diff --git a/R/adjacency.R b/R/adjacency.R index 9ebf52700c..ed18fa9ba1 100644 --- a/R/adjacency.R +++ b/R/adjacency.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.adjacency()` was renamed to `graph_from_adjacency_matrix()` to create a more +#' `graph.adjacency()` was renamed to [graph_from_adjacency_matrix()] to create a more #' consistent API. #' @inheritParams graph_from_adjacency_matrix #' @keywords internal diff --git a/R/assortativity.R b/R/assortativity.R index 3b7f6d7679..82af3004c5 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `assortativity.nominal()` was renamed to `assortativity_nominal()` to create a more +#' `assortativity.nominal()` was renamed to [assortativity_nominal()] to create a more #' consistent API. #' @inheritParams assortativity_nominal #' @keywords internal @@ -18,7 +18,7 @@ assortativity.nominal <- function(graph, types, directed = TRUE, normalized = TR #' @description #' `r lifecycle::badge("deprecated")` #' -#' `assortativity.degree()` was renamed to `assortativity_degree()` to create a more +#' `assortativity.degree()` was renamed to [assortativity_degree()] to create a more #' consistent API. #' @inheritParams assortativity_degree #' @keywords internal diff --git a/R/attributes.R b/R/attributes.R index bf37740a9d..c0908a0e9d 100644 --- a/R/attributes.R +++ b/R/attributes.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `set.vertex.attribute()` was renamed to `set_vertex_attr()` to create a more +#' `set.vertex.attribute()` was renamed to [set_vertex_attr()] to create a more #' consistent API. #' @inheritParams set_vertex_attr #' @keywords internal @@ -23,7 +23,7 @@ set.vertex.attribute <- function(graph, name, index = V(graph), value) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `set.graph.attribute()` was renamed to `set_graph_attr()` to create a more +#' `set.graph.attribute()` was renamed to [set_graph_attr()] to create a more #' consistent API. #' @inheritParams set_graph_attr #' @keywords internal @@ -43,7 +43,7 @@ set.graph.attribute <- function(graph, name, value) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `set.edge.attribute()` was renamed to `set_edge_attr()` to create a more +#' `set.edge.attribute()` was renamed to [set_edge_attr()] to create a more #' consistent API. #' @inheritParams set_edge_attr #' @keywords internal @@ -59,7 +59,7 @@ set.edge.attribute <- function(graph, name, index = E(graph), value) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `remove.vertex.attribute()` was renamed to `delete_vertex_attr()` to create a more +#' `remove.vertex.attribute()` was renamed to [delete_vertex_attr()] to create a more #' consistent API. #' @inheritParams delete_vertex_attr #' @keywords internal @@ -79,7 +79,7 @@ remove.vertex.attribute <- function(graph, name) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `remove.graph.attribute()` was renamed to `delete_graph_attr()` to create a more +#' `remove.graph.attribute()` was renamed to [delete_graph_attr()] to create a more #' consistent API. #' @inheritParams delete_graph_attr #' @keywords internal @@ -99,7 +99,7 @@ remove.graph.attribute <- function(graph, name) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `remove.edge.attribute()` was renamed to `delete_edge_attr()` to create a more +#' `remove.edge.attribute()` was renamed to [delete_edge_attr()] to create a more #' consistent API. #' @inheritParams delete_edge_attr #' @keywords internal @@ -119,7 +119,7 @@ remove.edge.attribute <- function(graph, name) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `list.vertex.attributes()` was renamed to `vertex_attr_names()` to create a more +#' `list.vertex.attributes()` was renamed to [vertex_attr_names()] to create a more #' consistent API. #' @inheritParams vertex_attr_names #' @keywords internal @@ -139,7 +139,7 @@ list.vertex.attributes <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `list.graph.attributes()` was renamed to `graph_attr_names()` to create a more +#' `list.graph.attributes()` was renamed to [graph_attr_names()] to create a more #' consistent API. #' @inheritParams graph_attr_names #' @keywords internal @@ -159,7 +159,7 @@ list.graph.attributes <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `list.edge.attributes()` was renamed to `edge_attr_names()` to create a more +#' `list.edge.attributes()` was renamed to [edge_attr_names()] to create a more #' consistent API. #' @inheritParams edge_attr_names #' @keywords internal @@ -179,7 +179,7 @@ list.edge.attributes <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.weighted()` was renamed to `is_weighted()` to create a more +#' `is.weighted()` was renamed to [is_weighted()] to create a more #' consistent API. #' @inheritParams is_weighted #' @keywords internal @@ -195,7 +195,7 @@ is.weighted <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.named()` was renamed to `is_named()` to create a more +#' `is.named()` was renamed to [is_named()] to create a more #' consistent API. #' @inheritParams is_named #' @keywords internal @@ -211,7 +211,7 @@ is.named <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.bipartite()` was renamed to `is_bipartite()` to create a more +#' `is.bipartite()` was renamed to [is_bipartite()] to create a more #' consistent API. #' @inheritParams is_bipartite #' @keywords internal @@ -227,7 +227,7 @@ is.bipartite <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.vertex.attribute()` was renamed to `vertex_attr()` to create a more +#' `get.vertex.attribute()` was renamed to [vertex_attr()] to create a more #' consistent API. #' @inheritParams vertex_attr #' @keywords internal @@ -243,7 +243,7 @@ get.vertex.attribute <- function(graph, name, index = V(graph)) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.graph.attribute()` was renamed to `graph_attr()` to create a more +#' `get.graph.attribute()` was renamed to [graph_attr()] to create a more #' consistent API. #' @inheritParams graph_attr #' @keywords internal @@ -259,7 +259,7 @@ get.graph.attribute <- function(graph, name) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.edge.attribute()` was renamed to `edge_attr()` to create a more +#' `get.edge.attribute()` was renamed to [edge_attr()] to create a more #' consistent API. #' @inheritParams edge_attr #' @keywords internal diff --git a/R/basic.R b/R/basic.R index a1bd383fa7..ac16ca80f9 100644 --- a/R/basic.R +++ b/R/basic.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.igraph()` was renamed to `is_igraph()` to create a more +#' `is.igraph()` was renamed to [is_igraph()] to create a more #' consistent API. #' @inheritParams is_igraph #' @keywords internal diff --git a/R/bipartite.R b/R/bipartite.R index b00edc7df5..70fafcaa13 100644 --- a/R/bipartite.R +++ b/R/bipartite.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `bipartite.projection.size()` was renamed to `bipartite_projection_size()` to create a more +#' `bipartite.projection.size()` was renamed to [bipartite_projection_size()] to create a more #' consistent API. #' @inheritParams bipartite_projection_size #' @keywords internal @@ -18,7 +18,7 @@ bipartite.projection.size <- function(graph, types = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `bipartite.projection()` was renamed to `bipartite_projection()` to create a more +#' `bipartite.projection()` was renamed to [bipartite_projection()] to create a more #' consistent API. #' @inheritParams bipartite_projection #' @keywords internal @@ -33,7 +33,7 @@ bipartite.projection <- function(graph, types = NULL, multiplicity = TRUE, probe #' @description #' `r lifecycle::badge("deprecated")` #' -#' `bipartite.mapping()` was renamed to `bipartite_mapping()` to create a more +#' `bipartite.mapping()` was renamed to [bipartite_mapping()] to create a more #' consistent API. #' @inheritParams bipartite_mapping #' @keywords internal diff --git a/R/centrality.R b/R/centrality.R index 4057ccb1b0..222d383e07 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `subgraph.centrality()` was renamed to `subgraph_centrality()` to create a more +#' `subgraph.centrality()` was renamed to [subgraph_centrality()] to create a more #' consistent API. #' @inheritParams subgraph_centrality #' @keywords internal @@ -18,7 +18,7 @@ subgraph.centrality <- function(graph, diag = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `page.rank()` was renamed to `page_rank()` to create a more +#' `page.rank()` was renamed to [page_rank()] to create a more #' consistent API. #' @inheritParams page_rank #' @keywords internal @@ -33,7 +33,7 @@ page.rank <- function(graph, algo = c("prpack", "arpack"), vids = V(graph), dire #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hub.score()` was renamed to `hub_score()` to create a more +#' `hub.score()` was renamed to [hub_score()] to create a more #' consistent API. #' @inheritParams hub_score #' @keywords internal @@ -48,7 +48,7 @@ hub.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defa #' @description #' `r lifecycle::badge("deprecated")` #' -#' `authority.score()` was renamed to `authority_score()` to create a more +#' `authority.score()` was renamed to [authority_score()] to create a more #' consistent API. #' @inheritParams authority_score #' @keywords internal @@ -63,7 +63,7 @@ authority.score <- function(graph, scale = TRUE, weights = NULL, options = arpac #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.strength()` was renamed to `strength()` to create a more +#' `graph.strength()` was renamed to [strength()] to create a more #' consistent API. #' @inheritParams strength #' @keywords internal @@ -78,7 +78,7 @@ graph.strength <- function(graph, vids = V(graph), mode = c("all", "out", "in", #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.eigen()` was renamed to `spectrum()` to create a more +#' `graph.eigen()` was renamed to [spectrum()] to create a more #' consistent API. #' @inheritParams spectrum #' @keywords internal @@ -93,7 +93,7 @@ graph.eigen <- function(graph, algorithm = c("arpack", "auto", "lapack", "comp_a #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.diversity()` was renamed to `diversity()` to create a more +#' `graph.diversity()` was renamed to [diversity()] to create a more #' consistent API. #' @inheritParams diversity #' @keywords internal @@ -108,7 +108,7 @@ graph.diversity <- function(graph, weights = NULL, vids = V(graph)) { # nocov st #' @description #' `r lifecycle::badge("deprecated")` #' -#' `evcent()` was renamed to `eigen_centrality()` to create a more +#' `evcent()` was renamed to [eigen_centrality()] to create a more #' consistent API. #' @inheritParams eigen_centrality #' @keywords internal @@ -123,7 +123,7 @@ evcent <- function(graph, directed = FALSE, scale = TRUE, weights = NULL, option #' @description #' `r lifecycle::badge("deprecated")` #' -#' `edge.betweenness()` was renamed to `edge_betweenness()` to create a more +#' `edge.betweenness()` was renamed to [edge_betweenness()] to create a more #' consistent API. #' @inheritParams edge_betweenness #' @keywords internal @@ -138,7 +138,7 @@ edge.betweenness <- function(graph, e = E(graph), directed = TRUE, weights = NUL #' @description #' `r lifecycle::badge("deprecated")` #' -#' `bonpow()` was renamed to `power_centrality()` to create a more +#' `bonpow()` was renamed to [power_centrality()] to create a more #' consistent API. #' @inheritParams power_centrality #' @keywords internal @@ -153,7 +153,7 @@ bonpow <- function(graph, nodes = V(graph), loops = FALSE, exponent = 1, rescale #' @description #' `r lifecycle::badge("deprecated")` #' -#' `alpha.centrality()` was renamed to `alpha_centrality()` to create a more +#' `alpha.centrality()` was renamed to [alpha_centrality()] to create a more #' consistent API. #' @inheritParams alpha_centrality #' @keywords internal @@ -188,7 +188,7 @@ alpha.centrality <- function(graph, nodes = V(graph), alpha = 1, loops = FALSE, #' @description #' `r lifecycle::badge("deprecated")` #' -#' Use [`betweenness()`] with the `cutoff` argument instead. +#' Use [betweenness()] with the `cutoff` argument instead. #' @param vids The vertices for which the vertex betweenness estimation will be #' calculated. #' @inheritParams betweenness @@ -351,7 +351,7 @@ edge_betweenness <- function(graph, e = E(graph), #' @description #' `r lifecycle::badge("deprecated")` #' -#' Use [`edge_betweenness()`] with the `cutoff` argument instead. +#' Use [edge_betweenness()] with the `cutoff` argument instead. #' @inheritParams edge_betweenness #' @keywords internal #' @export @@ -467,7 +467,7 @@ closeness <- function(graph, vids = V(graph), #' @description #' `r lifecycle::badge("deprecated")` #' -#' Use [`closeness()`] with the `cutoff` argument instead. +#' Use [closeness()] with the `cutoff` argument instead. #' @inheritParams closeness #' @keywords internal #' @export diff --git a/R/centralization.R b/R/centralization.R index 4dae746ea4..5e5bed2631 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralize.scores()` was renamed to `centralize()` to create a more +#' `centralize.scores()` was renamed to [centralize()] to create a more #' consistent API. #' @inheritParams centralize #' @keywords internal @@ -18,7 +18,7 @@ centralize.scores <- function(scores, theoretical.max = 0, normalized = TRUE) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.evcent.tmax()` was renamed to `centr_eigen_tmax()` to create a more +#' `centralization.evcent.tmax()` was renamed to [centr_eigen_tmax()] to create a more #' consistent API. #' @inheritParams centr_eigen_tmax #' @keywords internal @@ -33,7 +33,7 @@ centralization.evcent.tmax <- function(graph = NULL, nodes = 0, directed = FALSE #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.evcent()` was renamed to `centr_eigen()` to create a more +#' `centralization.evcent()` was renamed to [centr_eigen()] to create a more #' consistent API. #' @inheritParams centr_eigen #' @keywords internal @@ -48,7 +48,7 @@ centralization.evcent <- function(graph, directed = FALSE, scale = TRUE, options #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.degree.tmax()` was renamed to `centr_degree_tmax()` to create a more +#' `centralization.degree.tmax()` was renamed to [centr_degree_tmax()] to create a more #' consistent API. #' @inheritParams centr_degree_tmax #' @keywords internal @@ -63,7 +63,7 @@ centralization.degree.tmax <- function(graph = NULL, nodes = 0, mode = c("all", #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.degree()` was renamed to `centr_degree()` to create a more +#' `centralization.degree()` was renamed to [centr_degree()] to create a more #' consistent API. #' @inheritParams centr_degree #' @keywords internal @@ -78,7 +78,7 @@ centralization.degree <- function(graph, mode = c("all", "out", "in", "total"), #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.closeness.tmax()` was renamed to `centr_clo_tmax()` to create a more +#' `centralization.closeness.tmax()` was renamed to [centr_clo_tmax()] to create a more #' consistent API. #' @inheritParams centr_clo_tmax #' @keywords internal @@ -93,7 +93,7 @@ centralization.closeness.tmax <- function(graph = NULL, nodes = 0, mode = c("out #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.closeness()` was renamed to `centr_clo()` to create a more +#' `centralization.closeness()` was renamed to [centr_clo()] to create a more #' consistent API. #' @inheritParams centr_clo #' @keywords internal @@ -108,7 +108,7 @@ centralization.closeness <- function(graph, mode = c("out", "in", "all", "total" #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.betweenness.tmax()` was renamed to `centr_betw_tmax()` to create a more +#' `centralization.betweenness.tmax()` was renamed to [centr_betw_tmax()] to create a more #' consistent API. #' @inheritParams centr_betw_tmax #' @keywords internal @@ -123,7 +123,7 @@ centralization.betweenness.tmax <- function(graph = NULL, nodes = 0, directed = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `centralization.betweenness()` was renamed to `centr_betw()` to create a more +#' `centralization.betweenness()` was renamed to [centr_betw()] to create a more #' consistent API. #' @inheritParams centr_betw #' @keywords internal diff --git a/R/cliques.R b/R/cliques.R index 6093623bc8..6bd6ac7250 100644 --- a/R/cliques.R +++ b/R/cliques.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximal.independent.vertex.sets()` was renamed to `max_ivs()` to create a more +#' `maximal.independent.vertex.sets()` was renamed to [max_ivs()] to create a more #' consistent API. #' @inheritParams max_ivs #' @keywords internal @@ -18,7 +18,7 @@ maximal.independent.vertex.sets <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximal.cliques.count()` was renamed to `count_max_cliques()` to create a more +#' `maximal.cliques.count()` was renamed to [count_max_cliques()] to create a more #' consistent API. #' @inheritParams count_max_cliques #' @keywords internal @@ -33,7 +33,7 @@ maximal.cliques.count <- function(graph, min = NULL, max = NULL, subset = NULL) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximal.cliques()` was renamed to `max_cliques()` to create a more +#' `maximal.cliques()` was renamed to [max_cliques()] to create a more #' consistent API. #' @inheritParams max_cliques #' @keywords internal @@ -48,7 +48,7 @@ maximal.cliques <- function(graph, min = NULL, max = NULL, subset = NULL, file = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `largest.independent.vertex.sets()` was renamed to `largest_ivs()` to create a more +#' `largest.independent.vertex.sets()` was renamed to [largest_ivs()] to create a more #' consistent API. #' @inheritParams largest_ivs #' @keywords internal @@ -63,7 +63,7 @@ largest.independent.vertex.sets <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `largest.cliques()` was renamed to `largest_cliques()` to create a more +#' `largest.cliques()` was renamed to [largest_cliques()] to create a more #' consistent API. #' @inheritParams largest_cliques #' @keywords internal @@ -78,7 +78,7 @@ largest.cliques <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `independent.vertex.sets()` was renamed to `ivs()` to create a more +#' `independent.vertex.sets()` was renamed to [ivs()] to create a more #' consistent API. #' @inheritParams ivs #' @keywords internal @@ -93,7 +93,7 @@ independent.vertex.sets <- function(graph, min = NULL, max = NULL) { # nocov sta #' @description #' `r lifecycle::badge("deprecated")` #' -#' `independence.number()` was renamed to `ivs_size()` to create a more +#' `independence.number()` was renamed to [ivs_size()] to create a more #' consistent API. #' @inheritParams ivs_size #' @keywords internal @@ -108,7 +108,7 @@ independence.number <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `clique.number()` was renamed to `clique_num()` to create a more +#' `clique.number()` was renamed to [clique_num()] to create a more #' consistent API. #' @inheritParams clique_num #' @keywords internal @@ -174,7 +174,7 @@ clique.number <- function(graph) { # nocov start #' `NULL` means no limit. #' @return `cliques()`, `largest_cliques()` and `clique_num()` #' return a list containing numeric vectors of vertex ids. Each list element is -#' a clique, i.e. a vertex sequence of class [`igraph.vs()`][V]. +#' a clique, i.e. a vertex sequence of class [igraph.vs][V]. #' #' `max_cliques()` returns `NULL`, invisibly, if its `file` #' argument is not `NULL`. The output is written to the specified file in @@ -343,7 +343,7 @@ clique_num <- clique_number_impl #' or only the maximal ones (`TRUE`). #' @return `weighted_cliques()` and `largest_weighted_cliques()` return a #' list containing numeric vectors of vertex IDs. Each list element is a weighted -#' clique, i.e. a vertex sequence of class [`igraph.vs()`][V]. +#' clique, i.e. a vertex sequence of class [igraph.vs][V]. #' #' `weighted_clique_num()` returns an integer scalar. #' @@ -499,7 +499,7 @@ max_ivs <- function(graph) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximal_ivs()` was renamed to `max_ivs()` to create a more +#' `maximal_ivs()` was renamed to [max_ivs()] to create a more #' consistent API. #' @export #' @inheritParams max_ivs diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index 56cc339566..83f3e1fa61 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `exportPajek()` was renamed to `export_pajek()` to create a more +#' `exportPajek()` was renamed to [export_pajek()] to create a more #' consistent API. #' @inheritParams export_pajek #' @keywords internal @@ -18,7 +18,7 @@ exportPajek <- function(blocks, graph, file, project.file = TRUE) { # nocov star #' @description #' `r lifecycle::badge("deprecated")` #' -#' `plotHierarchy()` was renamed to `plot_hierarchy()` to create a more +#' `plotHierarchy()` was renamed to [plot_hierarchy()] to create a more #' consistent API. #' @inheritParams plot_hierarchy #' @keywords internal @@ -33,7 +33,7 @@ plotHierarchy <- function(blocks, layout = layout_as_tree(hierarchy(blocks), roo #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maxcohesion()` was renamed to `max_cohesion()` to create a more +#' `maxcohesion()` was renamed to [max_cohesion()] to create a more #' consistent API. #' @inheritParams max_cohesion #' @keywords internal @@ -48,7 +48,7 @@ maxcohesion <- function(blocks) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.cohesion()` was renamed to `cohesion()` to create a more +#' `graph.cohesion()` was renamed to [cohesion()] to create a more #' consistent API. #' @param x x #' @param ... passed to `cohesion()` @@ -64,7 +64,7 @@ graph.cohesion <- function(x, ...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `cohesive.blocks()` was renamed to `cohesive_blocks()` to create a more +#' `cohesive.blocks()` was renamed to [cohesive_blocks()] to create a more #' consistent API. #' @inheritParams cohesive_blocks #' @keywords internal @@ -79,7 +79,7 @@ cohesive.blocks <- function(graph, labels = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `blockGraphs()` was renamed to `graphs_from_cohesive_blocks()` to create a more +#' `blockGraphs()` was renamed to [graphs_from_cohesive_blocks()] to create a more #' consistent API. #' @inheritParams graphs_from_cohesive_blocks #' @keywords internal diff --git a/R/community.R b/R/community.R index fd9abd48e7..143085923b 100644 --- a/R/community.R +++ b/R/community.