality()}} Centrality measures -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/arpack.Rd b/man/arpack.Rd index aa876dbfb0a..b03d3d76471 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -217,37 +217,11 @@ Matrices. \emph{Linear Algebra and its Applications}, vol 88/89, pp 575-595, \code{\link[=eigen_centrality]{eigen_centrality()}}, \code{\link[=page_rank]{page_rank()}}, \code{\link[=hub_score]{hub_score()}}, \code{\link[=cluster_leading_eigen]{cluster_leading_eigen()}} are some of the functions in igraph that use ARPACK. - -Centrality measures -\code{\link{alpha_centrality}()}, -\code{\link{closeness}()}, -\code{\link{diversity}()}, -\code{\link{eigen_centrality}()}, -\code{\link{estimate_betweenness}()}, -\code{\link{harmonic_centrality}()}, -\code{\link{page_rank}()}, -\code{\link{power_centrality}()}, -\code{\link{spectrum}()}, -\code{\link{strength}()}, -\code{\link{subgraph_centrality}()} - -Centrality measures -\code{\link{alpha_centrality}()}, -\code{\link{closeness}()}, -\code{\link{diversity}()}, -\code{\link{eigen_centrality}()}, -\code{\link{estimate_betweenness}()}, -\code{\link{harmonic_centrality}()}, -\code{\link{page_rank}()}, -\code{\link{power_centrality}()}, -\code{\link{spectrum}()}, -\code{\link{strength}()}, -\code{\link{subgraph_centrality}()} } \author{ Rich Lehoucq, Kristi Maschhoff, Danny Sorensen, Chao Yang for ARPACK, Gabor Csardi \email{csardi.gabor@gmail.com} for the R interface. } -\concept{centrality} +\concept{arpack} \keyword{datasets} \keyword{graphs} diff --git a/man/as_ids.Rd b/man/as_ids.Rd index 8d38ef8bfa9..6574521678d 100644 --- a/man/as_ids.Rd +++ b/man/as_ids.Rd @@ -41,3 +41,17 @@ V(g)$name <- letters[1:10] as_ids(V(g)) as_ids(E(g)) } +\seealso{ +Other vertex and edge sequences: +\code{\link{E}()}, +\code{\link{V}()}, +\code{\link{igraph-es-attributes}}, +\code{\link{igraph-es-indexing2}}, +\code{\link{igraph-es-indexing}}, +\code{\link{igraph-vs-attributes}}, +\code{\link{igraph-vs-indexing2}}, +\code{\link{igraph-vs-indexing}}, +\code{\link{print.igraph.es}()}, +\code{\link{print.igraph.vs}()} +} +\concept{vertex and edge sequences} diff --git a/man/as_membership.Rd b/man/as_membership.Rd index e09a84f7449..fc3d64d31ca 100644 --- a/man/as_membership.Rd +++ b/man/as_membership.Rd @@ -40,7 +40,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/automorphism_group.Rd b/man/automorphism_group.Rd index e6db9ccc2b7..1def2b4d48a 100644 --- a/man/automorphism_group.Rd +++ b/man/automorphism_group.Rd @@ -72,10 +72,14 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \seealso{ \code{\link[=canonical_permutation]{canonical_permutation()}}, \code{\link[=permute]{permute()}}, \code{\link[=count_automorphisms]{count_automorphisms()}} + +Other graph automorphism: +\code{\link{count_automorphisms}()} } \author{ Tommi Junttila (\url{http://users.ics.aalto.fi/tjunttil/}) for BLISS, Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph glue code and Tamas Nepusz \email{ntamas@gmail.com} for this manual page. } +\concept{graph automorphism} \keyword{graphs} diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 64f6f711180..70f191eeb1d 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -135,11 +135,11 @@ of Mathematical Sociology} 25(2):163-177, 2001. Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, @@ -148,11 +148,11 @@ Centrality measures Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, @@ -161,11 +161,11 @@ Centrality measures Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/bfs.Rd b/man/bfs.Rd index 5360ec08326..e60f3ca9511 100644 --- a/man/bfs.Rd +++ b/man/bfs.Rd @@ -140,11 +140,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/bipartite_mapping.Rd b/man/bipartite_mapping.Rd index 5a074655143..d5a3f0c599f 100644 --- a/man/bipartite_mapping.Rd +++ b/man/bipartite_mapping.Rd @@ -53,7 +53,8 @@ bipartite_mapping(g3) } \seealso{ Bipartite graphs -\code{\link{bipartite_projection}()} +\code{\link{bipartite_projection}()}, +\code{\link{is_bipartite}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/bipartite_projection.Rd b/man/bipartite_projection.Rd index f0f256ca494..dc009fb2f99 100644 --- a/man/bipartite_projection.Rd +++ b/man/bipartite_projection.Rd @@ -91,7 +91,8 @@ print(proj2[[2]], g = TRUE, e = TRUE) } \seealso{ Bipartite graphs -\code{\link{bipartite_mapping}()} +\code{\link{bipartite_mapping}()}, +\code{\link{is_bipartite}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/canonical_permutation.Rd b/man/canonical_permutation.Rd index 8d28d06996a..8d714e09918 100644 --- a/man/canonical_permutation.Rd +++ b/man/canonical_permutation.Rd @@ -89,9 +89,20 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \code{\link[=permute]{permute()}} to apply a permutation to a graph, \code{\link[=graph.isomorphic]{graph.isomorphic()}} for deciding graph isomorphism, possibly based on canonical labels. + +Other graph isomorphism: +\code{\link{count_isomorphisms}()}, +\code{\link{count_subgraph_isomorphisms}()}, +\code{\link{graph_from_isomorphism_class}()}, +\code{\link{isomorphic}()}, +\code{\link{isomorphism_class}()}, +\code{\link{isomorphisms}()}, +\code{\link{subgraph_isomorphic}()}, +\code{\link{subgraph_isomorphisms}()} } \author{ Tommi Junttila for BLISS, Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph and R interfaces. } +\concept{graph isomorphism} \keyword{graphs} diff --git a/man/closeness.Rd b/man/closeness.Rd index 1ee2c66ef92..8a21fc3233b 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -90,11 +90,11 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239. Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/cluster_edge_betweenness.Rd b/man/cluster_edge_betweenness.Rd index 64b3ad4e666..991ee28ac25 100644 --- a/man/cluster_edge_betweenness.Rd +++ b/man/cluster_edge_betweenness.Rd @@ -123,7 +123,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_fast_greedy.Rd b/man/cluster_fast_greedy.Rd index 2df29dfed68..96ba6c2461c 100644 --- a/man/cluster_fast_greedy.Rd +++ b/man/cluster_fast_greedy.Rd @@ -82,7 +82,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_fluid_communities.Rd b/man/cluster_fluid_communities.Rd index 9627a4dd2d4..84369a92ae1 100644 --- a/man/cluster_fluid_communities.Rd +++ b/man/cluster_fluid_communities.Rd @@ -61,7 +61,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_infomap.Rd b/man/cluster_infomap.Rd index f092b83f404..c6686d98779 100644 --- a/man/cluster_infomap.Rd +++ b/man/cluster_infomap.Rd @@ -81,7 +81,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_label_prop.Rd b/man/cluster_label_prop.Rd index 67737483fec..9921b491296 100644 --- a/man/cluster_label_prop.Rd +++ b/man/cluster_label_prop.Rd @@ -83,7 +83,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_leading_eigen.Rd b/man/cluster_leading_eigen.Rd index f0fc6a1955c..9797582c908 100644 --- a/man/cluster_leading_eigen.Rd +++ b/man/cluster_leading_eigen.Rd @@ -135,7 +135,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_leiden.Rd b/man/cluster_leiden.Rd index d0ec9dd9d7a..dc97b8b91a4 100644 --- a/man/cluster_leiden.Rd +++ b/man/cluster_leiden.Rd @@ -143,7 +143,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_louvain.Rd b/man/cluster_louvain.Rd index a94f74111f6..8a746e3dcee 100644 --- a/man/cluster_louvain.Rd +++ b/man/cluster_louvain.Rd @@ -89,7 +89,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_optimal.Rd b/man/cluster_optimal.Rd index 433afd7b862..a5b9e5cb37d 100644 --- a/man/cluster_optimal.Rd +++ b/man/cluster_optimal.Rd @@ -88,7 +88,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_spinglass.Rd b/man/cluster_spinglass.Rd index 2ec4ac6438c..df0fdf794a9 100644 --- a/man/cluster_spinglass.Rd +++ b/man/cluster_spinglass.Rd @@ -159,7 +159,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/cluster_walktrap.Rd b/man/cluster_walktrap.Rd index 17c1630ab43..99d51a045f4 100644 --- a/man/cluster_walktrap.Rd +++ b/man/cluster_walktrap.Rd @@ -88,7 +88,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_spinglass}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/communities.Rd b/man/communities.Rd index cad7ebc7251..81aa4af09d4 100644 --- a/man/communities.Rd +++ b/man/communities.Rd @@ -289,7 +289,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -310,7 +309,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -331,7 +329,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -352,7 +349,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -373,7 +369,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -394,7 +389,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -415,7 +409,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -436,7 +429,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -457,7 +449,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -478,7 +469,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -499,7 +489,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -520,7 +509,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -541,7 +529,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -562,7 +549,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -583,7 +569,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -604,7 +589,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, @@ -625,7 +609,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{modularity.igraph}()}, diff --git a/man/compare.Rd b/man/compare.Rd index 281e95ce15a..8eef71fc439 100644 --- a/man/compare.Rd +++ b/man/compare.Rd @@ -89,7 +89,6 @@ Community detection \code{\link{cluster_optimal}()}, \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/complementer.Rd b/man/complementer.Rd index 21a95c4b3b8..2d28bf6c9d0 100644 --- a/man/complementer.Rd +++ b/man/complementer.Rd @@ -40,8 +40,35 @@ gu <- union(g, gc) gu graph.isomorphic(gu, make_full_graph(vcount(g))) +} +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/components.Rd b/man/components.Rd index 264977ca371..5cc9df3d4ee 100644 --- a/man/components.Rd +++ b/man/components.Rd @@ -92,11 +92,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/compose.Rd b/man/compose.Rd index e03bc87675b..5ee0634c6c2 100644 --- a/man/compose.Rd +++ b/man/compose.Rd @@ -70,8 +70,35 @@ gc <- compose(g1, g2) print_all(gc) print_all(simplify(gc)) +} +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/constraint.Rd b/man/constraint.Rd index 121d56d5398..1b53e1fcd1b 100644 --- a/man/constraint.Rd +++ b/man/constraint.Rd @@ -59,11 +59,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/contract.Rd b/man/contract.Rd index 51bf2d41e6b..91c22c2af77 100644 --- a/man/contract.Rd +++ b/man/contract.Rd @@ -46,29 +46,33 @@ print(g2, g = TRUE, v = TRUE, e = TRUE) } \seealso{ -Community detection -\code{\link{as_membership}()}, -\code{\link{cluster_edge_betweenness}()}, -\code{\link{cluster_fast_greedy}()}, -\code{\link{cluster_fluid_communities}()}, -\code{\link{cluster_infomap}()}, -\code{\link{cluster_label_prop}()}, -\code{\link{cluster_leading_eigen}()}, -\code{\link{cluster_leiden}()}, -\code{\link{cluster_louvain}()}, -\code{\link{cluster_optimal}()}, -\code{\link{cluster_spinglass}()}, -\code{\link{cluster_walktrap}()}, -\code{\link{compare}()}, -\code{\link{groups}()}, -\code{\link{make_clusters}()}, -\code{\link{membership}()}, -\code{\link{modularity.igraph}()}, -\code{\link{plot_dendrogram}()}, -\code{\link{split_join_distance}()} +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{community} +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/coreness.Rd b/man/coreness.Rd index 3d29621ac28..1a38d3e1897 100644 --- a/man/coreness.Rd +++ b/man/coreness.Rd @@ -55,11 +55,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/count_automorphisms.Rd b/man/count_automorphisms.Rd index 195450cd0e3..f980a2d8fea 100644 --- a/man/count_automorphisms.Rd +++ b/man/count_automorphisms.Rd @@ -71,10 +71,14 @@ Workshop on Analytic Algorithms and Combinatorics.} 2007. \code{\link[=canonical_permutation]{canonical_permutation()}}, \code{\link[=permute]{permute()}}, and \code{\link[=automorphism_group]{automorphism_group()}} for a compact representation of all automorphisms + +Other graph automorphism: +\code{\link{automorphism_group}()} } \author{ Tommi Junttila (\url{http://users.ics.aalto.fi/tjunttil/}) for BLISS and Gabor Csardi \email{csardi.gabor@gmail.com} for the igraph glue code and this manual page. } +\concept{graph automorphism} \keyword{graphs} diff --git a/man/count_isomorphisms.Rd b/man/count_isomorphisms.Rd index 23b82102fd9..e449bb8253c 100644 --- a/man/count_isomorphisms.Rd +++ b/man/count_isomorphisms.Rd @@ -46,6 +46,7 @@ on Graphbased Representations in Pattern Recognition}, 149--159, 2001. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, \code{\link{isomorphic}()}, diff --git a/man/count_motifs.Rd b/man/count_motifs.Rd index 66a5370da95..6d715eec10d 100644 --- a/man/count_motifs.Rd +++ b/man/count_motifs.Rd @@ -37,6 +37,7 @@ sample_motifs(g, 3) \code{\link[=isomorphism_class]{isomorphism_class()}} Other graph motifs: +\code{\link{dyad_census}()}, \code{\link{motifs}()}, \code{\link{sample_motifs}()} } diff --git a/man/count_subgraph_isomorphisms.Rd b/man/count_subgraph_isomorphisms.Rd index 5fd84c027b1..6aae8240b4f 100644 --- a/man/count_subgraph_isomorphisms.Rd +++ b/man/count_subgraph_isomorphisms.Rd @@ -78,6 +78,7 @@ C. Solnon: AllDifferent-based Filtering for Subgraph Isomorphism, } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, \code{\link{isomorphic}()}, diff --git a/man/count_triangles.Rd b/man/count_triangles.Rd index 56ee5bc0134..ea455b4ab67 100644 --- a/man/count_triangles.Rd +++ b/man/count_triangles.Rd @@ -1,11 +1,13 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/triangles.R -\name{count_triangles} +% Please edit documentation in R/aaa-auto.R, R/triangles.R +\name{triangles} +\alias{triangles} \alias{count_triangles} \alias{adjacent.triangles} -\alias{triangles} \title{Find triangles in graphs} \usage{ +triangles(graph) + count_triangles(graph, vids = V(graph)) } \arguments{ diff --git a/man/degree.Rd b/man/degree.Rd index 2d66893fe88..060a9fffccc 100644 --- a/man/degree.Rd +++ b/man/degree.Rd @@ -65,11 +65,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -89,11 +89,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/delete_edge_attr.Rd b/man/delete_edge_attr.Rd index 0f6c708d60d..933d737cd92 100644 --- a/man/delete_edge_attr.Rd +++ b/man/delete_edge_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_edge_attr(g, "name") edge_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, @@ -35,6 +35,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -44,4 +45,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/delete_edges.Rd b/man/delete_edges.Rd index c907ca1ec8b..448acc4573e 100644 --- a/man/delete_edges.Rd +++ b/man/delete_edges.Rd @@ -39,10 +39,25 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/delete_graph_attr.Rd b/man/delete_graph_attr.Rd index 8bea2ada25f..cb185a78dd2 100644 --- a/man/delete_graph_attr.Rd +++ b/man/delete_graph_attr.Rd @@ -25,7 +25,7 @@ g2 <- delete_graph_attr(g, "name") graph_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_vertex_attr}()}, \code{\link{edge_attr<-}()}, @@ -34,6 +34,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -43,4 +44,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/delete_vertex_attr.Rd b/man/delete_vertex_attr.Rd index b3ccb765274..3852e56e992 100644 --- a/man/delete_vertex_attr.Rd +++ b/man/delete_vertex_attr.Rd @@ -26,7 +26,7 @@ g2 <- delete_vertex_attr(g, "name") vertex_attr_names(g2) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{edge_attr<-}()}, @@ -35,6 +35,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -44,4 +45,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/delete_vertices.Rd b/man/delete_vertices.Rd index beb5f88a68b..ff96924401f 100644 --- a/man/delete_vertices.Rd +++ b/man/delete_vertices.Rd @@ -34,10 +34,25 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/dfs.Rd b/man/dfs.Rd index f18fe174db4..b413626c0af 100644 --- a/man/dfs.Rd +++ b/man/dfs.Rd @@ -132,11 +132,11 @@ Other structural.properties: \code{\link{constraint}()}, \code{\link{coreness}()}, \code{\link{degree}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/diameter.Rd b/man/diameter.Rd index 25e9d7f0400..7f3df2bf17b 100644 --- a/man/diameter.Rd +++ b/man/diameter.Rd @@ -67,32 +67,14 @@ get_diameter(g, weights = NA) \seealso{ \code{\link[=distances]{distances()}} -Other structural.properties: -\code{\link{bfs}()}, -\code{\link{component_distribution}()}, -\code{\link{connect}()}, -\code{\link{constraint}()}, -\code{\link{coreness}()}, -\code{\link{degree}()}, -\code{\link{dfs}()}, +Other paths: +\code{\link{all_simple_paths}()}, \code{\link{distance_table}()}, -\code{\link{edge_density}()}, -\code{\link{feedback_arc_set}()}, -\code{\link{girth}()}, -\code{\link{is_matching}()}, -\code{\link{knn}()}, -\code{\link{laplacian_matrix}()}, -\code{\link{reciprocity}()}, -\code{\link{subcomponent}()}, -\code{\link{subgraph}()}, -\code{\link{topo_sort}()}, -\code{\link{transitivity}()}, -\code{\link{unfold_tree}()}, -\code{\link{which_multiple}()}, -\code{\link{which_mutual}()} +\code{\link{eccentricity}()}, +\code{\link{radius}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{structural.properties} +\concept{paths} \keyword{graphs} diff --git a/man/difference.Rd b/man/difference.Rd index b256d9a1ca3..30e241b234d 100644 --- a/man/difference.Rd +++ b/man/difference.Rd @@ -21,3 +21,30 @@ and igraph vertex and edge sequences. See \code{\link[=difference.igraph]{difference.igraph()}}, and \code{\link[=difference.igraph.vs]{difference.