diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 4fc3be5a2f..087f0b05fc 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 287beb96fa..f7bce518e9 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 1c0c7f7722..24e4af01bb 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$name diff --git a/R/centrality.R b/R/centrality.R index 4006095bd2..df4a1e830a 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -303,7 +303,7 @@ estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "al } #' @rdname arpack -#' @family centrality +#' @family arpack #' @export arpack_defaults <- list( bmat = "I", n = 0, which = "XX", nev = 1, tol = 0.0, @@ -497,7 +497,7 @@ arpack_defaults <- list( #' which = "LM", maxiter = 2000 #' )) #' } -#' @family centrality +#' @family arpack #' @export arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults, env = parent.frame(), complex = !sym) { @@ -909,6 +909,7 @@ diversity <- diversity #' g2 <- make_ring(10) #' hub_score(g2)$vector #' authority_score(g2)$vector +#' @family centrality hub_score <- hub_score diff --git a/R/community.R b/R/community.R index 16325a8480..5b2b444e43 100644 --- a/R/community.R +++ b/R/community.R @@ -2548,6 +2548,6 @@ communities <- groups.communities #' ## combined using the 'toString' function. #' print(g2, g = TRUE, v = TRUE, e = TRUE) #' -#' @family community #' @export +#' @family functions for manipulating graph structure contract <- contract diff --git a/R/decomposition.R b/R/decomposition.R index e0503bb409..6215653a04 100644 --- a/R/decomposition.R +++ b/R/decomposition.R @@ -63,7 +63,7 @@ #' linear-time algorithms to test chordality of graphs, test acyclicity of #' hypergraphs, and selectively reduce acyclic hypergraphs. *SIAM Journal #' of Computation* 13, 566--579. -#' @family decomposition +#' @family chordal #' @export #' @keywords graphs #' @examples diff --git a/R/embedding.R b/R/embedding.R index deb923e296..96a6d4b7ba 100644 --- a/R/embedding.R +++ b/R/embedding.R @@ -88,6 +88,7 @@ #' }) #' RDP <- sample_dot_product(lpvs) #' embed <- embed_adjacency_matrix(RDP, 5) +#' @family embedding #' @export embed_adjacency_matrix <- embed_adjacency_matrix @@ -148,6 +149,7 @@ embed_adjacency_matrix <- embed_adjacency_matrix #' RDP.graph.3 <- sample_dot_product(lpvs.sph) #' dim_select(embed_adjacency_matrix(RDP.graph.3, 10)$D) #' +#' @family embedding #' @export dim_select <- dim_select diff --git a/R/epi.R b/R/epi.R index b60c2a5913..dbfbaa4cba 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 1a5f26f8c8..d92657672e 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 b6d263ca8c..4203918977 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 4eb30c2bc8..b1fe3c4122 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 c5cae425fe..ae6d548b40 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 0bc78d2140..0aa213fead 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 17dc2808e7..db017c1d06 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 c817f9c28f..477bba0370 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 2a36c14f17..0bc808f5e3 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 fb3fc4fec4..9d918ef45b 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 8f725439c0..259996526d 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 1a3d958a91..7441c8cb0f 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$cluster)^2 +#' @family scg scg_eps <- scg_eps diff --git a/R/simple.R b/R/simple.R index 7619abd715..9e812959f5 100644 --- a/R/simple.R +++ b/R/simple.R @@ -70,16 +70,19 @@ #' is_simple(simplify(g, remove.multiple = FALSE)) #' is_simple(simplify(g)) #' @family simple +#' @family functions for manipulating graph structure #' @export simplify <- simplify #' @family simple +#' @family functions for manipulating graph structure #' @export #' @rdname simplify is_simple <- is_simple #' @family isomorphism #' @family simple +#' @family functions for manipulating graph structure #' @export #' @rdname simplify simplify_and_colorize <- function(graph) { diff --git a/R/structural.properties.R b/R/structural.properties.R index 069536d26e..20cd556d34 100644 --- a/R/structural.properties.R +++ b/R/structural.properties.R @@ -58,7 +58,7 @@ #' } #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @seealso [distances()] -#' @family structural.properties +#' @family paths #' @export #' @keywords graphs #' @examples @@ -1418,6 +1418,7 @@ topo_sort <- function(graph, mode = c("out", "all", "in")) { #' 47:6, pp. 319-323, 1993 #' @keywords graphs #' @family structural.properties +#' @family cycles #' @export #' @examples #' @@ -1450,6 +1451,7 @@ feedback_arc_set <- feedback_arc_set #' graph *Proceedings of the ninth annual ACM symposium on Theory of #' computing*, 1-10, 1977 #' @family structural.properties +#' @family cycles #' @export #' @keywords graphs #' @examples diff --git a/R/topology.R b/R/topology.R index af564f4f91..d7bb403438 100644 --- a/R/topology.R +++ b/R/topology.R @@ -778,6 +778,7 @@ graph_from_isomorphism_class <- graph_from_isomorphism_class #' el1 <- el1[order(el1[, 1], el1[, 2]), ] #' el2 <- el2[order(el2[, 1], el2[, 2]), ] #' all(el1 == el2) +#' @family graph isomorphism #' @export canonical_permutation <- canonical_permutation @@ -820,6 +821,7 @@ canonical_permutation <- canonical_permutation #' E(g2)$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 d7279719f2..931a83c1a9 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 716a8ec029..51ebe64ad3 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 4d1e49048b..ef1cd750cc 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 804028b90e..7e05d7483a 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 d692626e80..d0911fac5d 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 273b5a5eec..0bba46fb2c 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 6f980120ec..4c3af0083f 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 aa876dbfb0..b03d3d7647 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 8d38ef8bfa..6574521678 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 e09a84f744..fc3d64d31c 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 e6db9ccc2b..1def2b4d48 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 64f6f71118..70f191eeb1 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 5360ec0832..e60f3ca951 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 5a07465514..d5a3f0c599 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 f0f256ca49..dc009fb2f9 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 8d28d06996..8d714e0991 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 1ee2c66ef9..8a21fc3233 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 64b3ad4e66..991ee28ac2 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 2df29dfed6..96ba6c2461 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 9627a4dd2d..84369a92ae 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 f092b83f40..c6686d9877 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 67737483fe..9921b49129 