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `create.communities()` was renamed to `make_clusters()` to create a more +#' `create.communities()` was renamed to [make_clusters()] to create a more #' consistent API. #' @inheritParams make_clusters #' @keywords internal @@ -18,7 +18,7 @@ create.communities <- function(graph, membership = NULL, algorithm = NULL, merge #' @description #' `r lifecycle::badge("deprecated")` #' -#' `walktrap.community()` was renamed to `cluster_walktrap()` to create a more +#' `walktrap.community()` was renamed to [cluster_walktrap()] to create a more #' consistent API. #' @inheritParams cluster_walktrap #' @keywords internal @@ -33,7 +33,7 @@ walktrap.community <- function(graph, weights = NULL, steps = 4, merges = TRUE, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `spinglass.community()` was renamed to `cluster_spinglass()` to create a more +#' `spinglass.community()` was renamed to [cluster_spinglass()] to create a more #' consistent API. #' @inheritParams cluster_spinglass #' @keywords internal @@ -48,7 +48,7 @@ spinglass.community <- function(graph, weights = NULL, vertex = NULL, spins = 25 #' @description #' `r lifecycle::badge("deprecated")` #' -#' `showtrace()` was renamed to `show_trace()` to create a more +#' `showtrace()` was renamed to [show_trace()] to create a more #' consistent API. #' @inheritParams show_trace #' @keywords internal @@ -63,7 +63,7 @@ showtrace <- function(communities) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `optimal.community()` was renamed to `cluster_optimal()` to create a more +#' `optimal.community()` was renamed to [cluster_optimal()] to create a more #' consistent API. #' @inheritParams cluster_optimal #' @keywords internal @@ -78,7 +78,7 @@ optimal.community <- function(graph, weights = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `multilevel.community()` was renamed to `cluster_louvain()` to create a more +#' `multilevel.community()` was renamed to [cluster_louvain()] to create a more #' consistent API. #' @inheritParams cluster_louvain #' @keywords internal @@ -93,7 +93,7 @@ multilevel.community <- function(graph, weights = NULL, resolution = 1) { # noco #' @description #' `r lifecycle::badge("deprecated")` #' -#' `mod.matrix()` was renamed to `modularity_matrix()` to create a more +#' `mod.matrix()` was renamed to [modularity_matrix()] to create a more #' consistent API. #' @inheritParams modularity_matrix #' @keywords internal @@ -108,7 +108,7 @@ mod.matrix <- function(graph, membership, weights = NULL, resolution = 1, direct #' @description #' `r lifecycle::badge("deprecated")` #' -#' `leading.eigenvector.community()` was renamed to `cluster_leading_eigen()` to create a more +#' `leading.eigenvector.community()` was renamed to [cluster_leading_eigen()] to create a more #' consistent API. #' @inheritParams cluster_leading_eigen #' @keywords internal @@ -123,7 +123,7 @@ leading.eigenvector.community <- function(graph, steps = -1, weights = NULL, sta #' @description #' `r lifecycle::badge("deprecated")` #' -#' `label.propagation.community()` was renamed to `cluster_label_prop()` to create a more +#' `label.propagation.community()` was renamed to [cluster_label_prop()] to create a more #' consistent API. #' @inheritParams cluster_label_prop #' @keywords internal @@ -138,7 +138,7 @@ label.propagation.community <- function(graph, weights = NULL, ..., mode = c("ou #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.hierarchical()` was renamed to `is_hierarchical()` to create a more +#' `is.hierarchical()` was renamed to [is_hierarchical()] to create a more #' consistent API. #' @inheritParams is_hierarchical #' @keywords internal @@ -153,7 +153,7 @@ is.hierarchical <- function(communities) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `infomap.community()` was renamed to `cluster_infomap()` to create a more +#' `infomap.community()` was renamed to [cluster_infomap()] to create a more #' consistent API. #' @inheritParams cluster_infomap #' @keywords internal @@ -168,7 +168,7 @@ infomap.community <- function(graph, e.weights = NULL, v.weights = NULL, nb.tria #' @description #' `r lifecycle::badge("deprecated")` #' -#' `fastgreedy.community()` was renamed to `cluster_fast_greedy()` to create a more +#' `fastgreedy.community()` was renamed to [cluster_fast_greedy()] to create a more #' consistent API. #' @inheritParams cluster_fast_greedy #' @keywords internal @@ -183,7 +183,7 @@ fastgreedy.community <- function(graph, merges = TRUE, modularity = TRUE, member #' @description #' `r lifecycle::badge("deprecated")` #' -#' `edge.betweenness.community()` was renamed to `cluster_edge_betweenness()` to create a more +#' `edge.betweenness.community()` was renamed to [cluster_edge_betweenness()] to create a more #' consistent API. #' @inheritParams cluster_edge_betweenness #' @keywords internal @@ -198,7 +198,7 @@ edge.betweenness.community <- function(graph, weights = NULL, directed = TRUE, e #' @description #' `r lifecycle::badge("deprecated")` #' -#' `dendPlot()` was renamed to `plot_dendrogram()` to create a more +#' `dendPlot()` was renamed to [plot_dendrogram()] to create a more #' consistent API. #' @inheritParams plot_dendrogram #' @keywords internal @@ -213,7 +213,7 @@ dendPlot <- function(x, mode = igraph_opt("dend.plot.type"), ...) { # nocov star #' @description #' `r lifecycle::badge("deprecated")` #' -#' `cutat()` was renamed to `cut_at()` to create a more +#' `cutat()` was renamed to [cut_at()] to create a more #' consistent API. #' @inheritParams cut_at #' @keywords internal @@ -228,7 +228,7 @@ cutat <- function(communities, no, steps) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `contract.vertices()` was renamed to `contract()` to create a more +#' `contract.vertices()` was renamed to [contract()] to create a more #' consistent API. #' @inheritParams contract #' @keywords internal @@ -243,7 +243,7 @@ contract.vertices <- function(graph, mapping, vertex.attr.comb = igraph_opt("ver #' @description #' `r lifecycle::badge("deprecated")` #' -#' `code.length()` was renamed to `code_len()` to create a more +#' `code.length()` was renamed to [code_len()] to create a more #' consistent API. #' @inheritParams code_len #' @keywords internal diff --git a/R/components.R b/R/components.R index 991cee4f5f..b41e9ec1b2 100644 --- a/R/components.R +++ b/R/components.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `no.clusters()` was renamed to `count_components()` to create a more +#' `no.clusters()` was renamed to [count_components()] to create a more #' consistent API. #' @inheritParams count_components #' @keywords internal @@ -18,7 +18,7 @@ no.clusters <- function(graph, mode = c("weak", "strong")) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `decompose.graph()` was renamed to `decompose()` to create a more +#' `decompose.graph()` was renamed to [decompose()] to create a more #' consistent API. #' @inheritParams decompose #' @keywords internal @@ -33,7 +33,7 @@ decompose.graph <- function(graph, mode = c("weak", "strong"), max.comps = NA, m #' @description #' `r lifecycle::badge("deprecated")` #' -#' `cluster.distribution()` was renamed to `component_distribution()` to create a more +#' `cluster.distribution()` was renamed to [component_distribution()] to create a more #' consistent API. #' @inheritParams component_distribution #' @keywords internal @@ -48,7 +48,7 @@ cluster.distribution <- function(graph, cumulative = FALSE, mul.size = FALSE, .. #' @description #' `r lifecycle::badge("deprecated")` #' -#' `biconnected.components()` was renamed to `biconnected_components()` to create a more +#' `biconnected.components()` was renamed to [biconnected_components()] to create a more #' consistent API. #' @inheritParams biconnected_components #' @keywords internal @@ -63,7 +63,7 @@ biconnected.components <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `articulation.points()` was renamed to `articulation_points()` to create a more +#' `articulation.points()` was renamed to [articulation_points()] to create a more #' consistent API. #' @inheritParams articulation_points #' @keywords internal diff --git a/R/console.R b/R/console.R index 43796e8b16..de57f5813c 100644 --- a/R/console.R +++ b/R/console.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.console()` was renamed to `console()` to create a more +#' `igraph.console()` was renamed to [console()] to create a more #' consistent API. #' #' @keywords internal diff --git a/R/conversion.R b/R/conversion.R index b68a3975df..6a9664ff61 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.to.graphNEL()` was renamed to `as_graphnel()` to create a more +#' `igraph.to.graphNEL()` was renamed to [as_graphnel()] to create a more #' consistent API. #' @inheritParams as_graphnel #' @keywords internal @@ -18,7 +18,7 @@ igraph.to.graphNEL <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.from.graphNEL()` was renamed to `graph_from_graphnel()` to create a more +#' `igraph.from.graphNEL()` was renamed to [graph_from_graphnel()] to create a more #' consistent API. #' @inheritParams graph_from_graphnel #' @keywords internal @@ -33,7 +33,7 @@ igraph.from.graphNEL <- function(graphNEL, name = TRUE, weight = TRUE, unlist.at #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.adjlist()` was renamed to `graph_from_adj_list()` to create a more +#' `graph.adjlist()` was renamed to [graph_from_adj_list()] to create a more #' consistent API. #' @inheritParams graph_from_adj_list #' @keywords internal @@ -48,7 +48,7 @@ graph.adjlist <- function(adjlist, mode = c("out", "in", "all", "total"), duplic #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.incidence()` was renamed to `as_biadjacency_matrix()` to create a more +#' `get.incidence()` was renamed to [as_biadjacency_matrix()] to create a more #' consistent API. #' @inheritParams as_biadjacency_matrix #' @keywords internal @@ -63,7 +63,7 @@ get.incidence <- function(graph, types = NULL, attr = NULL, names = TRUE, sparse #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.edgelist()` was renamed to `as_edgelist()` to create a more +#' `get.edgelist()` was renamed to [as_edgelist()] to create a more #' consistent API. #' @inheritParams as_edgelist #' @keywords internal @@ -78,7 +78,7 @@ get.edgelist <- function(graph, names = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.data.frame()` was renamed to `as_data_frame()` to create a more +#' `get.data.frame()` was renamed to [as_data_frame()] to create a more #' consistent API. #' @inheritParams as_data_frame #' @keywords internal @@ -93,7 +93,7 @@ get.data.frame <- function(x, what = c("edges", "vertices", "both")) { # nocov s #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.adjacency()` was renamed to `as_adjacency_matrix()` to create a more +#' `get.adjacency()` was renamed to [as_adjacency_matrix()] to create a more #' consistent API. #' @inheritParams as_adjacency_matrix #' @keywords internal @@ -108,7 +108,7 @@ get.adjacency <- function(graph, type = c("both", "upper", "lower"), attr = NULL #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.adjlist()` was renamed to `as_adj_list()` to create a more +#' `get.adjlist()` was renamed to [as_adj_list()] to create a more #' consistent API. #' @inheritParams as_adj_list #' @keywords internal @@ -123,7 +123,7 @@ get.adjlist <- function(graph, mode = c("all", "out", "in", "total"), loops = c( #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.adjedgelist()` was renamed to `as_adj_edge_list()` to create a more +#' `get.adjedgelist()` was renamed to [as_adj_edge_list()] to create a more #' consistent API. #' @inheritParams as_adj_edge_list #' @keywords internal @@ -995,7 +995,7 @@ as_biadjacency_matrix <- function(graph, types = NULL, attr = NULL, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `as_incidence_matrix()` was renamed to `as_biadjacency_matrix()` to create a more +#' `as_incidence_matrix()` was renamed to [as_biadjacency_matrix()] to create a more #' consistent API. #' @inheritParams as_biadjacency_matrix #' @keywords internal @@ -1174,7 +1174,7 @@ as_long_data_frame <- function(graph) { #' [as_adjacency_matrix()] or [as_edgelist()] #' depending on the value of `matrix.type`. #' -#' @param x object of class igraph, the network +#' @param x object of class `igraph`, the network #' @param matrix.type character, type of matrix to return, currently "adjacency" #' or "edgelist" are supported #' @param \dots other arguments to/from other methods @@ -1205,7 +1205,7 @@ as.matrix.igraph <- function(x, matrix.type = c("adjacency", "edgelist"), ...) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `as.directed()` was renamed to `as_directed()` to create a more +#' `as.directed()` was renamed to [as_directed()] to create a more #' consistent API. #' @inheritParams as_directed #' @keywords internal @@ -1220,7 +1220,7 @@ as.directed <- function(graph, mode = c("mutual", "arbitrary", "random", "acycli #' @description #' `r lifecycle::badge("deprecated")` #' -#' `as.undirected()` was renamed to `as_undirected()` to create a more +#' `as.undirected()` was renamed to [as_undirected()] to create a more #' consistent API. #' @inheritParams as_undirected #' @keywords internal @@ -1237,7 +1237,7 @@ as.undirected <- function(graph, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.edgelist()` was renamed to `graph_from_edgelist()` to create a more +#' `graph.edgelist()` was renamed to [graph_from_edgelist()] to create a more #' consistent API. #' @inheritParams graph_from_edgelist #' @keywords internal @@ -1252,7 +1252,7 @@ graph.edgelist <- function(el, directed = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.data.frame()` was renamed to `graph_from_data_frame()` to create a more +#' `graph.data.frame()` was renamed to [graph_from_data_frame()] to create a more #' consistent API. #' @inheritParams graph_from_data_frame #' @keywords internal diff --git a/R/decomposition.R b/R/decomposition.R index 2d75038e6f..50cbc36d06 100644 --- a/R/decomposition.R +++ b/R/decomposition.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.chordal()` was renamed to `is_chordal()` to create a more +#' `is.chordal()` was renamed to [is_chordal()] to create a more #' consistent API. #' @inheritParams is_chordal #' @keywords internal diff --git a/R/degseq.R b/R/degseq.R index 2e7943fac4..f0856e8c44 100644 --- a/R/degseq.R +++ b/R/degseq.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.graphical.degree.sequence()` was renamed to `is_graphical()` to create a more +#' `is.graphical.degree.sequence()` was renamed to [is_graphical()] to create a more #' consistent API. #' @inheritParams is_graphical #' @keywords internal @@ -18,7 +18,7 @@ is.graphical.degree.sequence <- function(out.deg, in.deg = NULL, allowed.edge.ty #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.degree.sequence()` was renamed to `is_degseq()` to create a more +#' `is.degree.sequence()` was renamed to [is_degseq()] to create a more #' consistent API. #' @inheritParams is_degseq #' @keywords internal diff --git a/R/demo.R b/R/demo.R index f1fee96a56..50b5bcfb26 100644 --- a/R/demo.R +++ b/R/demo.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraphdemo()` was renamed to `igraph_demo()` to create a more +#' `igraphdemo()` was renamed to [igraph_demo()] to create a more #' consistent API. #' @inheritParams igraph_demo #' @keywords internal diff --git a/R/fit.R b/R/fit.R index bf9202012b..c8074de02d 100644 --- a/R/fit.R +++ b/R/fit.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `power.law.fit()` was renamed to `fit_power_law()` to create a more +#' `power.law.fit()` was renamed to [fit_power_law()] to create a more #' consistent API. #' @inheritParams fit_power_law #' @keywords internal diff --git a/R/flow.R b/R/flow.R index 5746bd1b42..f3eba12091 100644 --- a/R/flow.R +++ b/R/flow.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `vertex.disjoint.paths()` was renamed to `vertex_disjoint_paths()` to create a more +#' `vertex.disjoint.paths()` was renamed to [vertex_disjoint_paths()] to create a more #' consistent API. #' @inheritParams vertex_disjoint_paths #' @keywords internal @@ -18,7 +18,7 @@ vertex.disjoint.paths <- function(graph, source = NULL, target = NULL) { # nocov #' @description #' `r lifecycle::badge("deprecated")` #' -#' `vertex.connectivity()` was renamed to `vertex_connectivity()` to create a more +#' `vertex.connectivity()` was renamed to [vertex_connectivity()] to create a more #' consistent API. #' @inheritParams vertex_connectivity #' @keywords internal @@ -33,7 +33,7 @@ vertex.connectivity <- function(graph, source = NULL, target = NULL, checks = TR #' @description #' `r lifecycle::badge("deprecated")` #' -#' `stMincuts()` was renamed to `st_min_cuts()` to create a more +#' `stMincuts()` was renamed to [st_min_cuts()] to create a more #' consistent API. #' @inheritParams st_min_cuts #' @keywords internal @@ -48,7 +48,7 @@ stMincuts <- function(graph, source, target, capacity = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `stCuts()` was renamed to `st_cuts()` to create a more +#' `stCuts()` was renamed to [st_cuts()] to create a more #' consistent API. #' @inheritParams st_cuts #' @keywords internal @@ -63,7 +63,7 @@ stCuts <- function(graph, source, target) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `minimum.size.separators()` was renamed to `min_separators()` to create a more +#' `minimum.size.separators()` was renamed to [min_separators()] to create a more #' consistent API. #' @inheritParams min_separators #' @keywords internal @@ -78,7 +78,7 @@ minimum.size.separators <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `minimal.st.separators()` was renamed to `min_st_separators()` to create a more +#' `minimal.st.separators()` was renamed to [min_st_separators()] to create a more #' consistent API. #' @inheritParams min_st_separators #' @keywords internal @@ -93,7 +93,7 @@ minimal.st.separators <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.separator()` was renamed to `is_separator()` to create a more +#' `is.separator()` was renamed to [is_separator()] to create a more #' consistent API. #' @inheritParams is_separator #' @keywords internal @@ -108,7 +108,7 @@ is.separator <- function(graph, candidate) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.minimal.separator()` was renamed to `is_min_separator()` to create a more +#' `is.minimal.separator()` was renamed to [is_min_separator()] to create a more #' consistent API. #' @inheritParams is_min_separator #' @keywords internal @@ -123,7 +123,7 @@ is.minimal.separator <- function(graph, candidate) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.mincut()` was renamed to `min_cut()` to create a more +#' `graph.mincut()` was renamed to [min_cut()] to create a more #' consistent API. #' @inheritParams min_cut #' @keywords internal @@ -138,7 +138,7 @@ graph.mincut <- function(graph, source = NULL, target = NULL, capacity = NULL, v #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.maxflow()` was renamed to `max_flow()` to create a more +#' `graph.maxflow()` was renamed to [max_flow()] to create a more #' consistent API. #' @inheritParams max_flow #' @keywords internal @@ -153,7 +153,7 @@ graph.maxflow <- function(graph, source, target, capacity = NULL) { # nocov star #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.adhesion()` was renamed to `adhesion()` to create a more +#' `graph.adhesion()` was renamed to [adhesion()] to create a more #' consistent API. #' @inheritParams adhesion #' @keywords internal @@ -168,7 +168,7 @@ graph.adhesion <- function(graph, checks = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `edge.disjoint.paths()` was renamed to `edge_connectivity()` to create a more +#' `edge.disjoint.paths()` was renamed to [edge_connectivity()] to create a more #' consistent API. #' @inheritParams edge_connectivity #' @keywords internal @@ -183,7 +183,7 @@ edge.disjoint.paths <- function(graph, source = NULL, target = NULL, checks = TR #' @description #' `r lifecycle::badge("deprecated")` #' -#' `edge.connectivity()` was renamed to `edge_connectivity()` to create a more +#' `edge.connectivity()` was renamed to [edge_connectivity()] to create a more #' consistent API. #' @inheritParams edge_connectivity #' @keywords internal @@ -198,7 +198,7 @@ edge.connectivity <- function(graph, source = NULL, target = NULL, checks = TRUE #' @description #' `r lifecycle::badge("deprecated")` #' -#' `dominator.tree()` was renamed to `dominator_tree()` to create a more +#' `dominator.tree()` was renamed to [dominator_tree()] to create a more #' consistent API. #' @inheritParams dominator_tree #' @keywords internal diff --git a/R/foreign.R b/R/foreign.R index 109be777a5..0b1f47f3c4 100644 --- a/R/foreign.R +++ b/R/foreign.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `write.graph()` was renamed to `write_graph()` to create a more +#' `write.graph()` was renamed to [write_graph()] to create a more #' consistent API. #' @inheritParams write_graph #' @keywords internal @@ -18,7 +18,7 @@ write.graph <- function(graph, file, format = c("edgelist", "pajek", "ncol", "lg #' @description #' `r lifecycle::badge("deprecated")` #' -#' `read.graph()` was renamed to `read_graph()` to create a more +#' `read.graph()` was renamed to [read_graph()] to create a more #' consistent API. #' @inheritParams read_graph #' @keywords internal @@ -33,7 +33,7 @@ read.graph <- function(file, format = c("edgelist", "pajek", "ncol", "lgl", "gra #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.graphdb()` was renamed to `graph_from_graphdb()` to create a more +#' `graph.graphdb()` was renamed to [graph_from_graphdb()] to create a more #' consistent API. #' @inheritParams graph_from_graphdb #' @keywords internal diff --git a/R/games.R b/R/games.R index 20a49a3366..d37d5eefec 100644 --- a/R/games.R +++ b/R/games.