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/difference.igraph.Rd b/man/difference.igraph.Rd index 0582635bea7..34a5e3e2f2b 100644 --- a/man/difference.igraph.Rd +++ b/man/difference.igraph.Rd @@ -60,7 +60,34 @@ G <- wheel \%m\% sstar print_all(G) plot(G, layout = layout_nicely(wheel)) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/dim_select.Rd b/man/dim_select.Rd index 5526b12f31a..6c916654f7b 100644 --- a/man/dim_select.Rd +++ b/man/dim_select.Rd @@ -68,8 +68,12 @@ Statistics and Data Analysis}, Vol. 51, 918--930. } \seealso{ \code{\link[=embed_adjacency_matrix]{embed_adjacency_matrix()}} + +Other embedding: +\code{\link{embed_adjacency_matrix}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{embedding} \keyword{graphs} diff --git a/man/disjoint_union.Rd b/man/disjoint_union.Rd index 1d4efb538b5..73c1c03fc86 100644 --- a/man/disjoint_union.Rd +++ b/man/disjoint_union.Rd @@ -51,7 +51,34 @@ g2 <- make_ring(10) V(g2)$name <- letters[11:20] print_all(g1 \%du\% g2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/distances.Rd b/man/distances.Rd index d128a78f71b..3f66f32af84 100644 --- a/man/distances.Rd +++ b/man/distances.Rd @@ -261,8 +261,8 @@ Saddle River, N.J.: Prentice Hall. \seealso{ Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{eccentricity}()}, -\code{\link{is_dag}()}, \code{\link{radius}()} Other structural.properties: @@ -273,10 +273,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -297,10 +297,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -321,10 +321,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -345,10 +345,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/diversity.Rd b/man/diversity.Rd index 4eea01e17ea..6042c723487 100644 --- a/man/diversity.Rd +++ b/man/diversity.Rd @@ -55,11 +55,11 @@ and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010. \seealso{ Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/dominator_tree.Rd b/man/dominator_tree.Rd index cae1865969c..817f5a2147b 100644 --- a/man/dominator_tree.Rd +++ b/man/dominator_tree.Rd @@ -73,6 +73,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/dyad_census.Rd b/man/dyad_census.Rd index a880a5878f0..a3f261eb783 100644 --- a/man/dyad_census.Rd +++ b/man/dyad_census.Rd @@ -37,8 +37,14 @@ Applications.} Cambridge: Cambridge University Press. 1994. \seealso{ \code{\link[=triad_census]{triad_census()}} for the same classification, but with triples. + +Other graph motifs: +\code{\link{count_motifs}()}, +\code{\link{motifs}()}, +\code{\link{sample_motifs}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{graph motifs} \keyword{graphs} diff --git a/man/eccentricity.Rd b/man/eccentricity.Rd index 9f7a5f1683a..33480743d96 100644 --- a/man/eccentricity.Rd +++ b/man/eccentricity.Rd @@ -48,8 +48,8 @@ Harary, F. Graph Theory. Reading, MA: Addison-Wesley, p. 35, Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{distance_table}()}, -\code{\link{is_dag}()}, \code{\link{radius}()} } \concept{paths} diff --git a/man/edge.Rd b/man/edge.Rd index 9e25de22cbc..cc4985cd90b 100644 --- a/man/edge.Rd +++ b/man/edge.Rd @@ -55,10 +55,50 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/edge_attr-set.Rd b/man/edge_attr-set.Rd index 1894fa936fc..7b14870552f 100644 --- a/man/edge_attr-set.Rd +++ b/man/edge_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -46,6 +46,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -55,4 +56,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_attr.Rd b/man/edge_attr.Rd index 19d7ac4c261..3782d289511 100644 --- a/man/edge_attr.Rd +++ b/man/edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g, edge.width = E(g)$weight) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -41,6 +41,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -50,4 +51,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_attr_names.Rd b/man/edge_attr_names.Rd index 1b5b1c26705..c51a641cb89 100644 --- a/man/edge_attr_names.Rd +++ b/man/edge_attr_names.Rd @@ -23,7 +23,7 @@ edge_attr_names(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -32,6 +32,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -41,4 +42,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/edge_connectivity.Rd b/man/edge_connectivity.Rd index 9d95ed3d480..9d695e23213 100644 --- a/man/edge_connectivity.Rd +++ b/man/edge_connectivity.Rd @@ -88,6 +88,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/edge_density.Rd b/man/edge_density.Rd index de181a83074..fcf573dfb6d 100644 --- a/man/edge_density.Rd +++ b/man/edge_density.Rd @@ -58,10 +58,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/ego.Rd b/man/ego.Rd index d5cde3925e5..c84294c1ab5 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -108,25 +108,30 @@ g <- connect(g, 2) } \seealso{ -Random graph models (games) -\code{\link{erdos.renyi.game}()}, -\code{\link{sample_bipartite}()}, -\code{\link{sample_degseq}()}, -\code{\link{sample_dot_product}()}, -\code{\link{sample_gnm}()}, -\code{\link{sample_gnp}()}, -\code{\link{sample_grg}()}, -\code{\link{sample_growing}()}, -\code{\link{sample_hierarchical_sbm}()}, -\code{\link{sample_islands}()}, -\code{\link{sample_k_regular}()}, -\code{\link{sample_last_cit}()}, -\code{\link{sample_pa_age}()}, -\code{\link{sample_pa}()}, -\code{\link{sample_pref}()}, -\code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} Other structural.properties: \code{\link{bfs}()}, @@ -135,11 +140,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -159,11 +164,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -183,11 +188,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -204,6 +209,6 @@ Other structural.properties: Gabor Csardi \email{csardi.gabor@gmail.com}, the first version was done by Vincent Matossian } -\concept{games} +\concept{functions for manipulating graph structure} \concept{structural.properties} \keyword{graphs} diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index f81fabbf749..176fc399c86 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -105,11 +105,11 @@ Measures. \emph{American Journal of Sociology}, 92, 1170-1182. \seealso{ Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/embed_adjacency_matrix.Rd b/man/embed_adjacency_matrix.Rd index ceb518b384b..3fde7ccf5be 100644 --- a/man/embed_adjacency_matrix.Rd +++ b/man/embed_adjacency_matrix.Rd @@ -93,5 +93,9 @@ Consistent Adjacency Spectral Embedding for Stochastic Blockmodel Graphs, } \seealso{ \code{\link[=sample_dot_product]{sample_dot_product()}} + +Other embedding: +\code{\link{dim_select}()} } +\concept{embedding} \keyword{graphs} diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 241f8871764..31bca89a7a8 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -68,10 +68,14 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -85,10 +89,13 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } \concept{games} \keyword{graphs} +\keyword{internal} diff --git a/man/feedback_arc_set.Rd b/man/feedback_arc_set.Rd index cbbfef93be4..1363d58fcfb 100644 --- a/man/feedback_arc_set.Rd +++ b/man/feedback_arc_set.Rd @@ -58,10 +58,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -73,6 +73,12 @@ Other structural.properties: \code{\link{unfold_tree}()}, \code{\link{which_multiple}()}, \code{\link{which_mutual}()} + +Graph cycles +\code{\link{girth}()}, +\code{\link{has_eulerian_path}()}, +\code{\link{is_dag}()} } +\concept{cycles} \concept{structural.properties} \keyword{graphs} diff --git a/man/girth.Rd b/man/girth.Rd index c73de4bdd14..6fa9b016770 100644 --- a/man/girth.Rd +++ b/man/girth.Rd @@ -59,10 +59,10 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -74,9 +74,15 @@ Other structural.properties: \code{\link{unfold_tree}()}, \code{\link{which_multiple}()}, \code{\link{which_mutual}()} + +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{has_eulerian_path}()}, +\code{\link{is_dag}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{cycles} \concept{structural.properties} \keyword{graphs} diff --git a/man/graph_attr-set.Rd b/man/graph_attr-set.Rd index ff1f6cdf4fc..8f0e6d340c6 100644 --- a/man/graph_attr-set.Rd +++ b/man/graph_attr-set.Rd @@ -34,7 +34,7 @@ graph_attr(g) <- list( plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -43,6 +43,7 @@ Other graph attributes: \code{\link{edge_attr}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -52,4 +53,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_attr.Rd b/man/graph_attr.Rd index 57cb7e108ca..24da90ff989 100644 --- a/man/graph_attr.Rd +++ b/man/graph_attr.Rd @@ -26,7 +26,7 @@ graph_attr(g) graph_attr(g, "name") } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -35,6 +35,7 @@ Other graph attributes: \code{\link{edge_attr}()}, \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -44,4 +45,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_attr_names.Rd b/man/graph_attr_names.Rd index a0af577ff35..8a91c0b3b11 100644 --- a/man/graph_attr_names.Rd +++ b/man/graph_attr_names.Rd @@ -22,7 +22,7 @@ g <- make_ring(10) graph_attr_names(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -31,6 +31,7 @@ Other graph attributes: \code{\link{edge_attr}()}, \code{\link{graph_attr<-}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -40,4 +41,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/graph_from_isomorphism_class.Rd b/man/graph_from_isomorphism_class.Rd index 86292c8798e..df9b0f5a049 100644 --- a/man/graph_from_isomorphism_class.Rd +++ b/man/graph_from_isomorphism_class.Rd @@ -27,6 +27,7 @@ vertices and undirected graphd with 3 to 6 vertices. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{isomorphic}()}, diff --git a/man/groups.Rd b/man/groups.Rd index f18005a25ea..a72ac54bb81 100644 --- a/man/groups.Rd +++ b/man/groups.Rd @@ -54,7 +54,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, \code{\link{modularity.igraph}()}, diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index f6cd8801261..ccfaecd8d9d 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -71,11 +71,11 @@ M. Marchiori and V. Latora, Harmony in the small-world, Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/has_eulerian_path.Rd b/man/has_eulerian_path.Rd index d28dbbc40ff..f09eb2bc1b7 100644 --- a/man/has_eulerian_path.Rd +++ b/man/has_eulerian_path.Rd @@ -56,5 +56,26 @@ has_eulerian_cycle(g) try(eulerian_cycle(g)) } -\concept{eulerian} +\seealso{ +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_dag}()} + +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_dag}()} + +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_dag}()} + +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_dag}()} +} +\concept{cycles} \keyword{graphs} diff --git a/man/hub_score.Rd b/man/hub_score.Rd index 973e15a32a0..11a4bf7889b 100644 --- a/man/hub_score.Rd +++ b/man/hub_score.Rd @@ -71,4 +71,18 @@ as IBM Research Report RJ 10076, May 1997. \code{\link[=eigen_centrality]{eigen_centrality()}} for eigenvector centrality, \code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for the underlining machinery of the computation. + +Centrality measures +\code{\link{alpha_centrality}()}, +\code{\link{closeness}()}, +\code{\link{diversity}()}, +\code{\link{eigen_centrality}()}, +\code{\link{estimate_betweenness}()}, +\code{\link{harmonic_centrality}()}, +\code{\link{page_rank}()}, +\code{\link{power_centrality}()}, +\code{\link{spectrum}()}, +\code{\link{strength}()}, +\code{\link{subgraph_centrality}()} } +\concept{centrality} diff --git a/man/igraph-attribute-combination.Rd b/man/igraph-attribute-combination.Rd index 444554ab5dc..2afea5b1b7a 100644 --- a/man/igraph-attribute-combination.Rd +++ b/man/igraph-attribute-combination.Rd @@ -105,8 +105,28 @@ simplify(g, edge.attr.comb = list( \code{\link[=graph_attr]{graph_attr()}}, \code{\link[=vertex_attr]{vertex_attr()}}, \code{\link[=edge_attr]{edge_attr()}} on how to use graph/vertex/edge attributes in general. \code{\link[=igraph_options]{igraph_options()}} on igraph parameters. + +Vertex, edge and graph attributes +\code{\link{delete_edge_attr}()}, +\code{\link{delete_graph_attr}()}, +\code{\link{delete_vertex_attr}()}, +\code{\link{edge_attr<-}()}, +\code{\link{edge_attr_names}()}, +\code{\link{edge_attr}()}, +\code{\link{graph_attr<-}()}, +\code{\link{graph_attr_names}()}, +\code{\link{graph_attr}()}, +\code{\link{igraph-dollar}}, +\code{\link{igraph-vs-attributes}}, +\code{\link{set_edge_attr}()}, +\code{\link{set_graph_attr}()}, +\code{\link{set_vertex_attr}()}, +\code{\link{vertex_attr<-}()}, +\code{\link{vertex_attr_names}()}, +\code{\link{vertex_attr}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{attributes} \keyword{graphs} diff --git a/man/igraph-dollar.Rd b/man/igraph-dollar.Rd index 106de6af007..141eb013e5e 100644 --- a/man/igraph-dollar.Rd +++ b/man/igraph-dollar.Rd @@ -29,7 +29,7 @@ g$name <- "10-ring" g$name } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -39,6 +39,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, \code{\link{set_graph_attr}()}, @@ -47,4 +48,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/igraph-es-attributes.Rd b/man/igraph-es-attributes.Rd index b7ecb446ded..e111087e95f 100644 --- a/man/igraph-es-attributes.Rd +++ b/man/igraph-es-attributes.Rd @@ -75,6 +75,7 @@ plot(g) Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, @@ -86,6 +87,7 @@ Other vertex and edge sequences: Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-es-indexing.Rd b/man/igraph-es-indexing.Rd index 8d4663a1faa..093de589a16 100644 --- a/man/igraph-es-indexing.Rd +++ b/man/igraph-es-indexing.Rd @@ -129,6 +129,7 @@ E(g)[.env$x] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-es-indexing2.Rd b/man/igraph-es-indexing2.Rd index 0e72acc4ec0..d65c5f83b9b 100644 --- a/man/igraph-es-indexing2.Rd +++ b/man/igraph-es-indexing2.Rd @@ -42,6 +42,7 @@ E(g)[[.inc("A")]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-minus.Rd b/man/igraph-minus.Rd index 46df8249f0f..f226b68c81e 100644 --- a/man/igraph-minus.Rd +++ b/man/igraph-minus.Rd @@ -61,10 +61,25 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/igraph-vs-attributes.Rd b/man/igraph-vs-attributes.Rd index 5f730900b60..bbc9f5e79f8 100644 --- a/man/igraph-vs-attributes.Rd +++ b/man/igraph-vs-attributes.Rd @@ -79,6 +79,7 @@ plot(g) Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, @@ -87,7 +88,7 @@ Other vertex and edge sequences: \code{\link{print.igraph.es}()}, \code{\link{print.igraph.vs}()} -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -97,6 +98,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{set_edge_attr}()}, \code{\link{set_graph_attr}()}, @@ -105,5 +107,5 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} \concept{vertex and edge sequences} diff --git a/man/igraph-vs-indexing.Rd b/man/igraph-vs-indexing.Rd index 0db1978020d..3c0dedba8fb 100644 --- a/man/igraph-vs-indexing.Rd +++ b/man/igraph-vs-indexing.Rd @@ -144,6 +144,7 @@ V(g)[.env$x] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/igraph-vs-indexing2.Rd b/man/igraph-vs-indexing2.Rd index 8fec612ec5a..854638f60a4 100644 --- a/man/igraph-vs-indexing2.Rd +++ b/man/igraph-vs-indexing2.Rd @@ -41,6 +41,7 @@ V(g)[[1:5]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/intersection.Rd b/man/intersection.Rd index 40e6910b7a0..a81426e2f7c 100644 --- a/man/intersection.Rd +++ b/man/intersection.Rd @@ -21,3 +21,30 @@ sequences. See \code{\link[=intersection.igraph]{intersection.igraph()}}, and \code{\link[=intersection.igraph.vs]{intersection.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/intersection.igraph.Rd b/man/intersection.igraph.Rd index 4f97995efe7..dc9c688975f 100644 --- a/man/intersection.igraph.Rd +++ b/man/intersection.igraph.Rd @@ -58,7 +58,34 @@ net1 <- graph_from_literal( net2 <- graph_from_literal(D - A:F:Y, B - A - X - F - H - Z, F - Y) print_all(net1 \%s\% net2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/is_chordal.Rd b/man/is_chordal.Rd index 38fa3410979..576094a3deb 100644 --- a/man/is_chordal.Rd +++ b/man/is_chordal.Rd @@ -80,9 +80,12 @@ of Computation} 13, 566--579. } \seealso{ \code{\link[=max_cardinality]{max_cardinality()}} + +Other chordal: +\code{\link{max_cardinality}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } -\concept{decomposition} +\concept{chordal} \keyword{graphs} diff --git a/man/is_dag.Rd b/man/is_dag.Rd index 30613bc0c00..35fcc59d5b0 100644 --- a/man/is_dag.Rd +++ b/man/is_dag.Rd @@ -30,15 +30,39 @@ g2 <- g + edge(5, 1) is_dag(g2) } \seealso{ -Other paths: -\code{\link{all_simple_paths}()}, +Graph cycles +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{has_eulerian_path}()} + +Other structural.properties: +\code{\link{bfs}()}, +\code{\link{component_distribution}()}, +\code{\link{connect}()}, +\code{\link{constraint}()}, +\code{\link{coreness}()}, +\code{\link{degree}()}, +\code{\link{dfs}()}, \code{\link{distance_table}()}, -\code{\link{eccentricity}()}, -\code{\link{radius}()} +\code{\link{edge_density}()}, +\code{\link{feedback_arc_set}()}, +\code{\link{girth}()}, +\code{\link{is_matching}()}, +\code{\link{knn}()}, +\code{\link{laplacian_matrix}()}, +\code{\link{reciprocity}()}, +\code{\link{subcomponent}()}, +\code{\link{subgraph}()}, +\code{\link{topo_sort}()}, +\code{\link{transitivity}()}, +\code{\link{unfold_tree}()}, +\code{\link{which_multiple}()}, +\code{\link{which_mutual}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} for the C code, Gabor Csardi \email{csardi.gabor@gmail.com} for the R interface. } -\concept{paths} +\concept{cycles} +\concept{structural.properties} \keyword{graphs} diff --git a/man/is_min_separator.Rd b/man/is_min_separator.Rd index 0c8b4f1ccf5..e1317d9f395 100644 --- a/man/is_min_separator.Rd +++ b/man/is_min_separator.Rd @@ -70,6 +70,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/is_separator.Rd b/man/is_separator.Rd index 303ab931200..c560724a2b3 100644 --- a/man/is_separator.Rd +++ b/man/is_separator.Rd @@ -40,6 +40,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/is_tree.Rd b/man/is_tree.Rd index 4bbfe66d9cc..7d3b3debf1f 100644 --- a/man/is_tree.Rd +++ b/man/is_tree.Rd @@ -47,6 +47,7 @@ is_tree(g, details = TRUE) } \seealso{ Other trees: +\code{\link{make_from_prufer}()}, \code{\link{sample_spanning_tree}()}, \code{\link{to_prufer}()} } diff --git a/man/isomorphic.Rd b/man/isomorphic.Rd index 5ed05c3a656..745a45c710c 100644 --- a/man/isomorphic.Rd +++ b/man/isomorphic.Rd @@ -134,6 +134,7 @@ on Graphbased Representations in Pattern Recognition}, 149--159, 2001. } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/isomorphism_class.Rd b/man/isomorphism_class.Rd index 45da27910a8..5a485b06df2 100644 --- a/man/isomorphism_class.Rd +++ b/man/isomorphism_class.Rd @@ -34,6 +34,7 @@ isomorphic(g1, g2) } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/isomorphisms.Rd b/man/isomorphisms.Rd index 75d004639ec..95ffdf50edb 100644 --- a/man/isomorphisms.Rd +++ b/man/isomorphisms.Rd @@ -26,6 +26,7 @@ Calculate all isomorphic mappings between the vertices of two graphs } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/knn.Rd b/man/knn.Rd index 3d1ff264c7e..a04f009b391 100644 --- a/man/knn.Rd +++ b/man/knn.Rd @@ -98,11 +98,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, diff --git a/man/laplacian_matrix.Rd b/man/laplacian_matrix.Rd index f95386f5925..eaf2808b739 100644 --- a/man/laplacian_matrix.Rd +++ b/man/laplacian_matrix.Rd @@ -66,11 +66,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{reciprocity}()}, diff --git a/man/layout_on_grid.Rd b/man/layout_on_grid.Rd index 43cd3145bc5..6f14eb395b6 100644 --- a/man/layout_on_grid.Rd +++ b/man/layout_on_grid.Rd @@ -85,3 +85,4 @@ Tamas Nepusz \email{ntamas@gmail.com} } \concept{graph layouts} \keyword{graphs} +\keyword{internal} diff --git a/man/make_bipartite_graph.Rd b/man/make_bipartite_graph.Rd index a7193699854..c431c006b8c 100644 --- a/man/make_bipartite_graph.Rd +++ b/man/make_bipartite_graph.Rd @@ -66,8 +66,13 @@ print(g, v = TRUE) } \seealso{ \code{\link[=graph]{graph()}} to create one-mode networks + +Bipartite graphs +\code{\link{bipartite_mapping}()}, +\code{\link{bipartite_projection}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{bipartite} \keyword{graphs} diff --git a/man/make_clusters.Rd b/man/make_clusters.Rd index 2ff44996a9d..2d43b04272d 100644 --- a/man/make_clusters.Rd +++ b/man/make_clusters.Rd @@ -52,7 +52,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{membership}()}, \code{\link{modularity.igraph}()}, diff --git a/man/make_from_prufer.Rd b/man/make_from_prufer.Rd index fc661752998..7bd4f49afd6 100644 --- a/man/make_from_prufer.Rd +++ b/man/make_from_prufer.Rd @@ -32,9 +32,14 @@ only two vertices in the remaining graph. g <- make_tree(13, 3) to_prufer(g) - } \seealso{ \code{\link[=to_prufer]{to_prufer()}} to convert a graph into its Prüfer sequence + +Other trees: +\code{\link{is_tree}()}, +\code{\link{sample_spanning_tree}()}, +\code{\link{to_prufer}()} } +\concept{trees} \keyword{graphs} diff --git a/man/matching.Rd b/man/matching.Rd index 5920e564b40..ee1e61fb382 100644 --- a/man/matching.Rd +++ b/man/matching.Rd @@ -122,11 +122,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, @@ -146,11 +146,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, @@ -170,11 +170,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, \code{\link{reciprocity}()}, diff --git a/man/max_cardinality.Rd b/man/max_cardinality.Rd index c549e872e57..970e29c6068 100644 --- a/man/max_cardinality.Rd +++ b/man/max_cardinality.Rd @@ -58,8 +58,12 @@ of Computation} 13, 566--579. } \seealso{ \code{\link[=is_chordal]{is_chordal()}} + +Other chordal: +\code{\link{is_chordal}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{chordal} \keyword{graphs} diff --git a/man/max_flow.Rd b/man/max_flow.Rd index 1048a445021..5bd36150011 100644 --- a/man/max_flow.Rd +++ b/man/max_flow.Rd @@ -83,6 +83,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_cut.Rd b/man/min_cut.Rd index 051ff986641..798dfdce4fb 100644 --- a/man/min_cut.Rd +++ b/man/min_cut.Rd @@ -90,6 +90,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{max_flow}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_separators.Rd b/man/min_separators.Rd index 456d6150a37..bfefead44fd 100644 --- a/man/min_separators.Rd +++ b/man/min_separators.Rd @@ -89,6 +89,7 @@ Other flow: \code{\link{is_separator}()}, \code{\link{max_flow}()}, \code{\link{min_cut}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} diff --git a/man/min_st_separators.Rd b/man/min_st_separators.Rd index 799b7728e30..4c929869545 100644 --- a/man/min_st_separators.Rd +++ b/man/min_st_separators.Rd @@ -42,7 +42,21 @@ the Minimal Separators of a Graph, In: Peter Widmayer, Gabriele Neyer and Stephan Eidenbenz (editors): \emph{Graph-theoretic concepts in computer science}, 1665, 167--172, 1999. Springer. } +\seealso{ +Other flow: +\code{\link{dominator_tree}()}, +\code{\link{edge_connectivity}()}, +\code{\link{is_min_separator}()}, +\code{\link{is_separator}()}, +\code{\link{max_flow}()}, +\code{\link{min_cut}()}, +\code{\link{min_separators}()}, +\code{\link{st_cuts}()}, +\code{\link{st_min_cuts}()}, +\code{\link{vertex_connectivity}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{flow} \keyword{graphs} diff --git a/man/modularity.igraph.Rd b/man/modularity.igraph.Rd index 9e90f9ac1e0..be8a1d40be7 100644 --- a/man/modularity.igraph.Rd +++ b/man/modularity.igraph.Rd @@ -118,7 +118,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, @@ -139,7 +138,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/motifs.Rd b/man/motifs.Rd index 044fd19d353..758cf8213ac 100644 --- a/man/motifs.Rd +++ b/man/motifs.Rd @@ -44,6 +44,7 @@ sample_motifs(g, 3) Other graph motifs: \code{\link{count_motifs}()}, +\code{\link{dyad_census}()}, \code{\link{sample_motifs}()} } \concept{graph motifs} diff --git a/man/page_rank.Rd b/man/page_rank.Rd index eebd9710800..283d67916a4 100644 --- a/man/page_rank.Rd +++ b/man/page_rank.Rd @@ -111,12 +111,12 @@ Other centrality scores: \code{\link[=closeness]{closeness()}}, Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, \code{\link{strength}()}, diff --git a/man/path.Rd b/man/path.Rd index 5fa00017dda..4268ff5ba81 100644 --- a/man/path.Rd +++ b/man/path.Rd @@ -49,10 +49,25 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/permute.Rd b/man/permute.Rd index 20d2d18444e..55ab931dba9 100644 --- a/man/permute.Rd +++ b/man/permute.Rd @@ -48,8 +48,34 @@ all(sort(E(g2)$weight) == sort(E(g)$weight)) } \seealso{ \code{\link[=canonical_permutation]{canonical_permutation()}} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/plot.sir.Rd b/man/plot.sir.Rd index a4e3d6a1200..f8d69ada435 100644 --- a/man/plot.sir.Rd +++ b/man/plot.sir.Rd @@ -85,12 +85,12 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=sir]{sir()}} for running the actual simulation. -Other epi: +Processes on graphs \code{\link{time_bins.sir}()} } \author{ Eric Kolaczyk (\url{http://math.bu.edu/people/kolaczyk/}) and Gabor Csardi \email{csardi.gabor@gmail.com}. } -\concept{epi} +\concept{processes} \keyword{graphs} diff --git a/man/plot_dendrogram.communities.Rd b/man/plot_dendrogram.communities.Rd index c3f254662af..46468919080 100644 --- a/man/plot_dendrogram.communities.Rd +++ b/man/plot_dendrogram.communities.Rd @@ -115,7 +115,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, @@ -136,7 +135,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/plus-.igraph.Rd b/man/plus-.igraph.Rd index aab9a78957b..def387d8766 100644 --- a/man/plus-.igraph.Rd +++ b/man/plus-.igraph.Rd @@ -105,11 +105,26 @@ plot(g) Other functions for manipulating graph structure: \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, \code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, \code{\link{vertex}()} } \concept{functions for manipulating graph structure} diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index fef36bd8078..31e6777caf7 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -137,12 +137,12 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.'' Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{spectrum}()}, \code{\link{strength}()}, diff --git a/man/print.igraph.es.Rd b/man/print.igraph.es.Rd index 5e5f15c1fbe..24352a9918e 100644 --- a/man/print.igraph.es.Rd +++ b/man/print.igraph.es.Rd @@ -57,6 +57,7 @@ E(g4)[[1:5]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/print.igraph.vs.Rd b/man/print.igraph.vs.Rd index 947944cfbaa..78ea8968048 100644 --- a/man/print.igraph.vs.Rd +++ b/man/print.igraph.vs.Rd @@ -55,6 +55,7 @@ V(g4)[[2:5, 7:8]] Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-attributes}}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, diff --git a/man/radius.Rd b/man/radius.Rd index d55f09441f7..874aea51bb9 100644 --- a/man/radius.Rd +++ b/man/radius.Rd @@ -48,8 +48,8 @@ calculations. Other paths: \code{\link{all_simple_paths}()}, +\code{\link{diameter}()}, \code{\link{distance_table}()}, -\code{\link{eccentricity}()}, -\code{\link{is_dag}()} +\code{\link{eccentricity}()} } \concept{paths} diff --git a/man/reciprocity.Rd b/man/reciprocity.Rd index f81e2b4a3df..2bf970cded8 100644 --- a/man/reciprocity.Rd +++ b/man/reciprocity.Rd @@ -51,11 +51,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/rep.igraph.Rd b/man/rep.igraph.Rd index beba58c15bb..249bf876102 100644 --- a/man/rep.igraph.Rd +++ b/man/rep.igraph.Rd @@ -28,3 +28,55 @@ of times, as unconnected components. \examples{ rings <- make_ring(5) * 5 } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/reverse_edges.Rd b/man/reverse_edges.Rd index 5af0656fef9..ea72fea1fa8 100644 --- a/man/reverse_edges.Rd +++ b/man/reverse_edges.Rd @@ -31,3 +31,55 @@ all edges, this operation is also known as graph transpose. g <- make_graph(~ 1 -+ 2, 2 -+ 3, 3 -+ 4) reverse_edges(g, 2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/sample_.Rd b/man/sample_.Rd index 2f80ebe2b4f..67173bc2b94 100644 --- a/man/sample_.Rd +++ b/man/sample_.Rd @@ -29,3 +29,31 @@ blocky2 <- pref_matrix \%>\% blocky3 <- pref_matrix \%>\% sample_(sbm(), n = 20, block.sizes = c(10, 10)) } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()} +} +\concept{games} diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index 4ced6d0ce12..c0cf409ffa9 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -77,10 +77,14 @@ sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") \code{\link[=sample_gnp]{sample_gnp()}} and \code{\link[=sample_gnm]{sample_gnm()}} for the unipartite version. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,13 +98,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -114,7 +124,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_correlated_gnp.Rd b/man/sample_correlated_gnp.Rd index 89285aa7f5f..de47064bc4a 100644 --- a/man/sample_correlated_gnp.Rd +++ b/man/sample_correlated_gnp.Rd @@ -57,4 +57,31 @@ graph matching for correlated Erdos-Renyi graphs. \seealso{ \code{\link[=sample_correlated_gnp_pair]{sample_correlated_gnp_pair()}}, \code{\link[=sample_gnp]{sample_gnp()}} + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } +\concept{games} diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index 35d2793e267..5ca3163aaa9 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -50,5 +50,32 @@ graph matching for correlated Erdos-Renyi graphs. \seealso{ \code{\link[=sample_correlated_gnp]{sample_correlated_gnp()}}, \code{\link[=sample_gnp]{sample_gnp()}}. + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } +\concept{games} \keyword{graphs} diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index 28d25e6df57..5bc18574036 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -109,10 +109,14 @@ all(degree(g5) == degs) \code{\link[=realize_degseq]{realize_degseq()}} for a deterministic variant. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -126,13 +130,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -146,7 +156,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index 5a0278020f2..40f6368f9c7 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -57,10 +57,14 @@ for social networks. Dissertation, Johns Hopkins University, Maryland, USA, and \code{\link[=sample_sphere_volume]{sample_sphere_volume()}} for sampling position vectors. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -74,13 +78,19 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,7 +104,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index 1736421078d..408b230ce79 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -78,7 +78,35 @@ Goh K-I, Kahng B, Kim D: Universal behaviour of load distribution in scale-free networks. \emph{Phys Rev Lett} 87(27):278701, 2001. } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} +} \author{ Tamas Nepusz \email{ntamas@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index c487ec9a93a..8d7957e5744 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -87,7 +87,35 @@ Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation transitions in scale-free networks under the Achlioptas process. \emph{Phys Rev Lett} 103:135702, 2009. } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} +} \author{ Tamas Nepusz \email{ntamas@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index a13743708fd..db2a5534067 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -71,8 +71,35 @@ conference on Knowledge discovery in data mining}, 177--187, 2005. \seealso{ \code{\link[=barabasi.game]{barabasi.game()}} for the basic preferential attachment model. + +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{games} \keyword{graphs} diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 075988365cc..6a1b076510d 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -47,11 +47,15 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -64,14 +68,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -84,7 +94,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index 701441c506d..b0ce3e69392 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -46,11 +46,15 @@ Mathematicae} 6, 290--297 (1959). \code{\link[=sample_gnm]{sample_gnm()}}, \code{\link[=sample_pa]{sample_pa()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -63,14 +67,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_grg}()}, \code{\link{sample_growing}()}, @@ -83,7 +93,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 9dd1088a0d4..58253883efd 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -48,11 +48,15 @@ g2 <- sample_grg(1000, 0.05, torus = TRUE) \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_growing}()}, @@ -65,14 +69,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_growing}()}, @@ -85,7 +95,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com}, first version was diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index d3d9f7fac11..cafb9e5bf19 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -45,11 +45,15 @@ g2 <- sample_growing(500, citation = TRUE) \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -62,14 +66,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -82,7 +92,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index 43fd3fce229..74de881742f 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -59,11 +59,15 @@ if (require(Matrix)) { \code{\link[=sbm.game]{sbm.game()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -76,14 +80,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -96,7 +106,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 9ec6aad7d29..04dcf2d1f1b 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -37,11 +37,15 @@ oc \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -54,7 +58,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Samuel Thiriot diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 9a4deb2431f..6808ab72f48 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -49,11 +49,15 @@ sapply(k10, plot, vertex.label = NA) sequence. Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -66,7 +70,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index 3f6b9ae864e..ec1259857a7 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -83,11 +83,15 @@ vertex only. } \seealso{ Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -100,14 +104,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -120,14 +130,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -140,14 +156,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -160,14 +182,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -180,14 +208,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -200,7 +234,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_motifs.Rd b/man/sample_motifs.Rd index 6fed53c8c10..a553bc04884 100644 --- a/man/sample_motifs.Rd +++ b/man/sample_motifs.Rd @@ -52,6 +52,7 @@ sample_motifs(g, 3) Other graph motifs: \code{\link{count_motifs}()}, +\code{\link{dyad_census}()}, \code{\link{motifs}()} } \concept{graph motifs} diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index 1dd9757eb49..53ccd385dea 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -131,11 +131,15 @@ de Solla Price, D. J. 1965. Networks of Scientific Papers \emph{Science}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -148,14 +152,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -168,7 +178,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index f90688e4c3e..cd940e879d1 