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 f0fc6a1955..9797582c90 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 d0ec9dd9d7..dc97b8b91a 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 a94f74111f..8a746e3dce 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 433afd7b86..a5b9e5cb37 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 2ec4ac6438..df0fdf794a 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 17c1630ab4..99d51a045f 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 cad7ebc725..81aa4af09d 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 281e95ce15..8eef71fc43 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 21a95c4b3b..2d28bf6c9d 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 264977ca37..5cc9df3d4e 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 e03bc87675..5ee0634c6c 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 121d56d539..1b53e1fcd1 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 51bf2d41e6..91c22c2af7 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 3d29621ac2..1a38d3e189 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 195450cd0e..f980a2d8fe 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 23b82102fd..e449bb8253 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 66a5370da9..6d715eec10 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 5fd84c027b..6aae8240b4 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 56ee5bc013..ea455b4ab6 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 2d66893fe8..060a9fffcc 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 0f6c708d60..933d737cd9 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 c907ca1ec8..448acc4573 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 8bea2ada25..cb185a78dd 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 b3ccb76527..3852e56e99 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 beb5f88a68..ff96924401 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 f18fe174db..b413626c0a 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 25e9d7f040..7f3df2bf17 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 b256d9a1ca..30e241b234 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 0582635bea..34a5e3e2f2 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 5526b12f31..6c916654f7 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 1d4efb538b..73c1c03fc8 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 d128a78f71..3f66f32af8 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 4eea01e17e..6042c72348 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 cae1865969..817f5a2147 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 a880a5878f..a3f261eb78 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 9f7a5f1683..33480743d9 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 9e25de22cb..cc4985cd90 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 1894fa936f..7b14870552 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 19d7ac4c26..3782d28951 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 1b5b1c2670..c51a641cb8 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 9d95ed3d48..9d695e2321 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 de181a8307..fcf573dfb6 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 d5cde3925e..c84294c1ab 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 f81fabbf74..176fc399c8 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 ceb518b384..3fde7ccf5b 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 241f887176..31bca89a7a 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 cbbfef93be..1363d58fcf 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 c73de4bdd1..6fa9b01677 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 ff1f6cdf4f..8f0e6d340c 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 57cb7e108c..24da90ff98 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 a0af577ff3..8a91c0b3b1 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 86292c8798..df9b0f5a04 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 f18005a25e..a72ac54bb8 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 f6cd880126..ccfaecd8d9 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 d28dbbc40f..f09eb2bc1b 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 973e15a32a..11a4bf7889 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 444554ab5d..2afea5b1b7 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 106de6af00..141eb013e5 100644 --- a/man/igraph-dollar.Rd +++ b/man/igraph-dollar.Rd @@ -29,7 +29,7 @@ g$name <- "10-ring" g$name } \seealso{ -Other graph attributes: +Vertex, edge and graph attributes \code{\link{delete_edge_attr}()}, \code{\link{delete_graph_attr}()}, \code{\link{delete_vertex_attr}()}, @@ -39,6 +39,7 @@ Other graph attributes: \code{\link{graph_attr<-}()}, \code{\link{graph_attr_names}()}, \code{\link{graph_attr}()}, +\code{\link{igraph-attribute-combination}}, \code{\link{igraph-vs-attributes}}, \code{\link{set_edge_attr}()}, \code{\link{set_graph_attr}()}, @@ -47,4 +48,4 @@ Other graph attributes: \code{\link{vertex_attr_names}()}, \code{\link{vertex_attr}()} } -\concept{graph attributes} +\concept{attributes} diff --git a/man/igraph-es-attributes.Rd b/man/igraph-es-attributes.Rd index b7ecb446de..e111087e95 100644 --- a/man/igraph-es-attributes.Rd +++ b/man/igraph-es-attributes.Rd @@ -75,6 +75,7 @@ plot(g) Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, @@ -86,6 +87,7 @@ Other vertex and edge sequences: Other vertex and edge sequences: \code{\link{E}()}, \code{\link{V}()}, +\code{\link{as_ids}()}, \code{\link{igraph-es-indexing2}}, \code{\link{igraph-es-indexing}}, \code{\link{igraph-vs-attributes}}, diff --git a/man/igraph-es-indexing.Rd b/man/igraph-es-indexing.Rd index 8d4663a1fa..093de589a1 100644 --- a/man/igraph-es-indexing.Rd +++ b/man/igraph-es-indexing.Rd @@ -129,6 +129,7 @@ E(g)[.env$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 0e72acc4ec..d65c5f83b9 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 46df8249f0..f226b68c81 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 5f730900b6..bbc9f5e79f 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 0db1978020..3c0dedba8f 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 8fec612ec5..854638f60a 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 40e6910b7a..a81426e2f7 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 4f97995efe..dc9c688975 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 38fa341097..576094a3de 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 30613bc0c0..35fcc59d5b 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 0c8b4f1ccf..e1317d9f39 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 303ab93120..c560724a2b 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 4bbfe66d9c..7d3b3debf1 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 5ed05c3a65..745a45c710 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 45da27910a..5a485b06df 