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `watts.strogatz.game()` was renamed to `sample_smallworld()` to create a more +#' `watts.strogatz.game()` was renamed to [sample_smallworld()] to create a more #' consistent API. #' @inheritParams sample_smallworld #' @keywords internal @@ -18,7 +18,7 @@ watts.strogatz.game <- function(dim, size, nei, p, loops = FALSE, multiple = FAL #' @description #' `r lifecycle::badge("deprecated")` #' -#' `static.power.law.game()` was renamed to `sample_fitness_pl()` to create a more +#' `static.power.law.game()` was renamed to [sample_fitness_pl()] to create a more #' consistent API. #' @inheritParams sample_fitness_pl #' @keywords internal @@ -33,7 +33,7 @@ static.power.law.game <- function(no.of.nodes, no.of.edges, exponent.out, expone #' @description #' `r lifecycle::badge("deprecated")` #' -#' `static.fitness.game()` was renamed to `sample_fitness()` to create a more +#' `static.fitness.game()` was renamed to [sample_fitness()] to create a more #' consistent API. #' @inheritParams sample_fitness #' @keywords internal @@ -48,7 +48,7 @@ static.fitness.game <- function(no.of.edges, fitness.out, fitness.in = NULL, loo #' @description #' `r lifecycle::badge("deprecated")` #' -#' `sbm.game()` was renamed to `sample_sbm()` to create a more +#' `sbm.game()` was renamed to [sample_sbm()] to create a more #' consistent API. #' @inheritParams sample_sbm #' @keywords internal @@ -63,7 +63,7 @@ sbm.game <- function(n, pref.matrix, block.sizes, directed = FALSE, loops = FALS #' @description #' `r lifecycle::badge("deprecated")` #' -#' `preference.game()` was renamed to `sample_pref()` to create a more +#' `preference.game()` was renamed to [sample_pref()] to create a more #' consistent API. #' @inheritParams sample_pref #' @keywords internal @@ -78,7 +78,7 @@ preference.game <- function(nodes, types, type.dist = rep(1, types), fixed.sizes #' @description #' `r lifecycle::badge("deprecated")` #' -#' `lastcit.game()` was renamed to `sample_last_cit()` to create a more +#' `lastcit.game()` was renamed to [sample_last_cit()] to create a more #' consistent API. #' @inheritParams sample_last_cit #' @keywords internal @@ -93,7 +93,7 @@ lastcit.game <- function(n, edges = 1, agebins = n / 7100, pref = (1:(agebins + #' @description #' `r lifecycle::badge("deprecated")` #' -#' `k.regular.game()` was renamed to `sample_k_regular()` to create a more +#' `k.regular.game()` was renamed to [sample_k_regular()] to create a more #' consistent API. #' @inheritParams sample_k_regular #' @keywords internal @@ -108,7 +108,7 @@ k.regular.game <- function(no.of.nodes, k, directed = FALSE, multiple = FALSE) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `interconnected.islands.game()` was renamed to `sample_islands()` to create a more +#' `interconnected.islands.game()` was renamed to [sample_islands()] to create a more #' consistent API. #' @inheritParams sample_islands #' @keywords internal @@ -123,7 +123,7 @@ interconnected.islands.game <- function(islands.n, islands.size, islands.pin, n. #' @description #' `r lifecycle::badge("deprecated")` #' -#' `grg.game()` was renamed to `sample_grg()` to create a more +#' `grg.game()` was renamed to [sample_grg()] to create a more #' consistent API. #' @inheritParams sample_grg #' @keywords internal @@ -138,7 +138,7 @@ grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) { # nocov sta #' @description #' `r lifecycle::badge("deprecated")` #' -#' `growing.random.game()` was renamed to `sample_growing()` to create a more +#' `growing.random.game()` was renamed to [sample_growing()] to create a more #' consistent API. #' @inheritParams sample_growing #' @keywords internal @@ -153,7 +153,7 @@ growing.random.game <- function(n, m = 1, directed = TRUE, citation = FALSE) { # #' @description #' `r lifecycle::badge("deprecated")` #' -#' `forest.fire.game()` was renamed to `sample_forestfire()` to create a more +#' `forest.fire.game()` was renamed to [sample_forestfire()] to create a more #' consistent API. #' @inheritParams sample_forestfire #' @keywords internal @@ -168,7 +168,7 @@ forest.fire.game <- function(nodes, fw.prob, bw.factor = 1, ambs = 1, directed = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `establishment.game()` was renamed to `sample_traits()` to create a more +#' `establishment.game()` was renamed to [sample_traits()] to create a more #' consistent API. #' @inheritParams sample_traits #' @keywords internal @@ -183,7 +183,7 @@ establishment.game <- function(nodes, types, k = 1, type.dist = rep(1, types), p #' @description #' `r lifecycle::badge("deprecated")` #' -#' `degree.sequence.game()` was renamed to `sample_degseq()` to create a more +#' `degree.sequence.game()` was renamed to [sample_degseq()] to create a more #' consistent API. #' @inheritParams sample_degseq #' @keywords internal @@ -198,7 +198,7 @@ degree.sequence.game <- function(out.deg, in.deg = NULL, method = c("simple", "v #' @description #' `r lifecycle::badge("deprecated")` #' -#' `connect.neighborhood()` was renamed to `connect()` to create a more +#' `connect.neighborhood()` was renamed to [connect()] to create a more #' consistent API. #' @inheritParams connect #' @keywords internal @@ -213,7 +213,7 @@ connect.neighborhood <- function(graph, order, mode = c("all", "out", "in", "tot #' @description #' `r lifecycle::badge("deprecated")` #' -#' `citing.cited.type.game()` was renamed to `sample_cit_cit_types()` to create a more +#' `citing.cited.type.game()` was renamed to [sample_cit_cit_types()] to create a more #' consistent API. #' @inheritParams sample_cit_cit_types #' @keywords internal @@ -228,7 +228,7 @@ citing.cited.type.game <- function(n, edges = 1, types = rep(0, n), pref = matri #' @description #' `r lifecycle::badge("deprecated")` #' -#' `cited.type.game()` was renamed to `sample_cit_types()` to create a more +#' `cited.type.game()` was renamed to [sample_cit_types()] to create a more #' consistent API. #' @inheritParams sample_cit_types #' @keywords internal @@ -243,7 +243,7 @@ cited.type.game <- function(n, edges = 1, types = rep(0, n), pref = rep(1, lengt #' @description #' `r lifecycle::badge("deprecated")` #' -#' `callaway.traits.game()` was renamed to `sample_traits_callaway()` to create a more +#' `callaway.traits.game()` was renamed to [sample_traits_callaway()] to create a more #' consistent API. #' @inheritParams sample_traits_callaway #' @keywords internal @@ -258,7 +258,7 @@ callaway.traits.game <- function(nodes, types, edge.per.step = 1, type.dist = re #' @description #' `r lifecycle::badge("deprecated")` #' -#' `bipartite.random.game()` was renamed to `sample_bipartite()` to create a more +#' `bipartite.random.game()` was renamed to [sample_bipartite()] to create a more #' consistent API. #' @inheritParams sample_bipartite #' @keywords internal @@ -276,7 +276,7 @@ bipartite.random.game <- function(n1, n2, type = c("gnp", "gnm"), p, m, directed #' @description #' `r lifecycle::badge("deprecated")` #' -#' `barabasi.game()` was renamed to `sample_pa()` to create a more +#' `barabasi.game()` was renamed to [sample_pa()] to create a more #' consistent API. #' @inheritParams sample_pa #' @keywords internal @@ -291,7 +291,7 @@ barabasi.game <- function(n, power = 1, m = NULL, out.dist = NULL, out.seq = NUL #' @description #' `r lifecycle::badge("deprecated")` #' -#' `ba.game()` was renamed to `sample_pa()` to create a more +#' `ba.game()` was renamed to [sample_pa()] to create a more #' consistent API. #' @inheritParams sample_pa #' @keywords internal @@ -306,7 +306,7 @@ ba.game <- function(n, power = 1, m = NULL, out.dist = NULL, out.seq = NULL, out #' @description #' `r lifecycle::badge("deprecated")` #' -#' `asymmetric.preference.game()` was renamed to `sample_asym_pref()` to create a more +#' `asymmetric.preference.game()` was renamed to [sample_asym_pref()] to create a more #' consistent API. #' @inheritParams sample_asym_pref #' @keywords internal @@ -321,7 +321,7 @@ asymmetric.preference.game <- function(nodes, types, type.dist.matrix = matrix(1 #' @description #' `r lifecycle::badge("deprecated")` #' -#' `aging.barabasi.game()` was renamed to `sample_pa_age()` to create a more +#' `aging.barabasi.game()` was renamed to [sample_pa_age()] to create a more #' consistent API. #' @inheritParams sample_pa_age #' @keywords internal @@ -336,7 +336,7 @@ aging.barabasi.game <- function(n, pa.exp, aging.exp, m = NULL, aging.bin = 300, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `aging.ba.game()` was renamed to `sample_pa_age()` to create a more +#' `aging.ba.game()` was renamed to [sample_pa_age()] to create a more #' consistent API. #' @inheritParams sample_pa_age #' @keywords internal @@ -351,7 +351,7 @@ aging.ba.game <- function(n, pa.exp, aging.exp, m = NULL, aging.bin = 300, out.d #' @description #' `r lifecycle::badge("deprecated")` #' -#' `aging.prefatt.game()` was renamed to `sample_pa_age()` to create a more +#' `aging.prefatt.game()` was renamed to [sample_pa_age()] to create a more #' consistent API. #' @inheritParams sample_pa_age #' @keywords internal @@ -1707,7 +1707,7 @@ cit_cit_types <- function(...) constructor_spec(sample_cit_cit_types, ...) #' Bipartite random graphs #' #' `r lifecycle::badge("deprecated")` Generate bipartite graphs using the Erdős-Rényi model. -#' Use [`sample_bipartite_gnm()`] and [`sample_bipartite_gnp()`] instead. +#' Use [sample_bipartite_gnm()] and [sample_bipartite_gnp()] instead. #' #' @param n1 Integer scalar, the number of bottom vertices. #' @param n2 Integer scalar, the number of top vertices. diff --git a/R/glet.R b/R/glet.R index e96e6dec20..2b755f259e 100644 --- a/R/glet.R +++ b/R/glet.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graphlets.project()` was renamed to `graphlet_proj()` to create a more +#' `graphlets.project()` was renamed to [graphlet_proj()] to create a more #' consistent API. #' @inheritParams graphlet_proj #' @keywords internal @@ -18,7 +18,7 @@ graphlets.project <- function(graph, weights = NULL, cliques, niter = 1000, Mu = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graphlets.candidate.basis()` was renamed to `graphlet_basis()` to create a more +#' `graphlets.candidate.basis()` was renamed to [graphlet_basis()] to create a more #' consistent API. #' @inheritParams graphlet_basis #' @keywords internal diff --git a/R/hrg.R b/R/hrg.R index 76431457bd..6a00790472 100644 --- a/R/hrg.R +++ b/R/hrg.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.predict()` was renamed to `predict_edges()` to create a more +#' `hrg.predict()` was renamed to [predict_edges()] to create a more #' consistent API. #' @inheritParams predict_edges #' @keywords internal @@ -18,7 +18,7 @@ hrg.predict <- function(graph, hrg = NULL, start = FALSE, num.samples = 10000, n #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.fit()` was renamed to `fit_hrg()` to create a more +#' `hrg.fit()` was renamed to [fit_hrg()] to create a more #' consistent API. #' @inheritParams fit_hrg #' @keywords internal @@ -33,7 +33,7 @@ hrg.fit <- function(graph, hrg = NULL, start = FALSE, steps = 0) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.game()` was renamed to `sample_hrg()` to create a more +#' `hrg.game()` was renamed to [sample_hrg()] to create a more #' consistent API. #' @inheritParams sample_hrg #' @keywords internal @@ -48,7 +48,7 @@ hrg.game <- function(hrg) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.dendrogram()` was renamed to `hrg_tree()` to create a more +#' `hrg.dendrogram()` was renamed to [hrg_tree()] to create a more #' consistent API. #' @inheritParams hrg_tree #' @keywords internal @@ -63,7 +63,7 @@ hrg.dendrogram <- function(hrg) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.create()` was renamed to `hrg()` to create a more +#' `hrg.create()` was renamed to [hrg()] to create a more #' consistent API. #' @inheritParams hrg #' @keywords internal @@ -78,7 +78,7 @@ hrg.create <- function(graph, prob) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `hrg.consensus()` was renamed to `consensus_tree()` to create a more +#' `hrg.consensus()` was renamed to [consensus_tree()] to create a more #' consistent API. #' @inheritParams consensus_tree #' @keywords internal diff --git a/R/incidence.R b/R/incidence.R index dd1118b735..de08219b99 100644 --- a/R/incidence.R +++ b/R/incidence.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.incidence()` was renamed to `graph_from_biadjacency_matrix()` to create a more +#' `graph.incidence()` was renamed to [graph_from_biadjacency_matrix()] to create a more #' consistent API. #' @inheritParams graph_from_biadjacency_matrix #' @keywords internal @@ -228,7 +228,7 @@ graph_from_biadjacency_matrix <- function(incidence, directed = FALSE, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph_from_incidence_matrix()` was renamed to `graph_from_biadjacency_matrix()` to create a more +#' `graph_from_incidence_matrix()` was renamed to [graph_from_biadjacency_matrix()] to create a more #' consistent API. #' @inheritParams graph_from_biadjacency_matrix #' @keywords internal @@ -246,7 +246,7 @@ from_incidence_matrix <- function(...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph_from_incidence_matrix()` was renamed to `graph_from_biadjacency_matrix()` to create a more +#' `graph_from_incidence_matrix()` was renamed to [graph_from_biadjacency_matrix()] to create a more #' consistent API. #' @inheritParams graph_from_biadjacency_matrix #' @keywords internal diff --git a/R/interface.R b/R/interface.R index 687f45a9fa..3c18f9aa27 100644 --- a/R/interface.R +++ b/R/interface.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.directed()` was renamed to `is_directed()` to create a more +#' `is.directed()` was renamed to [is_directed()] to create a more #' consistent API. #' @inheritParams is_directed #' @keywords internal @@ -18,7 +18,7 @@ is.directed <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `delete.vertices()` was renamed to `delete_vertices()` to create a more +#' `delete.vertices()` was renamed to [delete_vertices()] to create a more #' consistent API. #' @inheritParams delete_vertices #' @keywords internal @@ -33,7 +33,7 @@ delete.vertices <- function(graph, v) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `delete.edges()` was renamed to `delete_edges()` to create a more +#' `delete.edges()` was renamed to [delete_edges()] to create a more #' consistent API. #' @inheritParams delete_edges #' @keywords internal @@ -48,7 +48,7 @@ delete.edges <- function(graph, edges) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `add.vertices()` was renamed to `add_vertices()` to create a more +#' `add.vertices()` was renamed to [add_vertices()] to create a more #' consistent API. #' @inheritParams add_vertices #' @keywords internal @@ -63,7 +63,7 @@ add.vertices <- function(graph, nv, ..., attr = list()) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `add.edges()` was renamed to `add_edges()` to create a more +#' `add.edges()` was renamed to [add_edges()] to create a more #' consistent API. #' @inheritParams add_edges #' @keywords internal @@ -568,7 +568,7 @@ get_edge_ids <- function(graph, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.edge.ids()` was renamed to `get_edge_ids()` to create a more +#' `get.edge.ids()` was renamed to [get_edge_ids()] to create a more #' consistent API. #' @inheritParams get_edge_ids #' @param multi diff --git a/R/layout.R b/R/layout.R index fb2feef744..fec85d8067 100644 --- a/R/layout.R +++ b/R/layout.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `piecewise.layout()` was renamed to `layout_components()` to create a more +#' `piecewise.layout()` was renamed to [layout_components()] to create a more #' consistent API. #' @inheritParams layout_components #' @keywords internal @@ -18,7 +18,7 @@ piecewise.layout <- function(graph, layout = layout_with_kk, ...) { # nocov star #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.sugiyama()` was renamed to `layout_with_sugiyama()` to create a more +#' `layout.sugiyama()` was renamed to [layout_with_sugiyama()] to create a more #' consistent API. #' @inheritParams layout_with_sugiyama #' @keywords internal @@ -33,7 +33,7 @@ layout.sugiyama <- function(graph, layers = NULL, hgap = 1, vgap = 1, maxiter = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.star()` was renamed to `layout_as_star()` to create a more +#' `layout.star()` was renamed to [layout_as_star()] to create a more #' consistent API. #' @inheritParams layout_as_star #' @keywords internal @@ -48,7 +48,7 @@ layout.star <- function(graph, center = V(graph)[1], order = NULL) { # nocov sta #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.norm()` was renamed to `norm_coords()` to create a more +#' `layout.norm()` was renamed to [norm_coords()] to create a more #' consistent API. #' @inheritParams norm_coords #' @keywords internal @@ -63,7 +63,7 @@ layout.norm <- function(layout, xmin = -1, xmax = 1, ymin = -1, ymax = 1, zmin = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.merge()` was renamed to `merge_coords()` to create a more +#' `layout.merge()` was renamed to [merge_coords()] to create a more #' consistent API. #' @inheritParams merge_coords #' @keywords internal @@ -78,7 +78,7 @@ layout.merge <- function(graphs, layouts, method = "dla") { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.mds()` was renamed to `layout_with_mds()` to create a more +#' `layout.mds()` was renamed to [layout_with_mds()] to create a more #' consistent API. #' @inheritParams layout_with_mds #' @keywords internal @@ -93,7 +93,7 @@ layout.mds <- function(graph, dist = NULL, dim = 2, options = arpack_defaults()) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.grid()` was renamed to `layout_on_grid()` to create a more +#' `layout.grid()` was renamed to [layout_on_grid()] to create a more #' consistent API. #' @inheritParams layout_on_grid #' @keywords internal @@ -108,7 +108,7 @@ layout.grid <- function(graph, width = 0, height = 0, dim = 2) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.graphopt()` was renamed to `layout_with_graphopt()` to create a more +#' `layout.graphopt()` was renamed to [layout_with_graphopt()] to create a more #' consistent API. #' @inheritParams layout_with_graphopt #' @keywords internal @@ -123,7 +123,7 @@ layout.graphopt <- function(graph, start = NULL, niter = 500, charge = 0.001, ma #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.gem()` was renamed to `layout_with_gem()` to create a more +#' `layout.gem()` was renamed to [layout_with_gem()] to create a more #' consistent API. #' @inheritParams layout_with_gem #' @keywords internal @@ -138,7 +138,7 @@ layout.gem <- function(graph, coords = NULL, maxiter = 40 * vcount(graph)^2, tem #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.davidson.harel()` was renamed to `layout_with_dh()` to create a more +#' `layout.davidson.harel()` was renamed to [layout_with_dh()] to create a more #' consistent API. #' @inheritParams layout_with_dh #' @keywords internal @@ -153,7 +153,7 @@ layout.davidson.harel <- function(graph, coords = NULL, maxiter = 10, fineiter = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.bipartite()` was renamed to `layout_as_bipartite()` to create a more +#' `layout.bipartite()` was renamed to [layout_as_bipartite()] to create a more #' consistent API. #' @inheritParams layout_as_bipartite #' @keywords internal @@ -168,7 +168,7 @@ layout.bipartite <- function(graph, types = NULL, hgap = 1, vgap = 1, maxiter = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.auto()` was renamed to `layout_nicely()` to create a more +#' `layout.auto()` was renamed to [layout_nicely()] to create a more #' consistent API. #' @inheritParams layout_nicely #' @keywords internal @@ -638,7 +638,7 @@ as_tree <- function(...) layout_spec(layout_as_tree, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.reingold.tilford()` was renamed to `layout_as_tree()` to create a more +#' `layout.reingold.tilford()` was renamed to [layout_as_tree()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -699,7 +699,7 @@ in_circle <- function(...) layout_spec(layout_in_circle, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.circle()` was renamed to `layout_in_circle()` to create a more +#' `layout.circle()` was renamed to [layout_in_circle()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -929,7 +929,7 @@ on_sphere <- function(...) layout_spec(layout_on_sphere, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.sphere()` was renamed to `layout_on_sphere()` to create a more +#' `layout.sphere()` was renamed to [layout_on_sphere()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -982,7 +982,7 @@ randomly <- function(...) layout_spec(layout_randomly, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.random()` was renamed to `layout_randomly()` to create a more +#' `layout.random()` was renamed to [layout_randomly()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -1306,7 +1306,7 @@ with_fr <- function(...) layout_spec(layout_with_fr, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.fruchterman.reingold()` was renamed to `layout_with_fr()` to create a more +#' `layout.fruchterman.reingold()` was renamed to [layout_with_fr()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -1608,7 +1608,7 @@ with_kk <- function(...) layout_spec(layout_with_kk, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.kamada.kawai()` was renamed to `layout_with_kk()` to create a more +#' `layout.kamada.kawai()` was renamed to [layout_with_kk()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -1679,7 +1679,7 @@ with_lgl <- function(...) layout_spec(layout_with_lgl, ...) #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.lgl()` was renamed to `layout_with_lgl()` to create a more +#' `layout.lgl()` was renamed to [layout_with_lgl()] to create a more #' consistent API. #' @param ... Passed to the new layout functions. #' @param params Passed to the new layout functions as arguments. @@ -2260,7 +2260,7 @@ layout.spring <- function(graph, ...) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' Now it calls the Fruchterman-Reingold layout [`layout_with_fr()`]. +#' Now it calls the Fruchterman-Reingold layout [layout_with_fr()]. #' #' @param graph Input graph. #' @param ... Extra arguments are ignored. @@ -2279,7 +2279,7 @@ layout.svd <- function(graph, ...) { #' `r lifecycle::badge("deprecated")` #' #' -#' Now it calls the Fruchterman-Reingold layout [`layout_with_fr()`]. +#' Now it calls the Fruchterman-Reingold layout [layout_with_fr()]. #' #' @param graph Input graph. #' @param ... Extra arguments are ignored. @@ -2301,7 +2301,7 @@ layout.fruchterman.reingold.grid <- function(graph, ...) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `layout.drl()` was renamed to `layout_with_drl()` to create a more +#' `layout.drl()` was renamed to [layout_with_drl()] to create a more #' consistent API. #' @inheritParams layout_with_drl #' @keywords internal diff --git a/R/make.R b/R/make.R index 29a39fa7aa..b0120999b0 100644 --- a/R/make.R +++ b/R/make.