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -141,11 +141,15 @@ max(degree(g3)) \code{\link[=sample_pa]{sample_pa()}}, \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -158,14 +162,20 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -178,7 +188,9 @@ Random graph models (games) \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index 80ad19cf5ae..cf50ad99b19 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -102,11 +102,15 @@ tkplot(g, layout = layout_in_circle) \code{\link[=sample_traits_callaway]{sample_traits_callaway()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -119,14 +123,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -139,14 +149,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -159,14 +175,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -179,7 +201,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_sbm}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Tamas Nepusz \email{ntamas@gmail.com} and Gabor Csardi diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index 41748c9fa4f..3f7cf092f79 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -56,11 +56,15 @@ and evaluation. \emph{Social Networks}, 14, 5--61. \code{\link[=sample_gnp]{sample_gnp()}}, \code{\link[=sample_gnm]{sample_gnm()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -73,14 +77,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -93,7 +103,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_smallworld}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 70f5276d0ed..2106f3c4769 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -57,11 +57,15 @@ Duncan J Watts and Steven H Strogatz: Collective dynamics of \code{\link[=make_lattice]{make_lattice()}}, \code{\link[=rewire]{rewire()}} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -74,14 +78,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -94,7 +104,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_traits_callaway}()} +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_spanning_tree.Rd b/man/sample_spanning_tree.Rd index 93d29c9cba9..9a02c09d202 100644 --- a/man/sample_spanning_tree.Rd +++ b/man/sample_spanning_tree.Rd @@ -37,6 +37,7 @@ forest <- subgraph.edges(g, edges) Other trees: \code{\link{is_tree}()}, +\code{\link{make_from_prufer}()}, \code{\link{to_prufer}()} } \concept{trees} diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index 5f691f9439b..ada4f7db777 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -81,11 +81,15 @@ g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2 } \seealso{ Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -98,14 +102,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -118,14 +128,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -138,14 +154,20 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} Random graph models (games) -\code{\link{connect}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, \code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, \code{\link{sample_gnm}()}, \code{\link{sample_gnp}()}, \code{\link{sample_grg}()}, @@ -158,7 +180,9 @@ Random graph models (games) \code{\link{sample_pa}()}, \code{\link{sample_pref}()}, \code{\link{sample_sbm}()}, -\code{\link{sample_smallworld}()} +\code{\link{sample_smallworld}()}, +\code{\link{sample_tree}()}, +\code{\link{sample_}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} diff --git a/man/sample_tree.Rd b/man/sample_tree.Rd index e5d05561bb6..a96854b043d 100644 --- a/man/sample_tree.Rd +++ b/man/sample_tree.Rd @@ -35,4 +35,32 @@ given number of nodes with the same probability. g <- sample_tree(100, method = "lerw") } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_}()} +} +\concept{games} \keyword{graphs} diff --git a/man/scg-method.Rd b/man/scg-method.Rd index 15bee51f41d..00b2cbc4e3a 100644 --- a/man/scg-method.Rd +++ b/man/scg-method.Rd @@ -45,8 +45,17 @@ D. Gfeller, and P. De Los Rios, Spectral Coarse Graining of Complex Networks, \emph{Physical Review Letters}, \strong{99}(3), 2007. \url{https://arxiv.org/abs/0706.0812} } +\seealso{ +Spectral Coarse Graining +\code{\link{scg_eps}()}, +\code{\link{scg_group}()}, +\code{\link{scg_semi_proj}()}, +\code{\link{scg}()}, +\code{\link{stochastic_matrix}()} +} \author{ David Morton de Lachapelle, \url{http://people.epfl.ch/david.morton}. } +\concept{scg} \keyword{graphs} diff --git a/man/scg.Rd b/man/scg.Rd index d33cf020e3d..4896c313696 100644 --- a/man/scg.Rd +++ b/man/scg.Rd @@ -242,6 +242,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_group]{scg_group()}} and \code{\link[=scg_semi_proj]{scg_semi_proj()}}. Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_eps.Rd b/man/scg_eps.Rd index 7c3f89a1ab4..d317f1fb1ca 100644 --- a/man/scg_eps.Rd +++ b/man/scg_eps.Rd @@ -57,8 +57,16 @@ Matrix Analysis and Applications}, 2008. } \seealso{ \link{scg-method} and \code{\link[=scg]{scg()}}. + +Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_group}()}, +\code{\link{scg_semi_proj}()}, +\code{\link{scg}()}, +\code{\link{stochastic_matrix}()} } \author{ David Morton de Lachapelle, \url{http://people.epfl.ch/david.morton}. } +\concept{scg} diff --git a/man/scg_group.Rd b/man/scg_group.Rd index d09520bb38a..a2ec5d1be89 100644 --- a/man/scg_group.Rd +++ b/man/scg_group.Rd @@ -137,6 +137,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_eps]{scg_eps()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_semi_proj}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/scg_semi_proj.Rd b/man/scg_semi_proj.Rd index 6887229958c..8df8cb9f997 100644 --- a/man/scg_semi_proj.Rd +++ b/man/scg_semi_proj.Rd @@ -101,6 +101,8 @@ Matrix Analysis and Applications}, 2008. \code{\link[=scg_eps]{scg_eps()}}, \code{\link[=scg_group]{scg_group()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg}()}, \code{\link{stochastic_matrix}()} diff --git a/man/set_edge_attr.Rd b/man/set_edge_attr.Rd index 8dac8f8fff9..d188cdc00bb 100644 --- a/man/set_edge_attr.Rd +++ b/man/set_edge_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -42,6 +42,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_graph_attr}()}, @@ -50,4 +51,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/set_graph_attr.Rd b/man/set_graph_attr.Rd index 554fa10150b..0675b573428 100644 --- a/man/set_graph_attr.Rd +++ b/man/set_graph_attr.Rd @@ -27,7 +27,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -37,6 +37,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -45,4 +46,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/set_vertex_attr.Rd b/man/set_vertex_attr.Rd index 38ba253b9ec..3c0ef7f9fd9 100644 --- a/man/set_vertex_attr.Rd +++ b/man/set_vertex_attr.Rd @@ -32,7 +32,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -42,6 +42,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -50,4 +51,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/simplify.Rd b/man/simplify.Rd index 055f33c7308..cdf3ea03c2a 100644 --- a/man/simplify.Rd +++ b/man/simplify.Rd @@ -71,10 +71,86 @@ is_simple(simplify(g)) \code{\link[=which_loop]{which_loop()}}, \code{\link[=which_multiple]{which_multiple()}} and \code{\link[=count_multiple]{count_multiple()}}, \code{\link[=delete_edges]{delete_edges()}}, \code{\link[=delete_vertices]{delete_vertices()}} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()}, +\code{\link{vertex}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \concept{isomorphism} \concept{simple} \keyword{graphs} diff --git a/man/sir.Rd b/man/sir.Rd index bb8a7438abc..8e62895a788 100644 --- a/man/sir.Rd +++ b/man/sir.Rd @@ -106,18 +106,18 @@ infectious diseases and its applications (2nd ed.). London: Griffin. \seealso{ \code{\link[=plot.sir]{plot.sir()}} to conveniently plot the results -Other epi: +Processes on graphs \code{\link{plot.sir}()} -Other epi: +Processes on graphs \code{\link{plot.sir}()} -Other epi: +Processes on graphs \code{\link{plot.sir}()} } \author{ Gabor Csardi \email{csardi.gabor@gmail.com}. Eric Kolaczyk (\url{http://math.bu.edu/people/kolaczyk/}) wrote the initial version in R. } -\concept{epi} +\concept{processes} \keyword{graphs} diff --git a/man/spectrum.Rd b/man/spectrum.Rd index 5408d3c59c6..9a6ee9e2c0d 100644 --- a/man/spectrum.Rd +++ b/man/spectrum.Rd @@ -80,12 +80,12 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{strength}()}, diff --git a/man/split_join_distance.Rd b/man/split_join_distance.Rd index a51355238cc..241059882b1 100644 --- a/man/split_join_distance.Rd +++ b/man/split_join_distance.Rd @@ -56,7 +56,6 @@ Community detection \code{\link{cluster_spinglass}()}, \code{\link{cluster_walktrap}()}, \code{\link{compare}()}, -\code{\link{contract}()}, \code{\link{groups}()}, \code{\link{make_clusters}()}, \code{\link{membership}()}, diff --git a/man/srand.Rd b/man/srand.Rd index bc6bda18b94..9c3fad06c8f 100644 --- a/man/srand.Rd +++ b/man/srand.Rd @@ -22,3 +22,4 @@ Other other: Gabor Csardi \email{csardi.gabor@gmail.com} } \concept{other} +\keyword{internal} diff --git a/man/st_cuts.Rd b/man/st_cuts.Rd index d5a714d1812..68f3e27c91d 100644 --- a/man/st_cuts.Rd +++ b/man/st_cuts.Rd @@ -60,6 +60,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_min_cuts}()}, \code{\link{vertex_connectivity}()} } diff --git a/man/st_min_cuts.Rd b/man/st_min_cuts.Rd index ac514cb64c3..f9377611ba0 100644 --- a/man/st_min_cuts.Rd +++ b/man/st_min_cuts.Rd @@ -70,6 +70,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{vertex_connectivity}()} } diff --git a/man/stochastic_matrix.Rd b/man/stochastic_matrix.Rd index 66fa4bc2a26..74bd73bb93c 100644 --- a/man/stochastic_matrix.Rd +++ b/man/stochastic_matrix.Rd @@ -54,6 +54,8 @@ max(abs(rowSums(W)) - 1) \code{\link[=as_adj]{as_adj()}} Spectral Coarse Graining +\code{\link{scg-method}}, +\code{\link{scg_eps}()}, \code{\link{scg_group}()}, \code{\link{scg_semi_proj}()}, \code{\link{scg}()} diff --git a/man/strength.Rd b/man/strength.Rd index a3cc75a6a7c..2f31b0eed0c 100644 --- a/man/strength.Rd +++ b/man/strength.Rd @@ -57,12 +57,12 @@ Natl. Acad. Sci. USA 101, 3747 (2004) Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/subcomponent.Rd b/man/subcomponent.Rd index d47b97251c3..ebaabd50e71 100644 --- a/man/subcomponent.Rd +++ b/man/subcomponent.Rd @@ -46,11 +46,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/subgraph.Rd b/man/subgraph.Rd index 1362344b9af..33846981d6d 100644 --- a/man/subgraph.Rd +++ b/man/subgraph.Rd @@ -74,11 +74,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -98,11 +98,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, @@ -122,11 +122,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index 9c9ac335018..1e68a375d94 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -47,12 +47,12 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005). Centrality measures \code{\link{alpha_centrality}()}, -\code{\link{arpack_defaults}}, \code{\link{closeness}()}, \code{\link{diversity}()}, \code{\link{eigen_centrality}()}, \code{\link{estimate_betweenness}()}, \code{\link{harmonic_centrality}()}, +\code{\link{hub_score}()}, \code{\link{page_rank}()}, \code{\link{power_centrality}()}, \code{\link{spectrum}()}, diff --git a/man/subgraph_isomorphic.Rd b/man/subgraph_isomorphic.Rd index 129f79b07f9..cd5fa41a318 100644 --- a/man/subgraph_isomorphic.Rd +++ b/man/subgraph_isomorphic.Rd @@ -116,6 +116,7 @@ C. Solnon: AllDifferent-based Filtering for Subgraph Isomorphism, } \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/subgraph_isomorphisms.Rd b/man/subgraph_isomorphisms.Rd index 021996d4408..a36b15020bf 100644 --- a/man/subgraph_isomorphisms.Rd +++ b/man/subgraph_isomorphisms.Rd @@ -68,6 +68,7 @@ supply \code{NULL} for both of these arguments.} \seealso{ Other graph isomorphism: +\code{\link{canonical_permutation}()}, \code{\link{count_isomorphisms}()}, \code{\link{count_subgraph_isomorphisms}()}, \code{\link{graph_from_isomorphism_class}()}, diff --git a/man/to_prufer.Rd b/man/to_prufer.Rd index 17b90f8b425..c3ec1b2f110 100644 --- a/man/to_prufer.Rd +++ b/man/to_prufer.Rd @@ -35,6 +35,7 @@ Prüfer sequence Other trees: \code{\link{is_tree}()}, +\code{\link{make_from_prufer}()}, \code{\link{sample_spanning_tree}()} } \concept{trees} diff --git a/man/topo_sort.Rd b/man/topo_sort.Rd index 77dc7fb76af..84a34bc4116 100644 --- a/man/topo_sort.Rd +++ b/man/topo_sort.Rd @@ -46,11 +46,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/transitivity.Rd b/man/transitivity.Rd index eedf20bec72..56e15a76327 100644 --- a/man/transitivity.Rd +++ b/man/transitivity.Rd @@ -127,11 +127,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/triad_census.Rd b/man/triad_census.Rd index 392b41dbcde..1c06b3a361c 100644 --- a/man/triad_census.Rd +++ b/man/triad_census.Rd @@ -53,4 +53,5 @@ Mifflin. \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{motifs} \keyword{graphs} diff --git a/man/unfold_tree.Rd b/man/unfold_tree.Rd index 72af710a167..597f2478fb0 100644 --- a/man/unfold_tree.Rd +++ b/man/unfold_tree.Rd @@ -53,11 +53,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/union.Rd b/man/union.Rd index 46d6f04a272..c1629715531 100644 --- a/man/union.Rd +++ b/man/union.Rd @@ -21,3 +21,30 @@ sequences. See \code{\link[=union.igraph]{union.igraph()}}, and \code{\link[=union.igraph.vs]{union.igraph.vs()}}. } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{vertex}()} +} +\concept{functions for manipulating graph structure} diff --git a/man/union.igraph.Rd b/man/union.igraph.Rd index c5c14c328d9..60fb4d413d4 100644 --- a/man/union.igraph.Rd +++ b/man/union.igraph.Rd @@ -55,7 +55,34 @@ net1 <- graph_from_literal( net2 <- graph_from_literal(D - A:F:Y, B - A - X - F - H - Z, F - Y) print_all(net1 \%u\% net2) } +\seealso{ +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union}()}, +\code{\link{vertex}()} +} \author{ Gabor Csardi \email{csardi.gabor@gmail.com} } +\concept{functions for manipulating graph structure} \keyword{graphs} diff --git a/man/vertex.Rd b/man/vertex.Rd index b5f1d5dc546..375fe1e0d2c 100644 --- a/man/vertex.Rd +++ b/man/vertex.Rd @@ -42,10 +42,50 @@ Other functions for manipulating graph structure: \code{\link{+.igraph}()}, \code{\link{add_edges}()}, \code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, \code{\link{delete_edges}()}, \code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, \code{\link{edge}()}, \code{\link{igraph-minus}}, -\code{\link{path}()} +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()} + +Other functions for manipulating graph structure: +\code{\link{+.igraph}()}, +\code{\link{add_edges}()}, +\code{\link{add_vertices}()}, +\code{\link{complementer}()}, +\code{\link{compose}()}, +\code{\link{connect}()}, +\code{\link{contract}()}, +\code{\link{delete_edges}()}, +\code{\link{delete_vertices}()}, +\code{\link{difference.igraph}()}, +\code{\link{difference}()}, +\code{\link{disjoint_union}()}, +\code{\link{edge}()}, +\code{\link{igraph-minus}}, +\code{\link{intersection.igraph}()}, +\code{\link{intersection}()}, +\code{\link{path}()}, +\code{\link{permute}()}, +\code{\link{rep.igraph}()}, +\code{\link{reverse_edges}()}, +\code{\link{simplify}()}, +\code{\link{union.igraph}()}, +\code{\link{union}()} } \concept{functions for manipulating graph structure} diff --git a/man/vertex_attr-set.Rd b/man/vertex_attr-set.Rd index d4a88dcb59a..90469b00ba7 100644 --- a/man/vertex_attr-set.Rd +++ b/man/vertex_attr-set.Rd @@ -37,7 +37,7 @@ g plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -47,6 +47,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -55,4 +56,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_attr.Rd b/man/vertex_attr.Rd index 28519fb02fa..04b04357df4 100644 --- a/man/vertex_attr.Rd +++ b/man/vertex_attr.Rd @@ -33,7 +33,7 @@ vertex_attr(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -43,6 +43,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -51,4 +52,4 @@ Other graph attributes: \code{\link{vertex_attr<-}()}, \code{\link{vertex_attr_names}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_attr_names.Rd b/man/vertex_attr_names.Rd index 42cb85c43c2..d62dcfd92e2 100644 --- a/man/vertex_attr_names.Rd +++ b/man/vertex_attr_names.Rd @@ -24,7 +24,7 @@ vertex_attr_names(g) plot(g) } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -34,6 +34,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-dollar}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, @@ -42,4 +43,4 @@ Other graph attributes: \code{\link{vertex_attr<-}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/vertex_connectivity.Rd b/man/vertex_connectivity.Rd index 792d8f315b1..2f98c5e893d 100644 --- a/man/vertex_connectivity.Rd +++ b/man/vertex_connectivity.Rd @@ -104,6 +104,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()} @@ -115,6 +116,7 @@ Other flow: \code{\link{max_flow}()}, \code{\link{min_cut}()}, \code{\link{min_separators}()}, +\code{\link{min_st_separators}()}, \code{\link{st_cuts}()}, \code{\link{st_min_cuts}()} } diff --git a/man/which_multiple.Rd b/man/which_multiple.Rd index 0a1a52034ca..3beae30d8b1 100644 --- a/man/which_multiple.Rd +++ b/man/which_multiple.Rd @@ -89,11 +89,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()}, diff --git a/man/which_mutual.Rd b/man/which_mutual.Rd index 2cbdd06f72f..06597d17667 100644 --- a/man/which_mutual.Rd +++ b/man/which_mutual.Rd @@ -49,11 +49,11 @@ Other structural.properties: \code{\link{coreness}()}, \code{\link{degree}()}, \code{\link{dfs}()}, -\code{\link{diameter}()}, \code{\link{distance_table}()}, \code{\link{edge_density}()}, \code{\link{feedback_arc_set}()}, \code{\link{girth}()}, +\code{\link{is_dag}()}, \code{\link{is_matching}()}, \code{\link{knn}()}, \code{\link{laplacian_matrix}()},