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 75d004639e..95ffdf50ed 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 3d1ff264c7..a04f009b39 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 f95386f592..eaf2808b73 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 43cd3145bc..6f14eb395b 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 a719369985..c431c006b8 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 2ff44996a9..2d43b04272 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 fc66175299..7bd4f49afd 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 5920e564b4..ee1e61fb38 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 c549e872e5..970e29c606 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 1048a44502..5bd3615001 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 051ff98664..798dfdce4f 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 456d6150a3..bfefead44f 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 799b7728e3..4c92986954 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 9e90f9ac1e..be8a1d40be 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 044fd19d35..758cf8213a 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 eebd971080..283d67916a 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 5fa00017dd..4268ff5ba8 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 20d2d18444..55ab931dba 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 a4e3d6a120..f8d69ada43 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 c3f254662a..4646891908 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 aab9a78957..def387d876 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 fef36bd807..31e6777caf 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 5e5f15c1fb..24352a9918 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 947944cfba..78ea896804 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 d55f09441f..874aea51bb 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 f81e2b4a3d..2bf970cded 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 beba58c15b..249bf87610 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 5af0656fef..ea72fea1fa 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 2f80ebe2b4..67173bc2b9 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 4ced6d0ce1..c0cf409ffa 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 89285aa7f5..de47064bc4 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 35d2793e26..5ca3163aaa 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 28d25e6df5..5bc1857403 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 5a0278020f..40f6368f9c 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 1736421078..408b230ce7 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 c487ec9a93..8d7957e574 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 a13743708f..db2a553406 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 075988365c..6a1b076510 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 701441c506..b0ce3e6939 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 9dd1088a0d..58253883ef 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 d3d9f7fac1..cafb9e5bf1 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 43fd3fce22..74de881742 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 9ec6aad7d2..04dcf2d1f1 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 9a4deb2431..6808ab72f4 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 3f6b9ae864..ec1259857a 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 6fed53c8c1..a553bc0488 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 1dd9757eb4..53ccd385de 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 f90688e4c3..cd940e879d 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 80ad19cf5a..cf50ad99b1 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 41748c9fa4..3f7cf092f7 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 70f5276d0e..2106f3c476 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 93d29c9cba..9a02c09d20 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 5f691f9439..ada4f7db77 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 e5d05561bb..a96854b043 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 15bee51f41..00b2cbc4e3 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 d33cf020e3..4896c31369 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 7c3f89a1ab..d317f1fb1c 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 d09520bb38..a2ec5d1be8 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 6887229958..8df8cb9f99 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 8dac8f8fff..d188cdc00b 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 554fa10150..0675b57342 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 38ba253b9e..3c0ef7f9fd 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 055f33c730..cdf3ea03c2 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 bb8a7438ab..8e62895a78 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 5408d3c59c..9a6ee9e2c0 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 a51355238c..241059882b 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 bc6bda18b9..9c3fad06c8 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 d5a714d181..68f3e27c91 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 ac514cb64c..f9377611ba 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 66fa4bc2a2..74bd73bb93 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 a3cc75a6a7..2f31b0eed0 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 d47b97251c..ebaabd50e7 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 1362344b9a..33846981d6 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 9c9ac33501..1e68a375d9 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 129f79b07f..cd5fa41a31 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 021996d440..a36b15020b 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 17b90f8b42..c3ec1b2f11 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 77dc7fb76a..84a34bc411 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 eedf20bec7..56e15a7632 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 392b41dbcd..1c06b3a361 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 72af710a16..597f2478fb 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 46d6f04a27..c162971553 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 c5c14c328d..60fb4d413d 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 b5f1d5dc54..375fe1e0d2 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 d4a88dcb59..90469b00ba 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 28519fb02f..04b04357df 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 42cb85c43c..d62dcfd92e 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 792d8f315b..2f98c5e893 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 0a1a52034c..3beae30d8b 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 2cbdd06f72..06597d1766 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}()},