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph()` was renamed to `make_graph()` to create a more +#' `graph()` was renamed to [make_graph()] to create a more #' consistent API. #' @inheritParams make_graph #' @keywords internal @@ -96,7 +96,7 @@ graph <- function(edges, ..., n = max(edges), isolates = NULL, directed = TRUE, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.famous()` was renamed to `make_graph()` to create a more +#' `graph.famous()` was renamed to [make_graph()] to create a more #' consistent API. #' @inheritParams make_graph #' @keywords internal @@ -189,7 +189,7 @@ graph.famous <- function(edges, ..., n = max(edges), isolates = NULL, directed = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `line.graph()` was renamed to `make_line_graph()` to create a more +#' `line.graph()` was renamed to [make_line_graph()] to create a more #' consistent API. #' @inheritParams make_line_graph #' @keywords internal @@ -211,7 +211,7 @@ line.graph <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.ring()` was renamed to `make_ring()` to create a more +#' `graph.ring()` was renamed to [make_ring()] to create a more #' consistent API. #' @inheritParams make_ring #' @keywords internal @@ -236,7 +236,7 @@ graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) { # #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.tree()` was renamed to `make_tree()` to create a more +#' `graph.tree()` was renamed to [make_tree()] to create a more #' consistent API. #' @inheritParams make_tree #' @keywords internal @@ -268,7 +268,7 @@ graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) { # #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.star()` was renamed to `make_star()` to create a more +#' `graph.star()` was renamed to [make_star()] to create a more #' consistent API. #' @inheritParams make_star #' @keywords internal @@ -305,7 +305,7 @@ graph.star <- function(n, mode = c("in", "out", "mutual", "undirected"), center #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.lcf()` was renamed to `graph_from_lcf()` to create a more +#' `graph.lcf()` was renamed to [graph_from_lcf()] to create a more #' consistent API. #' @inheritParams graph_from_lcf #' @keywords internal @@ -333,7 +333,7 @@ graph.lcf <- function(n, shifts, repeats = 1) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.lattice()` was renamed to `make_lattice()` to create a more +#' `graph.lattice()` was renamed to [make_lattice()] to create a more #' consistent API. #' @inheritParams make_lattice #' @keywords internal @@ -385,7 +385,7 @@ graph.lattice <- function(dimvector = NULL, length = NULL, dim = NULL, nei = 1, #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.kautz()` was renamed to `make_kautz_graph()` to create a more +#' `graph.kautz()` was renamed to [make_kautz_graph()] to create a more #' consistent API. #' @inheritParams make_kautz_graph #' @keywords internal @@ -407,7 +407,7 @@ graph.kautz <- function(m, n) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.full.citation()` was renamed to `make_full_citation_graph()` to create a more +#' `graph.full.citation()` was renamed to [make_full_citation_graph()] to create a more #' consistent API. #' @inheritParams make_full_citation_graph #' @keywords internal @@ -431,7 +431,7 @@ graph.full.citation <- function(n, directed = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.full.bipartite()` was renamed to `make_full_bipartite_graph()` to create a more +#' `graph.full.bipartite()` was renamed to [make_full_bipartite_graph()] to create a more #' consistent API. #' @inheritParams make_full_bipartite_graph #' @keywords internal @@ -464,7 +464,7 @@ graph.full.bipartite <- function(n1, n2, directed = FALSE, mode = c("all", "out" #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.full()` was renamed to `make_full_graph()` to create a more +#' `graph.full()` was renamed to [make_full_graph()] to create a more #' consistent API. #' @inheritParams make_full_graph #' @keywords internal @@ -488,7 +488,7 @@ graph.full <- function(n, directed = FALSE, loops = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.formula()` was renamed to `graph_from_literal()` to create a more +#' `graph.formula()` was renamed to [graph_from_literal()] to create a more #' consistent API. #' @inheritParams graph_from_literal #' @keywords internal @@ -504,7 +504,7 @@ graph.formula <- function(..., simplify = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.extended.chordal.ring()` was renamed to `make_chordal_ring()` to create a more +#' `graph.extended.chordal.ring()` was renamed to [make_chordal_ring()] to create a more #' consistent API. #' @inheritParams make_chordal_ring #' @keywords internal @@ -528,7 +528,7 @@ graph.extended.chordal.ring <- function(n, w, directed = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.empty()` was renamed to `make_empty_graph()` to create a more +#' `graph.empty()` was renamed to [make_empty_graph()] to create a more #' consistent API. #' @inheritParams make_empty_graph #' @keywords internal @@ -551,7 +551,7 @@ graph.empty <- function(n = 0, directed = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.de.bruijn()` was renamed to `make_de_bruijn_graph()` to create a more +#' `graph.de.bruijn()` was renamed to [make_de_bruijn_graph()] to create a more #' consistent API. #' @inheritParams make_de_bruijn_graph #' @keywords internal @@ -573,7 +573,7 @@ graph.de.bruijn <- function(m, n) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.bipartite()` was renamed to `make_bipartite_graph()` to create a more +#' `graph.bipartite()` was renamed to [make_bipartite_graph()] to create a more #' consistent API. #' @inheritParams make_bipartite_graph #' @keywords internal @@ -612,7 +612,7 @@ graph.bipartite <- function(types, edges, directed = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.atlas()` was renamed to `graph_from_atlas()` to create a more +#' `graph.atlas()` was renamed to [graph_from_atlas()] to create a more #' consistent API. #' @inheritParams graph_from_atlas #' @keywords internal diff --git a/R/minimum.spanning.tree.R b/R/minimum.spanning.tree.R index e5aa1ef5dc..b151057da7 100644 --- a/R/minimum.spanning.tree.R +++ b/R/minimum.spanning.tree.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `minimum.spanning.tree()` was renamed to `mst()` to create a more +#' `minimum.spanning.tree()` was renamed to [mst()] to create a more #' consistent API. #' @inheritParams mst #' @keywords internal diff --git a/R/motifs.R b/R/motifs.R index 9ec772bb27..4196424073 100644 --- a/R/motifs.R +++ b/R/motifs.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `triad.census()` was renamed to `triad_census()` to create a more +#' `triad.census()` was renamed to [triad_census()] to create a more #' consistent API. #' @inheritParams triad_census #' @keywords internal @@ -18,7 +18,7 @@ triad.census <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.motifs.no()` was renamed to `count_motifs()` to create a more +#' `graph.motifs.no()` was renamed to [count_motifs()] to create a more #' consistent API. #' @inheritParams count_motifs #' @keywords internal @@ -34,7 +34,7 @@ graph.motifs.no <- function(graph, size = 3, cut.prob = rep(0, size)) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.motifs.est()` was renamed to `sample_motifs()` to create a more +#' `graph.motifs.est()` was renamed to [sample_motifs()] to create a more #' consistent API. #' @param cut.prob Numeric vector giving the probabilities that the search #' graph is cut at a certain level. Its length should be the same as the size @@ -53,7 +53,7 @@ graph.motifs.est <- function(graph, size = 3, cut.prob = rep(0, size), sample.si #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.motifs()` was renamed to `motifs()` to create a more +#' `graph.motifs()` was renamed to [motifs()] to create a more #' consistent API. #' @param cut.prob Numeric vector giving the probabilities that the search #' graph is cut at a certain level. Its length should be the same as the size @@ -72,7 +72,7 @@ graph.motifs <- function(graph, size = 3, cut.prob = rep(0, size)) { # nocov sta #' @description #' `r lifecycle::badge("deprecated")` #' -#' `dyad.census()` was renamed to `dyad_census()` to create a more +#' `dyad.census()` was renamed to [dyad_census()] to create a more #' consistent API. #' @inheritParams dyad_census #' @keywords internal diff --git a/R/operators.R b/R/operators.R index 750604dc1c..667596f475 100644 --- a/R/operators.R +++ b/R/operators.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.intersection()` was renamed to `intersection()` to create a more +#' `graph.intersection()` was renamed to [intersection()] to create a more #' consistent API. #' @inheritParams intersection #' @keywords internal @@ -18,7 +18,7 @@ graph.intersection <- function(...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.union()` was renamed to `union.igraph()` to create a more +#' `graph.union()` was renamed to [union.igraph()] to create a more #' consistent API. #' @inheritParams union.igraph #' @keywords internal @@ -33,7 +33,7 @@ graph.union <- function(..., byname = "auto") { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.difference()` was renamed to `difference()` to create a more +#' `graph.difference()` was renamed to [difference()] to create a more #' consistent API. #' @inheritParams difference #' @keywords internal @@ -48,7 +48,7 @@ graph.difference <- function(...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.disjoint.union()` was renamed to `disjoint_union()` to create a more +#' `graph.disjoint.union()` was renamed to [disjoint_union()] to create a more #' consistent API. #' @inheritParams disjoint_union #' @keywords internal @@ -63,7 +63,7 @@ graph.disjoint.union <- function(...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.compose()` was renamed to `compose()` to create a more +#' `graph.compose()` was renamed to [compose()] to create a more #' consistent API. #' @inheritParams compose #' @keywords internal @@ -78,7 +78,7 @@ graph.compose <- function(g1, g2, byname = "auto") { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.complementer()` was renamed to `complementer()` to create a more +#' `graph.complementer()` was renamed to [complementer()] to create a more #' consistent API. #' @inheritParams complementer #' @keywords internal diff --git a/R/other.R b/R/other.R index 983d42d4e9..02d39172f7 100644 --- a/R/other.R +++ b/R/other.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `running.mean()` was renamed to `running_mean()` to create a more +#' `running.mean()` was renamed to [running_mean()] to create a more #' consistent API. #' @inheritParams running_mean #' @keywords internal @@ -18,7 +18,7 @@ running.mean <- function(v, binwidth) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.sample()` was renamed to `sample_seq()` to create a more +#' `igraph.sample()` was renamed to [sample_seq()] to create a more #' consistent API. #' @inheritParams sample_seq #' @keywords internal @@ -33,7 +33,7 @@ igraph.sample <- function(low, high, length) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `convex.hull()` was renamed to `convex_hull()` to create a more +#' `convex.hull()` was renamed to [convex_hull()] to create a more #' consistent API. #' @inheritParams convex_hull #' @keywords internal diff --git a/R/par.R b/R/par.R index 0b37a47d5b..157b0f4557 100644 --- a/R/par.R +++ b/R/par.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.options()` was renamed to `igraph_options()` to create a more +#' `igraph.options()` was renamed to [igraph_options()] to create a more #' consistent API. #' @inheritParams igraph_options #' @keywords internal @@ -18,7 +18,7 @@ igraph.options <- function(...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `getIgraphOpt()` was renamed to `igraph_opt()` to create a more +#' `getIgraphOpt()` was renamed to [igraph_opt()] to create a more #' consistent API. #' @inheritParams igraph_opt #' @keywords internal diff --git a/R/paths.R b/R/paths.R index 79e5d1c1ab..be254799c0 100644 --- a/R/paths.R +++ b/R/paths.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `path.length.hist()` was renamed to `distance_table()` to create a more +#' `path.length.hist()` was renamed to [distance_table()] to create a more #' consistent API. #' @inheritParams distance_table #' @keywords internal @@ -18,7 +18,7 @@ path.length.hist <- function(graph, directed = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximum.cardinality.search()` was renamed to `max_cardinality()` to create a more +#' `maximum.cardinality.search()` was renamed to [max_cardinality()] to create a more #' consistent API. #' @inheritParams max_cardinality #' @keywords internal @@ -33,7 +33,7 @@ maximum.cardinality.search <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.dag()` was renamed to `is_dag()` to create a more +#' `is.dag()` was renamed to [is_dag()] to create a more #' consistent API. #' @inheritParams is_dag #' @keywords internal diff --git a/R/plot.common.R b/R/plot.common.R index 24f5928844..91a56b014e 100644 --- a/R/plot.common.R +++ b/R/plot.common.R @@ -449,7 +449,7 @@ NULL #' @description #' `r lifecycle::badge("deprecated")` #' -#' `autocurve.edges()` was renamed to `curve_multiple()` to create a more +#' `autocurve.edges()` was renamed to [curve_multiple()] to create a more #' consistent API. #' @inheritParams curve_multiple #' @keywords internal diff --git a/R/plot.shapes.R b/R/plot.shapes.R index 685dd7a958..1fafabf0ec 100644 --- a/R/plot.shapes.R +++ b/R/plot.shapes.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.shape.noplot()` was renamed to `shape_noplot()` to create a more +#' `igraph.shape.noplot()` was renamed to [shape_noplot()] to create a more #' consistent API. #' @inheritParams shape_noplot #' @keywords internal @@ -18,7 +18,7 @@ igraph.shape.noplot <- function(coords, v = NULL, params) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.shape.noclip()` was renamed to `shape_noclip()` to create a more +#' `igraph.shape.noclip()` was renamed to [shape_noclip()] to create a more #' consistent API. #' @inheritParams shape_noclip #' @keywords internal @@ -33,7 +33,7 @@ igraph.shape.noclip <- function(coords, el, params, end = c("both", "from", "to" #' @description #' `r lifecycle::badge("deprecated")` #' -#' `vertex.shapes()` was renamed to `shapes()` to create a more +#' `vertex.shapes()` was renamed to [shapes()] to create a more #' consistent API. #' @inheritParams shapes #' @keywords internal @@ -48,7 +48,7 @@ vertex.shapes <- function(shape = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `add.vertex.shape()` was renamed to `add_shape()` to create a more +#' `add.vertex.shape()` was renamed to [add_shape()] to create a more #' consistent API. #' @inheritParams add_shape #' @keywords internal diff --git a/R/similarity.R b/R/similarity.R index 5f1e38e88d..30273dec51 100644 --- a/R/similarity.R +++ b/R/similarity.R @@ -75,7 +75,7 @@ similarity <- function(graph, vids = V(graph), #' @description #' `r lifecycle::badge("deprecated")` #' -#' Please use [`similarity()`] with `method = "jaccard"` instead. +#' Please use [similarity()] with `method = "jaccard"` instead. #' @inheritParams similarity #' @keywords internal #' @export @@ -104,7 +104,7 @@ similarity.jaccard <- function(graph, #' @description #' `r lifecycle::badge("deprecated")` #' -#' Please use [`similarity()`] with `method = "dice"` instead. +#' Please use [similarity()] with `method = "dice"` instead. #' @inheritParams similarity #' @keywords internal #' @export @@ -133,7 +133,7 @@ similarity.dice <- function(graph, #' @description #' `r lifecycle::badge("deprecated")` #' -#' Please use [`similarity()`] with `method = "invlogweighted"` instead. +#' Please use [similarity()] with `method = "invlogweighted"` instead. #' @inheritParams similarity #' @keywords internal #' @export diff --git a/R/simple.R b/R/simple.R index f06f24851a..51037f6f22 100644 --- a/R/simple.R +++ b/R/simple.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.simple()` was renamed to `is_simple()` to create a more +#' `is.simple()` was renamed to [is_simple()] to create a more #' consistent API. #' @inheritParams is_simple #' @keywords internal diff --git a/R/stochastic_matrix.R b/R/stochastic_matrix.R index d5be60bfc1..ef8693bd8a 100644 --- a/R/stochastic_matrix.R +++ b/R/stochastic_matrix.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.stochastic()` was renamed to `stochastic_matrix()` to create a more +#' `get.stochastic()` was renamed to [stochastic_matrix()] to create a more #' consistent API. #' @inheritParams stochastic_matrix #' @keywords internal diff --git a/R/structural-properties.R b/R/structural-properties.R index 44fc17fc58..e133177e7c 100644 --- a/R/structural-properties.R +++ b/R/structural-properties.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.shortest.paths()` was renamed to `shortest_paths()` to create a more +#' `get.shortest.paths()` was renamed to [shortest_paths()] to create a more #' consistent API. #' @inheritParams shortest_paths #' @keywords internal @@ -18,7 +18,7 @@ get.shortest.paths <- function(graph, from, to = V(graph), mode = c("out", "all" #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.all.shortest.paths()` was renamed to `all_shortest_paths()` to create a more +#' `get.all.shortest.paths()` was renamed to [all_shortest_paths()] to create a more #' consistent API. #' @inheritParams all_shortest_paths #' @keywords internal @@ -33,7 +33,7 @@ get.all.shortest.paths <- function(graph, from, to = V(graph), mode = c("out", " #' @description #' `r lifecycle::badge("deprecated")` #' -#' `get.diameter()` was renamed to `get_diameter()` to create a more +#' `get.diameter()` was renamed to [get_diameter()] to create a more #' consistent API. #' @inheritParams get_diameter #' @keywords internal @@ -48,7 +48,7 @@ get.diameter <- function(graph, directed = TRUE, unconnected = TRUE, weights = N #' @description #' `r lifecycle::badge("deprecated")` #' -#' `unfold.tree()` was renamed to `unfold_tree()` to create a more +#' `unfold.tree()` was renamed to [unfold_tree()] to create a more #' consistent API. #' @inheritParams unfold_tree #' @keywords internal @@ -63,7 +63,7 @@ unfold.tree <- function(graph, mode = c("all", "out", "in", "total"), roots) { # #' @description #' `r lifecycle::badge("deprecated")` #' -#' `topological.sort()` was renamed to `topo_sort()` to create a more +#' `topological.sort()` was renamed to [topo_sort()] to create a more #' consistent API. #' @inheritParams topo_sort #' @keywords internal @@ -78,7 +78,7 @@ topological.sort <- function(graph, mode = c("out", "all", "in")) { # nocov star #' @description #' `r lifecycle::badge("deprecated")` #' -#' `shortest.paths()` was renamed to `distances()` to create a more +#' `shortest.paths()` was renamed to [distances()] to create a more #' consistent API. #' @inheritParams distances #' @keywords internal @@ -95,7 +95,7 @@ shortest.paths <- function(graph, v = V(graph), to = V(graph), mode = c("all", " #' @description #' `r lifecycle::badge("deprecated")` #' -#' `neighborhood.size()` was renamed to `ego_size()` to create a more +#' `neighborhood.size()` was renamed to [ego_size()] to create a more #' consistent API. #' @inheritParams ego_size #' @keywords internal @@ -110,7 +110,7 @@ neighborhood.size <- function(graph, order = 1, nodes = V(graph), mode = c("all" #' @description #' `r lifecycle::badge("deprecated")` #' -#' `maximum.bipartite.matching()` was renamed to `max_bipartite_match()` to create a more +#' `maximum.bipartite.matching()` was renamed to [max_bipartite_match()] to create a more #' consistent API. #' @inheritParams max_bipartite_match #' @keywords internal @@ -125,7 +125,7 @@ maximum.bipartite.matching <- function(graph, types = NULL, weights = NULL, eps #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.mutual()` was renamed to `which_mutual()` to create a more +#' `is.mutual()` was renamed to [which_mutual()] to create a more #' consistent API. #' @inheritParams which_mutual #' @keywords internal @@ -140,7 +140,7 @@ is.mutual <- function(graph, eids = E(graph), loops = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.multiple()` was renamed to `which_multiple()` to create a more +#' `is.multiple()` was renamed to [which_multiple()] to create a more #' consistent API. #' @inheritParams which_multiple #' @keywords internal @@ -155,7 +155,7 @@ is.multiple <- function(graph, eids = E(graph)) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.maximal.matching()` was renamed to `is_max_matching()` to create a more +#' `is.maximal.matching()` was renamed to [is_max_matching()] to create a more #' consistent API. #' @inheritParams is_max_matching #' @keywords internal @@ -170,7 +170,7 @@ is.maximal.matching <- function(graph, matching, types = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.matching()` was renamed to `is_matching()` to create a more +#' `is.matching()` was renamed to [is_matching()] to create a more #' consistent API. #' @inheritParams is_matching #' @keywords internal @@ -185,7 +185,7 @@ is.matching <- function(graph, matching, types = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.loop()` was renamed to `which_loop()` to create a more +#' `is.loop()` was renamed to [which_loop()] to create a more #' consistent API. #' @inheritParams which_loop #' @keywords internal @@ -200,7 +200,7 @@ is.loop <- function(graph, eids = E(graph)) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `is.connected()` was renamed to `is_connected()` to create a more +#' `is.connected()` was renamed to [is_connected()] to create a more #' consistent API. #' @inheritParams is_connected #' @keywords internal @@ -215,7 +215,7 @@ is.connected <- function(graph, mode = c("weak", "strong")) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `induced.subgraph()` was renamed to `induced_subgraph()` to create a more +#' `induced.subgraph()` was renamed to [induced_subgraph()] to create a more #' consistent API. #' @inheritParams induced_subgraph #' @keywords internal @@ -230,7 +230,7 @@ induced.subgraph <- function(graph, vids, impl = c("auto", "copy_and_delete", "c #' @description #' `r lifecycle::badge("deprecated")` #' -#' `has.multiple()` was renamed to `any_multiple()` to create a more +#' `has.multiple()` was renamed to [any_multiple()] to create a more #' consistent API. #' @inheritParams any_multiple #' @keywords internal @@ -245,7 +245,7 @@ has.multiple <- function(graph) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.neighborhood()` was renamed to `make_ego_graph()` to create a more +#' `graph.neighborhood()` was renamed to [make_ego_graph()] to create a more #' consistent API. #' @inheritParams make_ego_graph #' @keywords internal @@ -260,7 +260,7 @@ graph.neighborhood <- function(graph, order = 1, nodes = V(graph), mode = c("all #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.laplacian()` was renamed to `laplacian_matrix()` to create a more +#' `graph.laplacian()` was renamed to [laplacian_matrix()] to create a more #' consistent API. #' @inheritParams laplacian_matrix #' @keywords internal @@ -275,7 +275,7 @@ graph.laplacian <- function(graph, normalized = FALSE, weights = NULL, sparse = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.knn()` was renamed to `knn()` to create a more +#' `graph.knn()` was renamed to [knn()] to create a more #' consistent API. #' @inheritParams knn #' @keywords internal @@ -290,7 +290,7 @@ graph.knn <- function(graph, vids = V(graph), mode = c("all", "out", "in", "tota #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.dfs()` was renamed to `dfs()` to create a more +#' `graph.dfs()` was renamed to [dfs()] to create a more #' consistent API. #' @param father Logical scalar, whether to return the father of the vertices. #' @inheritParams dfs @@ -306,7 +306,7 @@ graph.dfs <- function(graph, root, mode = c("out", "in", "all", "total"), unreac #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.density()` was renamed to `edge_density()` to create a more +#' `graph.density()` was renamed to [edge_density()] to create a more #' consistent API. #' @inheritParams edge_density #' @keywords internal @@ -321,7 +321,7 @@ graph.density <- function(graph, loops = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.coreness()` was renamed to `coreness()` to create a more +#' `graph.coreness()` was renamed to [coreness()] to create a more #' consistent API. #' @inheritParams coreness #' @keywords internal @@ -336,7 +336,7 @@ graph.coreness <- function(graph, mode = c("all", "out", "in")) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.bfs()` was renamed to `bfs()` to create a more +#' `graph.bfs()` was renamed to [bfs()] to create a more #' consistent API. #' @inheritParams bfs #' @param father Logical scalar, whether to return the father of the vertices. @@ -352,7 +352,7 @@ graph.bfs <- function(graph, root, mode = c("out", "in", "all", "total"), unreac #' @description #' `r lifecycle::badge("deprecated")` #' -#' `farthest.nodes()` was renamed to `farthest_vertices()` to create a more +#' `farthest.nodes()` was renamed to [farthest_vertices()] to create a more #' consistent API. #' @inheritParams farthest_vertices #' @keywords internal @@ -367,7 +367,7 @@ farthest.nodes <- function(graph, directed = TRUE, unconnected = TRUE, weights = #' @description #' `r lifecycle::badge("deprecated")` #' -#' `degree.distribution()` was renamed to `degree_distribution()` to create a more +#' `degree.distribution()` was renamed to [degree_distribution()] to create a more #' consistent API. #' @inheritParams degree_distribution #' @keywords internal @@ -382,7 +382,7 @@ degree.distribution <- function(graph, cumulative = FALSE, ...) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `count.multiple()` was renamed to `count_multiple()` to create a more +#' `count.multiple()` was renamed to [count_multiple()] to create a more #' consistent API. #' @inheritParams count_multiple #' @keywords internal @@ -397,7 +397,7 @@ count.multiple <- function(graph, eids = E(graph)) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `clusters()` was renamed to `components()` to create a more +#' `clusters()` was renamed to [components()] to create a more #' consistent API. #' @inheritParams components #' @keywords internal @@ -412,7 +412,7 @@ clusters <- function(graph, mode = c("weak", "strong")) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `average.path.length()` was renamed to `mean_distance()` to create a more +#' `average.path.length()` was renamed to [mean_distance()] to create a more #' consistent API. #' @inheritParams mean_distance #' @keywords internal @@ -1249,7 +1249,7 @@ subgraph_from_edges <- function(graph, eids, delete.vertices = TRUE) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `subgraph.edges()` was renamed to `subgraph_from_edges()` to create a more +#' `subgraph.edges()` was renamed to [subgraph_from_edges()] to create a more #' consistent API. #' @inheritParams subgraph_from_edges #' @keywords internal diff --git a/R/structure.info.R b/R/structure.info.R index e67d5b5b24..4f605e0326 100644 --- a/R/structure.info.R +++ b/R/structure.info.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `are.connected()` was renamed to `are_adjacent()` to create a more +#' `are.connected()` was renamed to [are_adjacent()] to create a more #' consistent API. #' @inheritParams are_adjacent #' @keywords internal diff --git a/R/tkplot.R b/R/tkplot.R index 23420196e0..a8d47feaef 100644 --- a/R/tkplot.R +++ b/R/tkplot.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.setcoords()` was renamed to `tk_set_coords()` to create a more +#' `tkplot.setcoords()` was renamed to [tk_set_coords()] to create a more #' consistent API. #' @inheritParams tk_set_coords #' @keywords internal @@ -18,7 +18,7 @@ tkplot.setcoords <- function(tkp.id, coords) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.rotate()` was renamed to `tk_rotate()` to create a more +#' `tkplot.rotate()` was renamed to [tk_rotate()] to create a more #' consistent API. #' @inheritParams tk_rotate #' @keywords internal @@ -33,7 +33,7 @@ tkplot.rotate <- function(tkp.id, degree = NULL, rad = NULL) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.reshape()` was renamed to `tk_reshape()` to create a more +#' `tkplot.reshape()` was renamed to [tk_reshape()] to create a more #' consistent API. #' @inheritParams tk_reshape #' @keywords internal @@ -48,7 +48,7 @@ tkplot.reshape <- function(tkp.id, newlayout, ..., params) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.off()` was renamed to `tk_off()` to create a more +#' `tkplot.off()` was renamed to [tk_off()] to create a more #' consistent API. #' #' @keywords internal @@ -63,7 +63,7 @@ tkplot.off <- function() { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.getcoords()` was renamed to `tk_coords()` to create a more +#' `tkplot.getcoords()` was renamed to [tk_coords()] to create a more #' consistent API. #' @inheritParams tk_coords #' @keywords internal @@ -78,7 +78,7 @@ tkplot.getcoords <- function(tkp.id, norm = FALSE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.fit.to.screen()` was renamed to `tk_fit()` to create a more +#' `tkplot.fit.to.screen()` was renamed to [tk_fit()] to create a more #' consistent API. #' @inheritParams tk_fit #' @keywords internal @@ -93,7 +93,7 @@ tkplot.fit.to.screen <- function(tkp.id, width = NULL, height = NULL) { # nocov #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.export.postscript()` was renamed to `tk_postscript()` to create a more +#' `tkplot.export.postscript()` was renamed to [tk_postscript()] to create a more #' consistent API. #' @inheritParams tk_postscript #' @keywords internal @@ -108,7 +108,7 @@ tkplot.export.postscript <- function(tkp.id) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.close()` was renamed to `tk_close()` to create a more +#' `tkplot.close()` was renamed to [tk_close()] to create a more #' consistent API. #' @inheritParams tk_close #' @keywords internal @@ -123,7 +123,7 @@ tkplot.close <- function(tkp.id, window.close = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.center()` was renamed to `tk_center()` to create a more +#' `tkplot.center()` was renamed to [tk_center()] to create a more #' consistent API. #' @inheritParams tk_center #' @keywords internal @@ -138,7 +138,7 @@ tkplot.center <- function(tkp.id) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `tkplot.canvas()` was renamed to `tk_canvas()` to create a more +#' `tkplot.canvas()` was renamed to [tk_canvas()] to create a more #' consistent API. #' @inheritParams tk_canvas #' @keywords internal diff --git a/R/topology.R b/R/topology.R index 808f89eee2..ca552e9890 100644 --- a/R/topology.R +++ b/R/topology.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `permute.vertices()` was renamed to `permute()` to create a more +#' `permute.vertices()` was renamed to [permute()] to create a more #' consistent API. #' @inheritParams permute #' @keywords internal @@ -18,7 +18,7 @@ permute.vertices <- function(graph, permutation) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.isocreate()` was renamed to `graph_from_isomorphism_class()` to create a more +#' `graph.isocreate()` was renamed to [graph_from_isomorphism_class()] to create a more #' consistent API. #' @inheritParams graph_from_isomorphism_class #' @keywords internal @@ -33,7 +33,7 @@ graph.isocreate <- function(size, number, directed = TRUE) { # nocov start #' @description #' `r lifecycle::badge("deprecated")` #' -#' `graph.automorphisms()` was renamed to `count_automorphisms()` to create a more +#' `graph.automorphisms()` was renamed to [count_automorphisms()] to create a more #' consistent API. #' @inheritParams count_automorphisms #' @keywords internal @@ -48,7 +48,7 @@ graph.automorphisms <- function(graph, colors = NULL, sh = c("fm", "f", "fs", "f #' @description #' `r lifecycle::badge("deprecated")` #' -#' `canonical.permutation()` was renamed to `canonical_permutation()` to create a more +#' `canonical.permutation()` was renamed to [canonical_permutation()] to create a more #' consistent API. #' @inheritParams canonical_permutation #' @keywords internal @@ -63,7 +63,7 @@ canonical.permutation <- function(graph, colors = NULL, sh = c("fm", "f", "fs", #' @description #' `r lifecycle::badge("deprecated")` #' -#' `automorphisms()` was renamed to `count_automorphisms()` to create a more +#' `automorphisms()` was renamed to [count_automorphisms()] to create a more #' consistent API. #' @inheritParams count_automorphisms #' @keywords internal diff --git a/R/triangles.R b/R/triangles.R index 02605e45b2..340917114f 100644 --- a/R/triangles.R +++ b/R/triangles.R @@ -3,7 +3,7 @@ #' @description #' `r lifecycle::badge("deprecated")` #' -#' `adjacent.triangles()` was renamed to `count_triangles()` to create a more +#' `adjacent.triangles()` was renamed to [count_triangles()] to create a more #' consistent API. #' @inheritParams count_triangles #' @keywords internal diff --git a/R/versions.R b/R/versions.R index 4258d2c4cd..27c384b9d9 100644 --- a/R/versions.R +++ b/R/versions.R @@ -195,7 +195,7 @@ clear_native_ptr <- function(g) { #' @description #' `r lifecycle::badge("deprecated")` #' -#' `igraph.version()` was renamed to `igraph_version()` to create a more +#' `igraph.version()` was renamed to [igraph_version()] to create a more #' consistent API. #' #' @keywords internal diff --git a/man/add.edges.Rd b/man/add.edges.Rd index 2a057e5eb5..8a4660c337 100644 --- a/man/add.edges.Rd +++ b/man/add.edges.Rd @@ -23,7 +23,7 @@ below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{add.edges()} was renamed to \code{add_edges()} to create a more +\code{add.edges()} was renamed to \code{\link[=add_edges]{add_edges()}} to create a more consistent API. } \keyword{internal} diff --git a/man/add.vertex.shape.Rd b/man/add.vertex.shape.Rd index b5cc9497e2..0a21bc5552 100644 --- a/man/add.vertex.shape.Rd +++ b/man/add.vertex.shape.Rd @@ -31,7 +31,7 @@ a prefix \sQuote{\code{plot.}}. See Details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{add.vertex.shape()} was renamed to \code{add_shape()} to create a more +\code{add.vertex.shape()} was renamed to \code{\link[=add_shape]{add_shape()}} to create a more consistent API. } \keyword{internal} diff --git a/man/add.vertices.Rd b/man/add.vertices.Rd index 2b22dc9a34..4782a44a55 100644 --- a/man/add.vertices.Rd +++ b/man/add.vertices.Rd @@ -22,7 +22,7 @@ below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{add.vertices()} was renamed to \code{add_vertices()} to create a more +\code{add.vertices()} was renamed to \code{\link[=add_vertices]{add_vertices()}} to create a more consistent API. } \keyword{internal} diff --git a/man/adjacent.triangles.Rd b/man/adjacent.triangles.Rd index 4ad9cbae1b..cc4ea89893 100644 --- a/man/adjacent.triangles.Rd +++ b/man/adjacent.triangles.Rd @@ -17,7 +17,7 @@ named graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{adjacent.triangles()} was renamed to \code{count_triangles()} to create a more +\code{adjacent.triangles()} was renamed to \code{\link[=count_triangles]{count_triangles()}} to create a more consistent API. } \keyword{internal} diff --git a/man/aging.ba.game.Rd b/man/aging.ba.game.Rd index bec871f51d..a8e90f364b 100644 --- a/man/aging.ba.game.Rd +++ b/man/aging.ba.game.Rd @@ -68,7 +68,7 @@ attachment. See also details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{aging.ba.game()} was renamed to \code{sample_pa_age()} to create a more +\code{aging.ba.game()} was renamed to \code{\link[=sample_pa_age]{sample_pa_age()}} to create a more consistent API. } \keyword{internal} diff --git a/man/aging.barabasi.game.Rd b/man/aging.barabasi.game.Rd index 238f1a1d15..7d95fbdd19 100644 --- a/man/aging.barabasi.game.Rd +++ b/man/aging.barabasi.game.Rd @@ -68,7 +68,7 @@ attachment. See also details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{aging.barabasi.game()} was renamed to \code{sample_pa_age()} to create a more +\code{aging.barabasi.game()} was renamed to \code{\link[=sample_pa_age]{sample_pa_age()}} to create a more consistent API. } \keyword{internal} diff --git a/man/aging.prefatt.game.Rd b/man/aging.prefatt.game.Rd index 0ff7822cce..5d913f343e 100644 --- a/man/aging.prefatt.game.Rd +++ b/man/aging.prefatt.game.Rd @@ -68,7 +68,7 @@ attachment. See also details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{aging.prefatt.game()} was renamed to \code{sample_pa_age()} to create a more +\code{aging.prefatt.game()} was renamed to \code{\link[=sample_pa_age]{sample_pa_age()}} to create a more consistent API. } \keyword{internal} diff --git a/man/alpha.centrality.Rd b/man/alpha.centrality.Rd index 375e748d43..530eedc75c 100644 --- a/man/alpha.centrality.Rd +++ b/man/alpha.centrality.Rd @@ -51,7 +51,7 @@ support} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{alpha.centrality()} was renamed to \code{alpha_centrality()} to create a more +\code{alpha.centrality()} was renamed to \code{\link[=alpha_centrality]{alpha_centrality()}} to create a more consistent API. } \keyword{internal} diff --git a/man/are.connected.Rd b/man/are.connected.Rd index 00a5544ad5..1452add865 100644 --- a/man/are.connected.Rd +++ b/man/are.connected.Rd @@ -16,7 +16,7 @@ are.connected(graph, v1, v2) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{are.connected()} was renamed to \code{are_adjacent()} to create a more +\code{are.connected()} was renamed to \code{\link[=are_adjacent]{are_adjacent()}} to create a more consistent API. } \keyword{internal} diff --git a/man/articulation.points.Rd b/man/articulation.points.Rd index 87641c892a..90a5009d20 100644 --- a/man/articulation.points.Rd +++ b/man/articulation.points.Rd @@ -13,7 +13,7 @@ it is directed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{articulation.points()} was renamed to \code{articulation_points()} to create a more +\code{articulation.points()} was renamed to \code{\link[=articulation_points]{articulation_points()}} to create a more consistent API. } \keyword{internal} diff --git a/man/as.directed.Rd b/man/as.directed.Rd index d1711005cc..0d38ae8a78 100644 --- a/man/as.directed.Rd +++ b/man/as.directed.Rd @@ -17,7 +17,7 @@ as.directed(graph, mode = c("mutual", "arbitrary", "random", "acyclic")) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{as.directed()} was renamed to \code{as_directed()} to create a more +\code{as.directed()} was renamed to \code{\link[=as_directed]{as_directed()}} to create a more consistent API. } \keyword{internal} diff --git a/man/as.matrix.igraph.Rd b/man/as.matrix.igraph.Rd index b74331c37e..136377aa4c 100644 --- a/man/as.matrix.igraph.Rd +++ b/man/as.matrix.igraph.Rd @@ -7,7 +7,7 @@ \method{as.matrix}{igraph}(x, matrix.type = c("adjacency", "edgelist"), ...) } \arguments{ -\item{x}{object of class igraph, the network} +\item{x}{object of class \code{igraph}, the network} \item{matrix.type}{character, type of matrix to return, currently "adjacency" or "edgelist" are supported} diff --git a/man/as.undirected.Rd b/man/as.undirected.Rd index b12568f8b2..8cf4d939fc 100644 --- a/man/as.undirected.Rd +++ b/man/as.undirected.Rd @@ -27,7 +27,7 @@ this.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{as.undirected()} was renamed to \code{as_undirected()} to create a more +\code{as.undirected()} was renamed to \code{\link[=as_undirected]{as_undirected()}} to create a more consistent API. } \keyword{internal} diff --git a/man/as_incidence_matrix.Rd b/man/as_incidence_matrix.Rd index 50c68cb715..697644a63f 100644 --- a/man/as_incidence_matrix.Rd +++ b/man/as_incidence_matrix.Rd @@ -9,7 +9,7 @@ as_incidence_matrix(...) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{as_incidence_matrix()} was renamed to \code{as_biadjacency_matrix()} to create a more +\code{as_incidence_matrix()} was renamed to \code{\link[=as_biadjacency_matrix]{as_biadjacency_matrix()}} to create a more consistent API. } \details{ diff --git a/man/assortativity.degree.Rd b/man/assortativity.degree.Rd index e79639b9d0..2329687900 100644 --- a/man/assortativity.degree.Rd +++ b/man/assortativity.degree.Rd @@ -20,7 +20,7 @@ graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{assortativity.degree()} was renamed to \code{assortativity_degree()} to create a more +\code{assortativity.degree()} was renamed to \code{\link[=assortativity_degree]{assortativity_degree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/assortativity.nominal.Rd b/man/assortativity.nominal.Rd index 17d02b6ebf..08db8faf43 100644 --- a/man/assortativity.nominal.Rd +++ b/man/assortativity.nominal.Rd @@ -29,7 +29,7 @@ values at the two ends of edges.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{assortativity.nominal()} was renamed to \code{assortativity_nominal()} to create a more +\code{assortativity.nominal()} was renamed to \code{\link[=assortativity_nominal]{assortativity_nominal()}} to create a more consistent API. } \keyword{internal} diff --git a/man/asymmetric.preference.game.Rd b/man/asymmetric.preference.game.Rd index 2213cb9bb0..00b6b8a149 100644 --- a/man/asymmetric.preference.game.Rd +++ b/man/asymmetric.preference.game.Rd @@ -29,7 +29,7 @@ an undirected graph, it must be symmetric.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{asymmetric.preference.game()} was renamed to \code{sample_asym_pref()} to create a more +\code{asymmetric.preference.game()} was renamed to \code{\link[=sample_asym_pref]{sample_asym_pref()}} to create a more consistent API. } \keyword{internal} diff --git a/man/authority.score.Rd b/man/authority.score.Rd index bfbb0345b9..814d1a19f3 100644 --- a/man/authority.score.Rd +++ b/man/authority.score.Rd @@ -31,7 +31,7 @@ selected by the surfer.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{authority.score()} was renamed to \code{authority_score()} to create a more +\code{authority.score()} was renamed to \code{\link[=authority_score]{authority_score()}} to create a more consistent API. } \keyword{internal} diff --git a/man/autocurve.edges.Rd b/man/autocurve.edges.Rd index 08e3e3c5bc..58ebff2987 100644 --- a/man/autocurve.edges.Rd +++ b/man/autocurve.edges.Rd @@ -15,7 +15,7 @@ curvature between \code{-start} and \code{start}, spaced equally.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{autocurve.edges()} was renamed to \code{curve_multiple()} to create a more +\code{autocurve.edges()} was renamed to \code{\link[=curve_multiple]{curve_multiple()}} to create a more consistent API. } \keyword{internal} diff --git a/man/automorphisms.Rd b/man/automorphisms.Rd index fbc69d51f2..48b6202e2e 100644 --- a/man/automorphisms.Rd +++ b/man/automorphisms.Rd @@ -31,7 +31,7 @@ smallest maximally non-trivially connected non-singleton cell.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{automorphisms()} was renamed to \code{count_automorphisms()} to create a more +\code{automorphisms()} was renamed to \code{\link[=count_automorphisms]{count_automorphisms()}} to create a more consistent API. } \keyword{internal} diff --git a/man/average.path.length.Rd b/man/average.path.length.Rd index c18a9bdf9d..cb3e0bb2ee 100644 --- a/man/average.path.length.Rd +++ b/man/average.path.length.Rd @@ -38,7 +38,7 @@ the result when this parameter is set to \code{TRUE}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{average.path.length()} was renamed to \code{mean_distance()} to create a more +\code{average.path.length()} was renamed to \code{\link[=mean_distance]{mean_distance()}} to create a more consistent API. } \keyword{internal} diff --git a/man/ba.game.Rd b/man/ba.game.Rd index a60ce1509d..bcd3f83ee7 100644 --- a/man/ba.game.Rd +++ b/man/ba.game.Rd @@ -67,7 +67,7 @@ contain the out degrees of the new vertices only, not the ones in the \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{ba.game()} was renamed to \code{sample_pa()} to create a more +\code{ba.game()} was renamed to \code{\link[=sample_pa]{sample_pa()}} to create a more consistent API. } \keyword{internal} diff --git a/man/barabasi.game.Rd b/man/barabasi.game.Rd index a2bf7321b9..142526d7d7 100644 --- a/man/barabasi.game.Rd +++ b/man/barabasi.game.Rd @@ -67,7 +67,7 @@ contain the out degrees of the new vertices only, not the ones in the \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{barabasi.game()} was renamed to \code{sample_pa()} to create a more +\code{barabasi.game()} was renamed to \code{\link[=sample_pa]{sample_pa()}} to create a more consistent API. } \keyword{internal} diff --git a/man/biconnected.components.Rd b/man/biconnected.components.Rd index 4e5f79237d..33d3d69c88 100644 --- a/man/biconnected.components.Rd +++ b/man/biconnected.components.Rd @@ -13,7 +13,7 @@ it is directed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{biconnected.components()} was renamed to \code{biconnected_components()} to create a more +\code{biconnected.components()} was renamed to \code{\link[=biconnected_components]{biconnected_components()}} to create a more consistent API. } \keyword{internal} diff --git a/man/bipartite.mapping.Rd b/man/bipartite.mapping.Rd index 0253b5bba7..7eb0c1a517 100644 --- a/man/bipartite.mapping.Rd +++ b/man/bipartite.mapping.Rd @@ -12,7 +12,7 @@ bipartite.mapping(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{bipartite.mapping()} was renamed to \code{bipartite_mapping()} to create a more +\code{bipartite.mapping()} was renamed to \code{\link[=bipartite_mapping]{bipartite_mapping()}} to create a more consistent API. } \keyword{internal} diff --git a/man/bipartite.projection.Rd b/man/bipartite.projection.Rd index 7c2765c62d..bf9ab6f0de 100644 --- a/man/bipartite.projection.Rd +++ b/man/bipartite.projection.Rd @@ -45,7 +45,7 @@ default it will be removed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{bipartite.projection()} was renamed to \code{bipartite_projection()} to create a more +\code{bipartite.projection()} was renamed to \code{\link[=bipartite_projection]{bipartite_projection()}} to create a more consistent API. } \keyword{internal} diff --git a/man/bipartite.projection.size.Rd b/man/bipartite.projection.size.Rd index 0647a00cb3..8e3335dd8b 100644 --- a/man/bipartite.projection.size.Rd +++ b/man/bipartite.projection.size.Rd @@ -17,7 +17,7 @@ graph has no \sQuote{\code{type}} vertex attribute.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{bipartite.projection.size()} was renamed to \code{bipartite_projection_size()} to create a more +\code{bipartite.projection.size()} was renamed to \code{\link[=bipartite_projection_size]{bipartite_projection_size()}} to create a more consistent API. } \keyword{internal} diff --git a/man/bipartite.random.game.Rd b/man/bipartite.random.game.Rd index b21155f19e..5568114c2a 100644 --- a/man/bipartite.random.game.Rd +++ b/man/bipartite.random.game.Rd @@ -42,7 +42,7 @@ is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{bipartite.random.game()} was renamed to \code{sample_bipartite()} to create a more +\code{bipartite.random.game()} was renamed to \code{\link[=sample_bipartite]{sample_bipartite()}} to create a more consistent API. } \keyword{internal} diff --git a/man/blockGraphs.Rd b/man/blockGraphs.Rd index 547f1a0786..edd5ab7708 100644 --- a/man/blockGraphs.Rd +++ b/man/blockGraphs.Rd @@ -18,7 +18,7 @@ argument.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{blockGraphs()} was renamed to \code{graphs_from_cohesive_blocks()} to create a more +\code{blockGraphs()} was renamed to \code{\link[=graphs_from_cohesive_blocks]{graphs_from_cohesive_blocks()}} to create a more consistent API. } \keyword{internal} diff --git a/man/bonpow.Rd b/man/bonpow.Rd index 97a6598ca0..4377272047 100644 --- a/man/bonpow.Rd +++ b/man/bonpow.Rd @@ -40,7 +40,7 @@ support} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{bonpow()} was renamed to \code{power_centrality()} to create a more +\code{bonpow()} was renamed to \code{\link[=power_centrality]{power_centrality()}} to create a more consistent API. } \keyword{internal} diff --git a/man/callaway.traits.game.Rd b/man/callaway.traits.game.Rd index 866f619da7..532d56b26a 100644 --- a/man/callaway.traits.game.Rd +++ b/man/callaway.traits.game.Rd @@ -31,7 +31,7 @@ types. These should be probabilities, i.e. numbers between zero and one.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{callaway.traits.game()} was renamed to \code{sample_traits_callaway()} to create a more +\code{callaway.traits.game()} was renamed to \code{\link[=sample_traits_callaway]{sample_traits_callaway()}} to create a more consistent API. } \keyword{internal} diff --git a/man/canonical.permutation.Rd b/man/canonical.permutation.Rd index e772237e64..88a07204e0 100644 --- a/man/canonical.permutation.Rd +++ b/man/canonical.permutation.Rd @@ -26,7 +26,7 @@ for possible values.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{canonical.permutation()} was renamed to \code{canonical_permutation()} to create a more +\code{canonical.permutation()} was renamed to \code{\link[=canonical_permutation]{canonical_permutation()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.betweenness.Rd b/man/centralization.betweenness.Rd index e567a4f831..eb88b18f35 100644 --- a/man/centralization.betweenness.Rd +++ b/man/centralization.betweenness.Rd @@ -18,7 +18,7 @@ centrality score by dividing by the theoretical maximum.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.betweenness()} was renamed to \code{centr_betw()} to create a more +\code{centralization.betweenness()} was renamed to \code{\link[=centr_betw]{centr_betw()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.betweenness.tmax.Rd b/man/centralization.betweenness.tmax.Rd index 5d6d12288d..58da0f0319 100644 --- a/man/centralization.betweenness.tmax.Rd +++ b/man/centralization.betweenness.tmax.Rd @@ -20,7 +20,7 @@ given.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.betweenness.tmax()} was renamed to \code{centr_betw_tmax()} to create a more +\code{centralization.betweenness.tmax()} was renamed to \code{\link[=centr_betw_tmax]{centr_betw_tmax()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.closeness.Rd b/man/centralization.closeness.Rd index 12036dce49..d37f704897 100644 --- a/man/centralization.closeness.Rd +++ b/man/centralization.closeness.Rd @@ -22,7 +22,7 @@ centrality score by dividing by the theoretical maximum.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.closeness()} was renamed to \code{centr_clo()} to create a more +\code{centralization.closeness()} was renamed to \code{\link[=centr_clo]{centr_clo()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.closeness.tmax.Rd b/man/centralization.closeness.tmax.Rd index 1180dffd4a..f8399e84c6 100644 --- a/man/centralization.closeness.tmax.Rd +++ b/man/centralization.closeness.tmax.Rd @@ -23,7 +23,7 @@ given.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.closeness.tmax()} was renamed to \code{centr_clo_tmax()} to create a more +\code{centralization.closeness.tmax()} was renamed to \code{\link[=centr_clo_tmax]{centr_clo_tmax()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.degree.Rd b/man/centralization.degree.Rd index bed5088d21..6f6715dc4d 100644 --- a/man/centralization.degree.Rd +++ b/man/centralization.degree.Rd @@ -26,7 +26,7 @@ centrality score by dividing by the theoretical maximum.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.degree()} was renamed to \code{centr_degree()} to create a more +\code{centralization.degree()} was renamed to \code{\link[=centr_degree]{centr_degree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.degree.tmax.Rd b/man/centralization.degree.tmax.Rd index 67804f3523..fa664f658f 100644 --- a/man/centralization.degree.tmax.Rd +++ b/man/centralization.degree.tmax.Rd @@ -25,7 +25,7 @@ calculating the degree.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.degree.tmax()} was renamed to \code{centr_degree_tmax()} to create a more +\code{centralization.degree.tmax()} was renamed to \code{\link[=centr_degree_tmax]{centr_degree_tmax()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.evcent.Rd b/man/centralization.evcent.Rd index ed31018fb4..f5e794376c 100644 --- a/man/centralization.evcent.Rd +++ b/man/centralization.evcent.Rd @@ -30,7 +30,7 @@ centrality score by dividing by the theoretical maximum.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.evcent()} was renamed to \code{centr_eigen()} to create a more +\code{centralization.evcent()} was renamed to \code{\link[=centr_eigen]{centr_eigen()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralization.evcent.tmax.Rd b/man/centralization.evcent.tmax.Rd index 688913f841..b6e6f8b94e 100644 --- a/man/centralization.evcent.tmax.Rd +++ b/man/centralization.evcent.tmax.Rd @@ -27,7 +27,7 @@ eigenvector centralization requires normalized eigenvector centrality scores.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralization.evcent.tmax()} was renamed to \code{centr_eigen_tmax()} to create a more +\code{centralization.evcent.tmax()} was renamed to \code{\link[=centr_eigen_tmax]{centr_eigen_tmax()}} to create a more consistent API. } \keyword{internal} diff --git a/man/centralize.scores.Rd b/man/centralize.scores.Rd index 9e6aba7ad6..4db99dde6a 100644 --- a/man/centralize.scores.Rd +++ b/man/centralize.scores.Rd @@ -20,7 +20,7 @@ centrality score by dividing by the supplied theoretical maximum.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{centralize.scores()} was renamed to \code{centralize()} to create a more +\code{centralize.scores()} was renamed to \code{\link[=centralize]{centralize()}} to create a more consistent API. } \keyword{internal} diff --git a/man/cited.type.game.Rd b/man/cited.type.game.Rd index 68707d0354..97671da197 100644 --- a/man/cited.type.game.Rd +++ b/man/cited.type.game.Rd @@ -33,7 +33,7 @@ graph as a vertex attribute called \sQuote{\code{type}}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{cited.type.game()} was renamed to \code{sample_cit_types()} to create a more +\code{cited.type.game()} was renamed to \code{\link[=sample_cit_types]{sample_cit_types()}} to create a more consistent API. } \keyword{internal} diff --git a/man/citing.cited.type.game.Rd b/man/citing.cited.type.game.Rd index 340244a335..71f467eede 100644 --- a/man/citing.cited.type.game.Rd +++ b/man/citing.cited.type.game.Rd @@ -33,7 +33,7 @@ graph as a vertex attribute called \sQuote{\code{type}}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{citing.cited.type.game()} was renamed to \code{sample_cit_cit_types()} to create a more +\code{citing.cited.type.game()} was renamed to \code{\link[=sample_cit_cit_types]{sample_cit_cit_types()}} to create a more consistent API. } \keyword{internal} diff --git a/man/clique.number.Rd b/man/clique.number.Rd index ae8343274c..b09afd58b7 100644 --- a/man/clique.number.Rd +++ b/man/clique.number.Rd @@ -12,7 +12,7 @@ clique.number(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{clique.number()} was renamed to \code{clique_num()} to create a more +\code{clique.number()} was renamed to \code{\link[=clique_num]{clique_num()}} to create a more consistent API. } \keyword{internal} diff --git a/man/cliques.Rd b/man/cliques.Rd index dff5707cc2..fcf314fd78 100644 --- a/man/cliques.Rd +++ b/man/cliques.Rd @@ -67,7 +67,7 @@ or only the maximal ones (\code{TRUE}).} \value{ \code{cliques()}, \code{largest_cliques()} and \code{clique_num()} return a list containing numeric vectors of vertex ids. Each list element is -a clique, i.e. a vertex sequence of class \code{\link[=V]{igraph.vs()}}. +a clique, i.e. a vertex sequence of class \link[=V]{igraph.vs}. \code{max_cliques()} returns \code{NULL}, invisibly, if its \code{file} argument is not \code{NULL}. The output is written to the specified file in diff --git a/man/cluster.distribution.Rd b/man/cluster.distribution.Rd index 52a1801327..4732759264 100644 --- a/man/cluster.distribution.Rd +++ b/man/cluster.distribution.Rd @@ -21,7 +21,7 @@ by the cluster sizes.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{cluster.distribution()} was renamed to \code{component_distribution()} to create a more +\code{cluster.distribution()} was renamed to \code{\link[=component_distribution]{component_distribution()}} to create a more consistent API. } \keyword{internal} diff --git a/man/clusters.Rd b/man/clusters.Rd index df8f58701c..1105d119b5 100644 --- a/man/clusters.Rd +++ b/man/clusters.Rd @@ -16,7 +16,7 @@ connected components to search. It is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{clusters()} was renamed to \code{components()} to create a more +\code{clusters()} was renamed to \code{\link[=components]{components()}} to create a more consistent API. } \keyword{internal} diff --git a/man/code.length.Rd b/man/code.length.Rd index be96cd67b3..940946cb5d 100644 --- a/man/code.length.Rd +++ b/man/code.length.Rd @@ -9,7 +9,7 @@ code.length(communities) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{code.length()} was renamed to \code{code_len()} to create a more +\code{code.length()} was renamed to \code{\link[=code_len]{code_len()}} to create a more consistent API. } \keyword{internal} diff --git a/man/cohesive.blocks.Rd b/man/cohesive.blocks.Rd index 363c6c420f..83cbd9e125 100644 --- a/man/cohesive.blocks.Rd +++ b/man/cohesive.blocks.Rd @@ -22,7 +22,7 @@ cohesive blocks.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{cohesive.blocks()} was renamed to \code{cohesive_blocks()} to create a more +\code{cohesive.blocks()} was renamed to \code{\link[=cohesive_blocks]{cohesive_blocks()}} to create a more consistent API. } \keyword{internal} diff --git a/man/connect.neighborhood.Rd b/man/connect.neighborhood.Rd index 13aa7e4048..2c09f9529e 100644 --- a/man/connect.neighborhood.Rd +++ b/man/connect.neighborhood.Rd @@ -23,7 +23,7 @@ argument is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{connect.neighborhood()} was renamed to \code{connect()} to create a more +\code{connect.neighborhood()} was renamed to \code{\link[=connect]{connect()}} to create a more consistent API. } \keyword{internal} diff --git a/man/contract.vertices.Rd b/man/contract.vertices.Rd index da5f8eeb38..ebf7f683aa 100644 --- a/man/contract.vertices.Rd +++ b/man/contract.vertices.Rd @@ -23,7 +23,7 @@ the new graph. Please see \code{\link[=attribute.combination]{attribute.combinat \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{contract.vertices()} was renamed to \code{contract()} to create a more +\code{contract.vertices()} was renamed to \code{\link[=contract]{contract()}} to create a more consistent API. } \keyword{internal} diff --git a/man/convex.hull.Rd b/man/convex.hull.Rd index ebe8dd49ac..39b9370599 100644 --- a/man/convex.hull.Rd +++ b/man/convex.hull.Rd @@ -12,7 +12,7 @@ convex.hull(data) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{convex.hull()} was renamed to \code{convex_hull()} to create a more +\code{convex.hull()} was renamed to \code{\link[=convex_hull]{convex_hull()}} to create a more consistent API. } \keyword{internal} diff --git a/man/count.multiple.Rd b/man/count.multiple.Rd index 87fe902580..d219ce32b3 100644 --- a/man/count.multiple.Rd +++ b/man/count.multiple.Rd @@ -15,7 +15,7 @@ all edges in the graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{count.multiple()} was renamed to \code{count_multiple()} to create a more +\code{count.multiple()} was renamed to \code{\link[=count_multiple]{count_multiple()}} to create a more consistent API. } \keyword{internal} diff --git a/man/create.communities.Rd b/man/create.communities.Rd index a5a295fba5..92118662bc 100644 --- a/man/create.communities.Rd +++ b/man/create.communities.Rd @@ -32,7 +32,7 @@ modularity values is calculated automatically.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{create.communities()} was renamed to \code{make_clusters()} to create a more +\code{create.communities()} was renamed to \code{\link[=make_clusters]{make_clusters()}} to create a more consistent API. } \keyword{internal} diff --git a/man/cutat.Rd b/man/cutat.Rd index 76ddf29d58..4b8e37faee 100644 --- a/man/cutat.Rd +++ b/man/cutat.Rd @@ -17,7 +17,7 @@ communities. Exactly one of \code{no} and \code{steps} must be supplied.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{cutat()} was renamed to \code{cut_at()} to create a more +\code{cutat()} was renamed to \code{\link[=cut_at]{cut_at()}} to create a more consistent API. } \keyword{internal} diff --git a/man/decompose.graph.Rd b/man/decompose.graph.Rd index 2d0da7dde1..ea7705e22a 100644 --- a/man/decompose.graph.Rd +++ b/man/decompose.graph.Rd @@ -31,7 +31,7 @@ isolate vertices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{decompose.graph()} was renamed to \code{decompose()} to create a more +\code{decompose.graph()} was renamed to \code{\link[=decompose]{decompose()}} to create a more consistent API. } \keyword{internal} diff --git a/man/degree.distribution.Rd b/man/degree.distribution.Rd index 73d1893eba..1a0fe90bcc 100644 --- a/man/degree.distribution.Rd +++ b/man/degree.distribution.Rd @@ -17,7 +17,7 @@ be calculated.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{degree.distribution()} was renamed to \code{degree_distribution()} to create a more +\code{degree.distribution()} was renamed to \code{\link[=degree_distribution]{degree_distribution()}} to create a more consistent API. } \keyword{internal} diff --git a/man/degree.sequence.game.Rd b/man/degree.sequence.game.Rd index e19c9cc5e6..b9db2f8951 100644 --- a/man/degree.sequence.game.Rd +++ b/man/degree.sequence.game.Rd @@ -24,7 +24,7 @@ should be even. For directed graphs its sum should be the same as the sum of \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{degree.sequence.game()} was renamed to \code{sample_degseq()} to create a more +\code{degree.sequence.game()} was renamed to \code{\link[=sample_degseq]{sample_degseq()}} to create a more consistent API. } \keyword{internal} diff --git a/man/delete.edges.Rd b/man/delete.edges.Rd index 8782d65668..760b9a84c0 100644 --- a/man/delete.edges.Rd +++ b/man/delete.edges.Rd @@ -17,7 +17,7 @@ containing the IDs or names of the source and target vertices, separated by \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{delete.edges()} was renamed to \code{delete_edges()} to create a more +\code{delete.edges()} was renamed to \code{\link[=delete_edges]{delete_edges()}} to create a more consistent API. } \keyword{internal} diff --git a/man/delete.vertices.Rd b/man/delete.vertices.Rd index 4d605ba4cb..ab97018be6 100644 --- a/man/delete.vertices.Rd +++ b/man/delete.vertices.Rd @@ -14,7 +14,7 @@ delete.vertices(graph, v) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{delete.vertices()} was renamed to \code{delete_vertices()} to create a more +\code{delete.vertices()} was renamed to \code{\link[=delete_vertices]{delete_vertices()}} to create a more consistent API. } \keyword{internal} diff --git a/man/dendPlot.Rd b/man/dendPlot.Rd index 63f2e7940a..20732492af 100644 --- a/man/dendPlot.Rd +++ b/man/dendPlot.Rd @@ -18,7 +18,7 @@ function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{dendPlot()} was renamed to \code{plot_dendrogram()} to create a more +\code{dendPlot()} was renamed to \code{\link[=plot_dendrogram]{plot_dendrogram()}} to create a more consistent API. } \keyword{internal} diff --git a/man/dominator.tree.Rd b/man/dominator.tree.Rd index 98eb4ec1c0..7e45489d3d 100644 --- a/man/dominator.tree.Rd +++ b/man/dominator.tree.Rd @@ -21,7 +21,7 @@ the original one in the input graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{dominator.tree()} was renamed to \code{dominator_tree()} to create a more +\code{dominator.tree()} was renamed to \code{\link[=dominator_tree]{dominator_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/dyad.census.Rd b/man/dyad.census.Rd index ef0b7eb4b4..8ad215cf62 100644 --- a/man/dyad.census.Rd +++ b/man/dyad.census.Rd @@ -12,7 +12,7 @@ dyad.census(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{dyad.census()} was renamed to \code{dyad_census()} to create a more +\code{dyad.census()} was renamed to \code{\link[=dyad_census]{dyad_census()}} to create a more consistent API. } \keyword{internal} diff --git a/man/edge.betweenness.Rd b/man/edge.betweenness.Rd index 7846d7e6f9..8087a6c8c8 100644 --- a/man/edge.betweenness.Rd +++ b/man/edge.betweenness.Rd @@ -31,7 +31,7 @@ betweenness. If negative, then there is no such limit.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{edge.betweenness()} was renamed to \code{edge_betweenness()} to create a more +\code{edge.betweenness()} was renamed to \code{\link[=edge_betweenness]{edge_betweenness()}} to create a more consistent API. } \keyword{internal} diff --git a/man/edge.betweenness.community.Rd b/man/edge.betweenness.community.Rd index 8c0bf1cfeb..bfeb5b97d5 100644 --- a/man/edge.betweenness.community.Rd +++ b/man/edge.betweenness.community.Rd @@ -59,7 +59,7 @@ vector corresponding to the highest possible modularity score.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{edge.betweenness.community()} was renamed to \code{cluster_edge_betweenness()} to create a more +\code{edge.betweenness.community()} was renamed to \code{\link[=cluster_edge_betweenness]{cluster_edge_betweenness()}} to create a more consistent API. } \keyword{internal} diff --git a/man/edge.connectivity.Rd b/man/edge.connectivity.Rd index 6f14a79fdc..b7210bf2c5 100644 --- a/man/edge.connectivity.Rd +++ b/man/edge.connectivity.Rd @@ -26,7 +26,7 @@ thanks Peter.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{edge.connectivity()} was renamed to \code{edge_connectivity()} to create a more +\code{edge.connectivity()} was renamed to \code{\link[=edge_connectivity]{edge_connectivity()}} to create a more consistent API. } \keyword{internal} diff --git a/man/edge.disjoint.paths.Rd b/man/edge.disjoint.paths.Rd index 35ca4184ca..0b5b8b9b21 100644 --- a/man/edge.disjoint.paths.Rd +++ b/man/edge.disjoint.paths.Rd @@ -26,7 +26,7 @@ thanks Peter.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{edge.disjoint.paths()} was renamed to \code{edge_connectivity()} to create a more +\code{edge.disjoint.paths()} was renamed to \code{\link[=edge_connectivity]{edge_connectivity()}} to create a more consistent API. } \keyword{internal} diff --git a/man/establishment.game.Rd b/man/establishment.game.Rd index fdf872fe2d..5147127c9b 100644 --- a/man/establishment.game.Rd +++ b/man/establishment.game.Rd @@ -31,7 +31,7 @@ types. These should be probabilities, i.e. numbers between zero and one.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{establishment.game()} was renamed to \code{sample_traits()} to create a more +\code{establishment.game()} was renamed to \code{\link[=sample_traits]{sample_traits()}} to create a more consistent API. } \keyword{internal} diff --git a/man/evcent.Rd b/man/evcent.Rd index 52ab935afa..5cb6f2e539 100644 --- a/man/evcent.Rd +++ b/man/evcent.Rd @@ -39,7 +39,7 @@ weights spread the centrality better.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{evcent()} was renamed to \code{eigen_centrality()} to create a more +\code{evcent()} was renamed to \code{\link[=eigen_centrality]{eigen_centrality()}} to create a more consistent API. } \keyword{internal} diff --git a/man/exportPajek.Rd b/man/exportPajek.Rd index f5d0b564d5..e29f44bd35 100644 --- a/man/exportPajek.Rd +++ b/man/exportPajek.Rd @@ -34,7 +34,7 @@ See details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{exportPajek()} was renamed to \code{export_pajek()} to create a more +\code{exportPajek()} was renamed to \code{\link[=export_pajek]{export_pajek()}} to create a more consistent API. } \keyword{internal} diff --git a/man/farthest.nodes.Rd b/man/farthest.nodes.Rd index bb61fa87a4..33594b6af0 100644 --- a/man/farthest.nodes.Rd +++ b/man/farthest.nodes.Rd @@ -25,7 +25,7 @@ used by default.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{farthest.nodes()} was renamed to \code{farthest_vertices()} to create a more +\code{farthest.nodes()} was renamed to \code{\link[=farthest_vertices]{farthest_vertices()}} to create a more consistent API. } \keyword{internal} diff --git a/man/fastgreedy.community.Rd b/man/fastgreedy.community.Rd index 81c47dc11f..920f114a0e 100644 --- a/man/fastgreedy.community.Rd +++ b/man/fastgreedy.community.Rd @@ -36,7 +36,7 @@ edge weight means a stronger connection for this function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{fastgreedy.community()} was renamed to \code{cluster_fast_greedy()} to create a more +\code{fastgreedy.community()} was renamed to \code{\link[=cluster_fast_greedy]{cluster_fast_greedy()}} to create a more consistent API. } \keyword{internal} diff --git a/man/forest.fire.game.Rd b/man/forest.fire.game.Rd index fac253a8b4..574211f1df 100644 --- a/man/forest.fire.game.Rd +++ b/man/forest.fire.game.Rd @@ -21,7 +21,7 @@ probability is calculated as \code{bw.factor*fw.prob}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{forest.fire.game()} was renamed to \code{sample_forestfire()} to create a more +\code{forest.fire.game()} was renamed to \code{\link[=sample_forestfire]{sample_forestfire()}} to create a more consistent API. } \keyword{internal} diff --git a/man/from_incidence_matrix.Rd b/man/from_incidence_matrix.Rd index 4b54c6d616..3db111359c 100644 --- a/man/from_incidence_matrix.Rd +++ b/man/from_incidence_matrix.Rd @@ -9,7 +9,7 @@ from_incidence_matrix(...) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph_from_incidence_matrix()} was renamed to \code{graph_from_biadjacency_matrix()} to create a more +\code{graph_from_incidence_matrix()} was renamed to \code{\link[=graph_from_biadjacency_matrix]{graph_from_biadjacency_matrix()}} to create a more consistent API. } \details{ diff --git a/man/get.adjacency.Rd b/man/get.adjacency.Rd index 20dfed6329..4b4b3e0b66 100644 --- a/man/get.adjacency.Rd +++ b/man/get.adjacency.Rd @@ -49,7 +49,7 @@ matrices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.adjacency()} was renamed to \code{as_adjacency_matrix()} to create a more +\code{get.adjacency()} was renamed to \code{\link[=as_adjacency_matrix]{as_adjacency_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.adjedgelist.Rd b/man/get.adjedgelist.Rd index e3f48eff32..922825e654 100644 --- a/man/get.adjedgelist.Rd +++ b/man/get.adjedgelist.Rd @@ -25,7 +25,7 @@ is not allowed for directed graphs and will be replaced with \code{"once"}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.adjedgelist()} was renamed to \code{as_adj_edge_list()} to create a more +\code{get.adjedgelist()} was renamed to \code{\link[=as_adj_edge_list]{as_adj_edge_list()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.adjlist.Rd b/man/get.adjlist.Rd index c595650131..46526385b1 100644 --- a/man/get.adjlist.Rd +++ b/man/get.adjlist.Rd @@ -29,7 +29,7 @@ of each set of parallel edges.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.adjlist()} was renamed to \code{as_adj_list()} to create a more +\code{get.adjlist()} was renamed to \code{\link[=as_adj_list]{as_adj_list()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.all.shortest.paths.Rd b/man/get.all.shortest.paths.Rd index 84a0c2c2d1..502d277d74 100644 --- a/man/get.all.shortest.paths.Rd +++ b/man/get.all.shortest.paths.Rd @@ -40,7 +40,7 @@ of a path is the sum of the weights of its constituent edges.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.all.shortest.paths()} was renamed to \code{all_shortest_paths()} to create a more +\code{get.all.shortest.paths()} was renamed to \code{\link[=all_shortest_paths]{all_shortest_paths()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.data.frame.Rd b/man/get.data.frame.Rd index 9e0091f561..2985d73993 100644 --- a/man/get.data.frame.Rd +++ b/man/get.data.frame.Rd @@ -15,7 +15,7 @@ edges, or both. The default is \sQuote{edges}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.data.frame()} was renamed to \code{as_data_frame()} to create a more +\code{get.data.frame()} was renamed to \code{\link[=as_data_frame]{as_data_frame()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.diameter.Rd b/man/get.diameter.Rd index 8fdad82829..d567873801 100644 --- a/man/get.diameter.Rd +++ b/man/get.diameter.Rd @@ -25,7 +25,7 @@ used by default.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.diameter()} was renamed to \code{get_diameter()} to create a more +\code{get.diameter()} was renamed to \code{\link[=get_diameter]{get_diameter()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.edge.attribute.Rd b/man/get.edge.attribute.Rd index 0a7ba9ac7c..94c36d66ee 100644 --- a/man/get.edge.attribute.Rd +++ b/man/get.edge.attribute.Rd @@ -18,7 +18,7 @@ for a subset of edges.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.edge.attribute()} was renamed to \code{edge_attr()} to create a more +\code{get.edge.attribute()} was renamed to \code{\link[=edge_attr]{edge_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.edge.ids.Rd b/man/get.edge.ids.Rd index 292bf6bce5..e83ef82509 100644 --- a/man/get.edge.ids.Rd +++ b/man/get.edge.ids.Rd @@ -26,7 +26,7 @@ returned for the non-existant edge(s).} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.edge.ids()} was renamed to \code{get_edge_ids()} to create a more +\code{get.edge.ids()} was renamed to \code{\link[=get_edge_ids]{get_edge_ids()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.edgelist.Rd b/man/get.edgelist.Rd index 3ec792add9..60d2b6258b 100644 --- a/man/get.edgelist.Rd +++ b/man/get.edgelist.Rd @@ -16,7 +16,7 @@ vertex ids.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.edgelist()} was renamed to \code{as_edgelist()} to create a more +\code{get.edgelist()} was renamed to \code{\link[=as_edgelist]{as_edgelist()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.graph.attribute.Rd b/man/get.graph.attribute.Rd index 71fff1eac3..b63e6badcc 100644 --- a/man/get.graph.attribute.Rd +++ b/man/get.graph.attribute.Rd @@ -15,7 +15,7 @@ attributes are returned in a list.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.graph.attribute()} was renamed to \code{graph_attr()} to create a more +\code{get.graph.attribute()} was renamed to \code{\link[=graph_attr]{graph_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.incidence.Rd b/man/get.incidence.Rd index e89865d804..d197bdd45c 100644 --- a/man/get.incidence.Rd +++ b/man/get.incidence.Rd @@ -32,7 +32,7 @@ created, you will need the \code{Matrix} package for this.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.incidence()} was renamed to \code{as_biadjacency_matrix()} to create a more +\code{get.incidence()} was renamed to \code{\link[=as_biadjacency_matrix]{as_biadjacency_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.shortest.paths.Rd b/man/get.shortest.paths.Rd index d91e6d048b..f1c6516e4a 100644 --- a/man/get.shortest.paths.Rd +++ b/man/get.shortest.paths.Rd @@ -76,7 +76,7 @@ used, regardless of this argument.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.shortest.paths()} was renamed to \code{shortest_paths()} to create a more +\code{get.shortest.paths()} was renamed to \code{\link[=shortest_paths]{shortest_paths()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.stochastic.Rd b/man/get.stochastic.Rd index 499b6456cb..cf4c94141a 100644 --- a/man/get.stochastic.Rd +++ b/man/get.stochastic.Rd @@ -22,7 +22,7 @@ sum up to one; otherwise it is the columns.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.stochastic()} was renamed to \code{stochastic_matrix()} to create a more +\code{get.stochastic()} was renamed to \code{\link[=stochastic_matrix]{stochastic_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/get.vertex.attribute.Rd b/man/get.vertex.attribute.Rd index 9834c56247..4fb9cd66eb 100644 --- a/man/get.vertex.attribute.Rd +++ b/man/get.vertex.attribute.Rd @@ -18,7 +18,7 @@ for these vertices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{get.vertex.attribute()} was renamed to \code{vertex_attr()} to create a more +\code{get.vertex.attribute()} was renamed to \code{\link[=vertex_attr]{vertex_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/getIgraphOpt.Rd b/man/getIgraphOpt.Rd index ca7b7a6a29..1c319890d4 100644 --- a/man/getIgraphOpt.Rd +++ b/man/getIgraphOpt.Rd @@ -16,7 +16,7 @@ whether it is set and setting it separately if not.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{getIgraphOpt()} was renamed to \code{igraph_opt()} to create a more +\code{getIgraphOpt()} was renamed to \code{\link[=igraph_opt]{igraph_opt()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.Rd b/man/graph.Rd index 0ff4f9fcc0..45201a87de 100644 --- a/man/graph.Rd +++ b/man/graph.Rd @@ -55,7 +55,7 @@ Do not give both of them.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph()} was renamed to \code{make_graph()} to create a more +\code{graph()} was renamed to \code{\link[=make_graph]{make_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.adhesion.Rd b/man/graph.adhesion.Rd index 75064997cb..55d01dbab6 100644 --- a/man/graph.adhesion.Rd +++ b/man/graph.adhesion.Rd @@ -20,7 +20,7 @@ thanks Peter.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.adhesion()} was renamed to \code{adhesion()} to create a more +\code{graph.adhesion()} was renamed to \code{\link[=adhesion]{adhesion()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.adjacency.Rd b/man/graph.adjacency.Rd index 70609e73bd..432e1f18c5 100644 --- a/man/graph.adjacency.Rd +++ b/man/graph.adjacency.Rd @@ -51,7 +51,7 @@ former is ignored.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.adjacency()} was renamed to \code{graph_from_adjacency_matrix()} to create a more +\code{graph.adjacency()} was renamed to \code{\link[=graph_from_adjacency_matrix]{graph_from_adjacency_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.adjlist.Rd b/man/graph.adjlist.Rd index dfa897ac47..75aa45a095 100644 --- a/man/graph.adjlist.Rd +++ b/man/graph.adjlist.Rd @@ -27,7 +27,7 @@ This argument is ignored if \code{mode} is \code{out} or \verb{in}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.adjlist()} was renamed to \code{graph_from_adj_list()} to create a more +\code{graph.adjlist()} was renamed to \code{\link[=graph_from_adj_list]{graph_from_adj_list()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.atlas.Rd b/man/graph.atlas.Rd index e2623ab8ef..630bc053d1 100644 --- a/man/graph.atlas.Rd +++ b/man/graph.atlas.Rd @@ -12,7 +12,7 @@ graph.atlas(n) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.atlas()} was renamed to \code{graph_from_atlas()} to create a more +\code{graph.atlas()} was renamed to \code{\link[=graph_from_atlas]{graph_from_atlas()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.automorphisms.Rd b/man/graph.automorphisms.Rd index 9327097411..fc35bb93d4 100644 --- a/man/graph.automorphisms.Rd +++ b/man/graph.automorphisms.Rd @@ -31,7 +31,7 @@ smallest maximally non-trivially connected non-singleton cell.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.automorphisms()} was renamed to \code{count_automorphisms()} to create a more +\code{graph.automorphisms()} was renamed to \code{\link[=count_automorphisms]{count_automorphisms()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.bfs.Rd b/man/graph.bfs.Rd index 0f53f00c77..cb6d7d54b6 100644 --- a/man/graph.bfs.Rd +++ b/man/graph.bfs.Rd @@ -70,7 +70,7 @@ from igraph 1.3.0; use \code{mode} instead.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.bfs()} was renamed to \code{bfs()} to create a more +\code{graph.bfs()} was renamed to \code{\link[=bfs]{bfs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.bipartite.Rd b/man/graph.bipartite.Rd index 42dd393b12..c4b17fbe22 100644 --- a/man/graph.bipartite.Rd +++ b/man/graph.bipartite.Rd @@ -24,7 +24,7 @@ bipartite graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.bipartite()} was renamed to \code{make_bipartite_graph()} to create a more +\code{graph.bipartite()} was renamed to \code{\link[=make_bipartite_graph]{make_bipartite_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.cohesion.Rd b/man/graph.cohesion.Rd index dec4a7e983..15a340b47d 100644 --- a/man/graph.cohesion.Rd +++ b/man/graph.cohesion.Rd @@ -14,7 +14,7 @@ graph.cohesion(x, ...) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.cohesion()} was renamed to \code{cohesion()} to create a more +\code{graph.cohesion()} was renamed to \code{\link[=cohesion]{cohesion()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.complementer.Rd b/man/graph.complementer.Rd index fb80a6cb9b..0eea465a41 100644 --- a/man/graph.complementer.Rd +++ b/man/graph.complementer.Rd @@ -14,7 +14,7 @@ graph.complementer(graph, loops = FALSE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.complementer()} was renamed to \code{complementer()} to create a more +\code{graph.complementer()} was renamed to \code{\link[=complementer]{complementer()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.compose.Rd b/man/graph.compose.Rd index 45ffa7b8fe..7523e3c898 100644 --- a/man/graph.compose.Rd +++ b/man/graph.compose.Rd @@ -20,7 +20,7 @@ but not both graphs are named.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.compose()} was renamed to \code{compose()} to create a more +\code{graph.compose()} was renamed to \code{\link[=compose]{compose()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.coreness.Rd b/man/graph.coreness.Rd index b1c2f45a87..f6cb0f5b4f 100644 --- a/man/graph.coreness.Rd +++ b/man/graph.coreness.Rd @@ -17,7 +17,7 @@ argument is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.coreness()} was renamed to \code{coreness()} to create a more +\code{graph.coreness()} was renamed to \code{\link[=coreness]{coreness()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.data.frame.Rd b/man/graph.data.frame.Rd index ecc3c28a69..2ec0b6ca4a 100644 --- a/man/graph.data.frame.Rd +++ b/man/graph.data.frame.Rd @@ -21,7 +21,7 @@ with \code{as.data.frame}, if not \code{NULL}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.data.frame()} was renamed to \code{graph_from_data_frame()} to create a more +\code{graph.data.frame()} was renamed to \code{\link[=graph_from_data_frame]{graph_from_data_frame()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.de.bruijn.Rd b/man/graph.de.bruijn.Rd index 79918ad3ce..2cc74e9598 100644 --- a/man/graph.de.bruijn.Rd +++ b/man/graph.de.bruijn.Rd @@ -14,7 +14,7 @@ graph.de.bruijn(m, n) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.de.bruijn()} was renamed to \code{make_de_bruijn_graph()} to create a more +\code{graph.de.bruijn()} was renamed to \code{\link[=make_de_bruijn_graph]{make_de_bruijn_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.density.Rd b/man/graph.density.Rd index c952e7b3d8..a13d8df4d0 100644 --- a/man/graph.density.Rd +++ b/man/graph.density.Rd @@ -17,7 +17,7 @@ the result will not be meaningful.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.density()} was renamed to \code{edge_density()} to create a more +\code{graph.density()} was renamed to \code{\link[=edge_density]{edge_density()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.dfs.Rd b/man/graph.dfs.Rd index 71a57578bb..dd6833395f 100644 --- a/man/graph.dfs.Rd +++ b/man/graph.dfs.Rd @@ -63,7 +63,7 @@ algorithm. See details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.dfs()} was renamed to \code{dfs()} to create a more +\code{graph.dfs()} was renamed to \code{\link[=dfs]{dfs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.difference.Rd b/man/graph.difference.Rd index 81537597a0..f266a7b110 100644 --- a/man/graph.difference.Rd +++ b/man/graph.difference.Rd @@ -13,7 +13,7 @@ the function that implements \code{difference()}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.difference()} was renamed to \code{difference()} to create a more +\code{graph.difference()} was renamed to \code{\link[=difference]{difference()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.disjoint.union.Rd b/man/graph.disjoint.union.Rd index c6b1c7d427..b81cbea50f 100644 --- a/man/graph.disjoint.union.Rd +++ b/man/graph.disjoint.union.Rd @@ -12,7 +12,7 @@ graph.disjoint.union(...) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.disjoint.union()} was renamed to \code{disjoint_union()} to create a more +\code{graph.disjoint.union()} was renamed to \code{\link[=disjoint_union]{disjoint_union()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.diversity.Rd b/man/graph.diversity.Rd index 05b55d5ca8..02d7a817d6 100644 --- a/man/graph.diversity.Rd +++ b/man/graph.diversity.Rd @@ -18,7 +18,7 @@ that this measure is not defined for unweighted graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.diversity()} was renamed to \code{diversity()} to create a more +\code{graph.diversity()} was renamed to \code{\link[=diversity]{diversity()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.edgelist.Rd b/man/graph.edgelist.Rd index cf4fa74f4d..289f8682de 100644 --- a/man/graph.edgelist.Rd +++ b/man/graph.edgelist.Rd @@ -14,7 +14,7 @@ graph.edgelist(el, directed = TRUE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.edgelist()} was renamed to \code{graph_from_edgelist()} to create a more +\code{graph.edgelist()} was renamed to \code{\link[=graph_from_edgelist]{graph_from_edgelist()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.eigen.Rd b/man/graph.eigen.Rd index 2a374fac92..ebd3bb38c1 100644 --- a/man/graph.eigen.Rd +++ b/man/graph.eigen.Rd @@ -27,7 +27,7 @@ the corresponding eigenvector is calculated.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.eigen()} was renamed to \code{spectrum()} to create a more +\code{graph.eigen()} was renamed to \code{\link[=spectrum]{spectrum()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.empty.Rd b/man/graph.empty.Rd index 10e43e0614..3aa773805b 100644 --- a/man/graph.empty.Rd +++ b/man/graph.empty.Rd @@ -14,7 +14,7 @@ graph.empty(n = 0, directed = TRUE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.empty()} was renamed to \code{make_empty_graph()} to create a more +\code{graph.empty()} was renamed to \code{\link[=make_empty_graph]{make_empty_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.extended.chordal.ring.Rd b/man/graph.extended.chordal.ring.Rd index 6bb8c5004b..9166334f8a 100644 --- a/man/graph.extended.chordal.ring.Rd +++ b/man/graph.extended.chordal.ring.Rd @@ -17,7 +17,7 @@ details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.extended.chordal.ring()} was renamed to \code{make_chordal_ring()} to create a more +\code{graph.extended.chordal.ring()} was renamed to \code{\link[=make_chordal_ring]{make_chordal_ring()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.famous.Rd b/man/graph.famous.Rd index d5bb7f4a00..d06866188e 100644 --- a/man/graph.famous.Rd +++ b/man/graph.famous.Rd @@ -55,7 +55,7 @@ Do not give both of them.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.famous()} was renamed to \code{make_graph()} to create a more +\code{graph.famous()} was renamed to \code{\link[=make_graph]{make_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.formula.Rd b/man/graph.formula.Rd index dcf759191d..fcc871c91e 100644 --- a/man/graph.formula.Rd +++ b/man/graph.formula.Rd @@ -18,7 +18,7 @@ multiple edges are removed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.formula()} was renamed to \code{graph_from_literal()} to create a more +\code{graph.formula()} was renamed to \code{\link[=graph_from_literal]{graph_from_literal()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.full.Rd b/man/graph.full.Rd index b466b68847..daeb623a77 100644 --- a/man/graph.full.Rd +++ b/man/graph.full.Rd @@ -16,7 +16,7 @@ graph.full(n, directed = FALSE, loops = FALSE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.full()} was renamed to \code{make_full_graph()} to create a more +\code{graph.full()} was renamed to \code{\link[=make_full_graph]{make_full_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.full.bipartite.Rd b/man/graph.full.bipartite.Rd index f59e7f010b..37346a98be 100644 --- a/man/graph.full.bipartite.Rd +++ b/man/graph.full.bipartite.Rd @@ -22,7 +22,7 @@ ignored for undirected graphs.x} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.full.bipartite()} was renamed to \code{make_full_bipartite_graph()} to create a more +\code{graph.full.bipartite()} was renamed to \code{\link[=make_full_bipartite_graph]{make_full_bipartite_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.full.citation.Rd b/man/graph.full.citation.Rd index 64eca86958..37b55e0745 100644 --- a/man/graph.full.citation.Rd +++ b/man/graph.full.citation.Rd @@ -14,7 +14,7 @@ graph.full.citation(n, directed = TRUE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.full.citation()} was renamed to \code{make_full_citation_graph()} to create a more +\code{graph.full.citation()} was renamed to \code{\link[=make_full_citation_graph]{make_full_citation_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.graphdb.Rd b/man/graph.graphdb.Rd index 9f5b4ce278..c4b76001b5 100644 --- a/man/graph.graphdb.Rd +++ b/man/graph.graphdb.Rd @@ -50,7 +50,7 @@ suffix is added to the filename.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.graphdb()} was renamed to \code{graph_from_graphdb()} to create a more +\code{graph.graphdb()} was renamed to \code{\link[=graph_from_graphdb]{graph_from_graphdb()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.incidence.Rd b/man/graph.incidence.Rd index 1f0922a443..83db1f0009 100644 --- a/man/graph.incidence.Rd +++ b/man/graph.incidence.Rd @@ -50,7 +50,7 @@ type) will be added.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.incidence()} was renamed to \code{graph_from_biadjacency_matrix()} to create a more +\code{graph.incidence()} was renamed to \code{\link[=graph_from_biadjacency_matrix]{graph_from_biadjacency_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.intersection.Rd b/man/graph.intersection.Rd index 6f937f6a66..02d7a01053 100644 --- a/man/graph.intersection.Rd +++ b/man/graph.intersection.Rd @@ -13,7 +13,7 @@ the function that implements \code{intersection()}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.intersection()} was renamed to \code{intersection()} to create a more +\code{graph.intersection()} was renamed to \code{\link[=intersection]{intersection()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.isocreate.Rd b/man/graph.isocreate.Rd index a1b02f4dcc..7db881837d 100644 --- a/man/graph.isocreate.Rd +++ b/man/graph.isocreate.Rd @@ -16,7 +16,7 @@ graph.isocreate(size, number, directed = TRUE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.isocreate()} was renamed to \code{graph_from_isomorphism_class()} to create a more +\code{graph.isocreate()} was renamed to \code{\link[=graph_from_isomorphism_class]{graph_from_isomorphism_class()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.kautz.Rd b/man/graph.kautz.Rd index be6751fd79..dc3f41474f 100644 --- a/man/graph.kautz.Rd +++ b/man/graph.kautz.Rd @@ -14,7 +14,7 @@ graph.kautz(m, n) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.kautz()} was renamed to \code{make_kautz_graph()} to create a more +\code{graph.kautz()} was renamed to \code{\link[=make_kautz_graph]{make_kautz_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.knn.Rd b/man/graph.knn.Rd index 82f2ebf636..7b8202a3a6 100644 --- a/man/graph.knn.Rd +++ b/man/graph.knn.Rd @@ -39,7 +39,7 @@ Weights are are used to calculate a weighted degree (also called \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.knn()} was renamed to \code{knn()} to create a more +\code{graph.knn()} was renamed to \code{\link[=knn]{knn()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.laplacian.Rd b/man/graph.laplacian.Rd index 0f9d422662..d72126e7b0 100644 --- a/man/graph.laplacian.Rd +++ b/man/graph.laplacian.Rd @@ -28,7 +28,7 @@ matrix. The \code{Matrix} package is required for sparse matrices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.laplacian()} was renamed to \code{laplacian_matrix()} to create a more +\code{graph.laplacian()} was renamed to \code{\link[=laplacian_matrix]{laplacian_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.lattice.Rd b/man/graph.lattice.Rd index 0435ebc746..58b4d735ff 100644 --- a/man/graph.lattice.Rd +++ b/man/graph.lattice.Rd @@ -41,7 +41,7 @@ be extended to boolean vector with dimvector length.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.lattice()} was renamed to \code{make_lattice()} to create a more +\code{graph.lattice()} was renamed to \code{\link[=make_lattice]{make_lattice()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.lcf.Rd b/man/graph.lcf.Rd index 561f84b459..2ba86e80bc 100644 --- a/man/graph.lcf.Rd +++ b/man/graph.lcf.Rd @@ -16,7 +16,7 @@ graph.lcf(n, shifts, repeats = 1) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.lcf()} was renamed to \code{graph_from_lcf()} to create a more +\code{graph.lcf()} was renamed to \code{\link[=graph_from_lcf]{graph_from_lcf()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.maxflow.Rd b/man/graph.maxflow.Rd index ba39c71a56..a441a5a868 100644 --- a/man/graph.maxflow.Rd +++ b/man/graph.maxflow.Rd @@ -20,7 +20,7 @@ Note that the \code{weight} edge attribute is not used by this function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.maxflow()} was renamed to \code{max_flow()} to create a more +\code{graph.maxflow()} was renamed to \code{\link[=max_flow]{max_flow()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.mincut.Rd b/man/graph.mincut.Rd index bfd204590c..a2a6a43020 100644 --- a/man/graph.mincut.Rd +++ b/man/graph.mincut.Rd @@ -29,7 +29,7 @@ partitions are also returned.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.mincut()} was renamed to \code{min_cut()} to create a more +\code{graph.mincut()} was renamed to \code{\link[=min_cut]{min_cut()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.motifs.Rd b/man/graph.motifs.Rd index a39940bdb8..5d6ffcf8a2 100644 --- a/man/graph.motifs.Rd +++ b/man/graph.motifs.Rd @@ -20,7 +20,7 @@ If \verb{rep(0, size))}, the default, no cuts are made.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.motifs()} was renamed to \code{motifs()} to create a more +\code{graph.motifs()} was renamed to \code{\link[=motifs]{motifs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.motifs.est.Rd b/man/graph.motifs.est.Rd index 59302b12fd..d2284e800c 100644 --- a/man/graph.motifs.est.Rd +++ b/man/graph.motifs.est.Rd @@ -33,7 +33,7 @@ starting point for finding motifs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.motifs.est()} was renamed to \code{sample_motifs()} to create a more +\code{graph.motifs.est()} was renamed to \code{\link[=sample_motifs]{sample_motifs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.motifs.no.Rd b/man/graph.motifs.no.Rd index 15e01bcec7..801430b8fa 100644 --- a/man/graph.motifs.no.Rd +++ b/man/graph.motifs.no.Rd @@ -19,7 +19,7 @@ If \code{NULL}, the default, no cuts are made.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.motifs.no()} was renamed to \code{count_motifs()} to create a more +\code{graph.motifs.no()} was renamed to \code{\link[=count_motifs]{count_motifs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.neighborhood.Rd b/man/graph.neighborhood.Rd index 9ecda49445..5e322a65d4 100644 --- a/man/graph.neighborhood.Rd +++ b/man/graph.neighborhood.Rd @@ -33,7 +33,7 @@ argument is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.neighborhood()} was renamed to \code{make_ego_graph()} to create a more +\code{graph.neighborhood()} was renamed to \code{\link[=make_ego_graph]{make_ego_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.ring.Rd b/man/graph.ring.Rd index ec1d13c8b6..462ce3e011 100644 --- a/man/graph.ring.Rd +++ b/man/graph.ring.Rd @@ -21,7 +21,7 @@ vertex has one child.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.ring()} was renamed to \code{make_ring()} to create a more +\code{graph.ring()} was renamed to \code{\link[=make_ring]{make_ring()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.star.Rd b/man/graph.star.Rd index f2efd88215..ad3809bbc3 100644 --- a/man/graph.star.Rd +++ b/man/graph.star.Rd @@ -20,7 +20,7 @@ are undirected.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.star()} was renamed to \code{make_star()} to create a more +\code{graph.star()} was renamed to \code{\link[=make_star]{make_star()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.strength.Rd b/man/graph.strength.Rd index 23ee3b847c..b0a556be30 100644 --- a/man/graph.strength.Rd +++ b/man/graph.strength.Rd @@ -32,7 +32,7 @@ attribute, then this is used by default. If the graph does not have a \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.strength()} was renamed to \code{strength()} to create a more +\code{graph.strength()} was renamed to \code{\link[=strength]{strength()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.tree.Rd b/man/graph.tree.Rd index 1bcb300157..1c8b229932 100644 --- a/man/graph.tree.Rd +++ b/man/graph.tree.Rd @@ -21,7 +21,7 @@ graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.tree()} was renamed to \code{make_tree()} to create a more +\code{graph.tree()} was renamed to \code{\link[=make_tree]{make_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph.union.Rd b/man/graph.union.Rd index 48d65bebb3..37dfa718af 100644 --- a/man/graph.union.Rd +++ b/man/graph.union.Rd @@ -18,7 +18,7 @@ graphs are named.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph.union()} was renamed to \code{union.igraph()} to create a more +\code{graph.union()} was renamed to \code{\link[=union.igraph]{union.igraph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graph_from_incidence_matrix.Rd b/man/graph_from_incidence_matrix.Rd index c7f6cf1df1..dd357fafaf 100644 --- a/man/graph_from_incidence_matrix.Rd +++ b/man/graph_from_incidence_matrix.Rd @@ -9,7 +9,7 @@ graph_from_incidence_matrix(...) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graph_from_incidence_matrix()} was renamed to \code{graph_from_biadjacency_matrix()} to create a more +\code{graph_from_incidence_matrix()} was renamed to \code{\link[=graph_from_biadjacency_matrix]{graph_from_biadjacency_matrix()}} to create a more consistent API. } \details{ diff --git a/man/graphlets.candidate.basis.Rd b/man/graphlets.candidate.basis.Rd index 7a6a12a12b..917e3f93d7 100644 --- a/man/graphlets.candidate.basis.Rd +++ b/man/graphlets.candidate.basis.Rd @@ -17,7 +17,7 @@ attribute is used.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graphlets.candidate.basis()} was renamed to \code{graphlet_basis()} to create a more +\code{graphlets.candidate.basis()} was renamed to \code{\link[=graphlet_basis]{graphlet_basis()}} to create a more consistent API. } \keyword{internal} diff --git a/man/graphlets.project.Rd b/man/graphlets.project.Rd index e16e9554f4..2ad48efd98 100644 --- a/man/graphlets.project.Rd +++ b/man/graphlets.project.Rd @@ -30,7 +30,7 @@ projection.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{graphlets.project()} was renamed to \code{graphlet_proj()} to create a more +\code{graphlets.project()} was renamed to \code{\link[=graphlet_proj]{graphlet_proj()}} to create a more consistent API. } \keyword{internal} diff --git a/man/grg.game.Rd b/man/grg.game.Rd index e5858787f3..4c430f572d 100644 --- a/man/grg.game.Rd +++ b/man/grg.game.Rd @@ -20,7 +20,7 @@ as vertex attributes called \sQuote{\code{x}} and \sQuote{\code{y}}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{grg.game()} was renamed to \code{sample_grg()} to create a more +\code{grg.game()} was renamed to \code{\link[=sample_grg]{sample_grg()}} to create a more consistent API. } \keyword{internal} diff --git a/man/growing.random.game.Rd b/man/growing.random.game.Rd index 4d575cb50f..0059c10d36 100644 --- a/man/growing.random.game.Rd +++ b/man/growing.random.game.Rd @@ -19,7 +19,7 @@ each time step the added edges are originating from the new vertex.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{growing.random.game()} was renamed to \code{sample_growing()} to create a more +\code{growing.random.game()} was renamed to \code{\link[=sample_growing]{sample_growing()}} to create a more consistent API. } \keyword{internal} diff --git a/man/has.multiple.Rd b/man/has.multiple.Rd index d7c9c6d88a..1c928b34ae 100644 --- a/man/has.multiple.Rd +++ b/man/has.multiple.Rd @@ -12,7 +12,7 @@ has.multiple(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{has.multiple()} was renamed to \code{any_multiple()} to create a more +\code{has.multiple()} was renamed to \code{\link[=any_multiple]{any_multiple()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.consensus.Rd b/man/hrg.consensus.Rd index a2cf893ed4..cffdc7dc09 100644 --- a/man/hrg.consensus.Rd +++ b/man/hrg.consensus.Rd @@ -23,7 +23,7 @@ missing edge prediction.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.consensus()} was renamed to \code{consensus_tree()} to create a more +\code{hrg.consensus()} was renamed to \code{\link[=consensus_tree]{consensus_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.create.Rd b/man/hrg.create.Rd index 86bcf73482..c1e72dcdcf 100644 --- a/man/hrg.create.Rd +++ b/man/hrg.create.Rd @@ -15,7 +15,7 @@ vertex ids.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.create()} was renamed to \code{hrg()} to create a more +\code{hrg.create()} was renamed to \code{\link[=hrg]{hrg()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.dendrogram.Rd b/man/hrg.dendrogram.Rd index f163c00e3f..9b544ba36c 100644 --- a/man/hrg.dendrogram.Rd +++ b/man/hrg.dendrogram.Rd @@ -12,7 +12,7 @@ hrg.dendrogram(hrg) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.dendrogram()} was renamed to \code{hrg_tree()} to create a more +\code{hrg.dendrogram()} was renamed to \code{\link[=hrg_tree]{hrg_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.fit.Rd b/man/hrg.fit.Rd index 0684aa2651..7f931185fe 100644 --- a/man/hrg.fit.Rd +++ b/man/hrg.fit.Rd @@ -23,7 +23,7 @@ MCMC procedure is performed until convergence.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.fit()} was renamed to \code{fit_hrg()} to create a more +\code{hrg.fit()} was renamed to \code{\link[=fit_hrg]{fit_hrg()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.game.Rd b/man/hrg.game.Rd index b58e25dad6..573826f3f8 100644 --- a/man/hrg.game.Rd +++ b/man/hrg.game.Rd @@ -12,7 +12,7 @@ hrg.game(hrg) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.game()} was renamed to \code{sample_hrg()} to create a more +\code{hrg.game()} was renamed to \code{\link[=sample_hrg]{sample_hrg()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hrg.predict.Rd b/man/hrg.predict.Rd index 5a833edbfb..015abe0a66 100644 --- a/man/hrg.predict.Rd +++ b/man/hrg.predict.Rd @@ -33,7 +33,7 @@ number for a more accurate prediction.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hrg.predict()} was renamed to \code{predict_edges()} to create a more +\code{hrg.predict()} was renamed to \code{\link[=predict_edges]{predict_edges()}} to create a more consistent API. } \keyword{internal} diff --git a/man/hub.score.Rd b/man/hub.score.Rd index 53822e7665..64216c3c11 100644 --- a/man/hub.score.Rd +++ b/man/hub.score.Rd @@ -26,7 +26,7 @@ selected by the surfer.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{hub.score()} was renamed to \code{hub_score()} to create a more +\code{hub.score()} was renamed to \code{\link[=hub_score]{hub_score()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.console.Rd b/man/igraph.console.Rd index 6b526fbe87..6903d3c1bd 100644 --- a/man/igraph.console.Rd +++ b/man/igraph.console.Rd @@ -9,7 +9,7 @@ igraph.console() \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.console()} was renamed to \code{console()} to create a more +\code{igraph.console()} was renamed to \code{\link[=console]{console()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.from.graphNEL.Rd b/man/igraph.from.graphNEL.Rd index 2731a8d70c..451b91f241 100644 --- a/man/igraph.from.graphNEL.Rd +++ b/man/igraph.from.graphNEL.Rd @@ -24,7 +24,7 @@ whenever possible, before adding them to the igraph graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.from.graphNEL()} was renamed to \code{graph_from_graphnel()} to create a more +\code{igraph.from.graphNEL()} was renamed to \code{\link[=graph_from_graphnel]{graph_from_graphnel()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.options.Rd b/man/igraph.options.Rd index 2dcb1ded5a..819399bb70 100644 --- a/man/igraph.options.Rd +++ b/man/igraph.options.Rd @@ -14,7 +14,7 @@ given. See the Value and Details sections for explanation.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.options()} was renamed to \code{igraph_options()} to create a more +\code{igraph.options()} was renamed to \code{\link[=igraph_options]{igraph_options()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.sample.Rd b/man/igraph.sample.Rd index 7b9b6a3ab8..a4e6fab216 100644 --- a/man/igraph.sample.Rd +++ b/man/igraph.sample.Rd @@ -16,7 +16,7 @@ igraph.sample(low, high, length) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.sample()} was renamed to \code{sample_seq()} to create a more +\code{igraph.sample()} was renamed to \code{\link[=sample_seq]{sample_seq()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.shape.noclip.Rd b/man/igraph.shape.noclip.Rd index 56b7a86d52..f3c32d1c89 100644 --- a/man/igraph.shape.noclip.Rd +++ b/man/igraph.shape.noclip.Rd @@ -9,7 +9,7 @@ igraph.shape.noclip(coords, el, params, end = c("both", "from", "to")) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.shape.noclip()} was renamed to \code{shape_noclip()} to create a more +\code{igraph.shape.noclip()} was renamed to \code{\link[=shape_noclip]{shape_noclip()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.shape.noplot.Rd b/man/igraph.shape.noplot.Rd index d824ee3df3..c97f1fc969 100644 --- a/man/igraph.shape.noplot.Rd +++ b/man/igraph.shape.noplot.Rd @@ -9,7 +9,7 @@ igraph.shape.noplot(coords, v = NULL, params) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.shape.noplot()} was renamed to \code{shape_noplot()} to create a more +\code{igraph.shape.noplot()} was renamed to \code{\link[=shape_noplot]{shape_noplot()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.to.graphNEL.Rd b/man/igraph.to.graphNEL.Rd index 7825b1e456..80a31e9dc8 100644 --- a/man/igraph.to.graphNEL.Rd +++ b/man/igraph.to.graphNEL.Rd @@ -12,7 +12,7 @@ igraph.to.graphNEL(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.to.graphNEL()} was renamed to \code{as_graphnel()} to create a more +\code{igraph.to.graphNEL()} was renamed to \code{\link[=as_graphnel]{as_graphnel()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraph.version.Rd b/man/igraph.version.Rd index b782b69ed0..0588348ab9 100644 --- a/man/igraph.version.Rd +++ b/man/igraph.version.Rd @@ -9,7 +9,7 @@ igraph.version() \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraph.version()} was renamed to \code{igraph_version()} to create a more +\code{igraph.version()} was renamed to \code{\link[=igraph_version]{igraph_version()}} to create a more consistent API. } \keyword{internal} diff --git a/man/igraphdemo.Rd b/man/igraphdemo.Rd index a03b308fd1..08141022cd 100644 --- a/man/igraphdemo.Rd +++ b/man/igraphdemo.Rd @@ -13,7 +13,7 @@ Otherwise it should be either a filename or the name of an igraph demo.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{igraphdemo()} was renamed to \code{igraph_demo()} to create a more +\code{igraphdemo()} was renamed to \code{\link[=igraph_demo]{igraph_demo()}} to create a more consistent API. } \keyword{internal} diff --git a/man/independence.number.Rd b/man/independence.number.Rd index 23d7d3f336..1b58e94416 100644 --- a/man/independence.number.Rd +++ b/man/independence.number.Rd @@ -12,7 +12,7 @@ independence.number(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{independence.number()} was renamed to \code{ivs_size()} to create a more +\code{independence.number()} was renamed to \code{\link[=ivs_size]{ivs_size()}} to create a more consistent API. } \keyword{internal} diff --git a/man/independent.vertex.sets.Rd b/man/independent.vertex.sets.Rd index a400e074a2..007cf945fb 100644 --- a/man/independent.vertex.sets.Rd +++ b/man/independent.vertex.sets.Rd @@ -18,7 +18,7 @@ vertex sets to find. \code{NULL} means no limit.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{independent.vertex.sets()} was renamed to \code{ivs()} to create a more +\code{independent.vertex.sets()} was renamed to \code{\link[=ivs]{ivs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/induced.subgraph.Rd b/man/induced.subgraph.Rd index a10f45624a..bdd39ecd4e 100644 --- a/man/induced.subgraph.Rd +++ b/man/induced.subgraph.Rd @@ -28,7 +28,7 @@ result graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{induced.subgraph()} was renamed to \code{induced_subgraph()} to create a more +\code{induced.subgraph()} was renamed to \code{\link[=induced_subgraph]{induced_subgraph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/infomap.community.Rd b/man/infomap.community.Rd index 89b326dac0..6814f95b1c 100644 --- a/man/infomap.community.Rd +++ b/man/infomap.community.Rd @@ -37,7 +37,7 @@ of the detected community structure.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{infomap.community()} was renamed to \code{cluster_infomap()} to create a more +\code{infomap.community()} was renamed to \code{\link[=cluster_infomap]{cluster_infomap()}} to create a more consistent API. } \keyword{internal} diff --git a/man/interconnected.islands.game.Rd b/man/interconnected.islands.game.Rd index 93d945f8cf..e7876315b3 100644 --- a/man/interconnected.islands.game.Rd +++ b/man/interconnected.islands.game.Rd @@ -19,7 +19,7 @@ island.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{interconnected.islands.game()} was renamed to \code{sample_islands()} to create a more +\code{interconnected.islands.game()} was renamed to \code{\link[=sample_islands]{sample_islands()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.bipartite.Rd b/man/is.bipartite.Rd index 91d02ae47a..3df3b59a5c 100644 --- a/man/is.bipartite.Rd +++ b/man/is.bipartite.Rd @@ -12,7 +12,7 @@ is.bipartite(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.bipartite()} was renamed to \code{is_bipartite()} to create a more +\code{is.bipartite()} was renamed to \code{\link[=is_bipartite]{is_bipartite()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.chordal.Rd b/man/is.chordal.Rd index d11da48415..9a6926bde6 100644 --- a/man/is.chordal.Rd +++ b/man/is.chordal.Rd @@ -32,7 +32,7 @@ that is given..} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.chordal()} was renamed to \code{is_chordal()} to create a more +\code{is.chordal()} was renamed to \code{\link[=is_chordal]{is_chordal()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.connected.Rd b/man/is.connected.Rd index 5b9d7aaab5..41e307952a 100644 --- a/man/is.connected.Rd +++ b/man/is.connected.Rd @@ -16,7 +16,7 @@ connected components to search. It is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.connected()} was renamed to \code{is_connected()} to create a more +\code{is.connected()} was renamed to \code{\link[=is_connected]{is_connected()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.dag.Rd b/man/is.dag.Rd index 7aa7333df9..5ebd55f8c4 100644 --- a/man/is.dag.Rd +++ b/man/is.dag.Rd @@ -13,7 +13,7 @@ is.dag(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.dag()} was renamed to \code{is_dag()} to create a more +\code{is.dag()} was renamed to \code{\link[=is_dag]{is_dag()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.degree.sequence.Rd b/man/is.degree.sequence.Rd index a094c08539..e382eaf150 100644 --- a/man/is.degree.sequence.Rd +++ b/man/is.degree.sequence.Rd @@ -16,7 +16,7 @@ should be \code{NULL}. For directed graphs it specifies the in-degrees.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.degree.sequence()} was renamed to \code{is_degseq()} to create a more +\code{is.degree.sequence()} was renamed to \code{\link[=is_degseq]{is_degseq()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.directed.Rd b/man/is.directed.Rd index 6504ec7b97..800f842bff 100644 --- a/man/is.directed.Rd +++ b/man/is.directed.Rd @@ -12,7 +12,7 @@ is.directed(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.directed()} was renamed to \code{is_directed()} to create a more +\code{is.directed()} was renamed to \code{\link[=is_directed]{is_directed()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.graphical.degree.sequence.Rd b/man/is.graphical.degree.sequence.Rd index 083dd3dffd..a17e74ebd0 100644 --- a/man/is.graphical.degree.sequence.Rd +++ b/man/is.graphical.degree.sequence.Rd @@ -27,7 +27,7 @@ allowed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.graphical.degree.sequence()} was renamed to \code{is_graphical()} to create a more +\code{is.graphical.degree.sequence()} was renamed to \code{\link[=is_graphical]{is_graphical()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.hierarchical.Rd b/man/is.hierarchical.Rd index 585e656a36..0df3d516d3 100644 --- a/man/is.hierarchical.Rd +++ b/man/is.hierarchical.Rd @@ -9,7 +9,7 @@ is.hierarchical(communities) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.hierarchical()} was renamed to \code{is_hierarchical()} to create a more +\code{is.hierarchical()} was renamed to \code{\link[=is_hierarchical]{is_hierarchical()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.igraph.Rd b/man/is.igraph.Rd index 53d26bbb24..7baebadadb 100644 --- a/man/is.igraph.Rd +++ b/man/is.igraph.Rd @@ -12,7 +12,7 @@ is.igraph(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.igraph()} was renamed to \code{is_igraph()} to create a more +\code{is.igraph()} was renamed to \code{\link[=is_igraph]{is_igraph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.loop.Rd b/man/is.loop.Rd index f4f73f0b03..81f9d1d070 100644 --- a/man/is.loop.Rd +++ b/man/is.loop.Rd @@ -15,7 +15,7 @@ all edges in the graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.loop()} was renamed to \code{which_loop()} to create a more +\code{is.loop()} was renamed to \code{\link[=which_loop]{which_loop()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.matching.Rd b/man/is.matching.Rd index 308558038f..e034615d00 100644 --- a/man/is.matching.Rd +++ b/man/is.matching.Rd @@ -20,7 +20,7 @@ are taken from the \sQuote{\code{type}} vertex attribute, if present.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.matching()} was renamed to \code{is_matching()} to create a more +\code{is.matching()} was renamed to \code{\link[=is_matching]{is_matching()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.maximal.matching.Rd b/man/is.maximal.matching.Rd index 16bcb97589..f48288c578 100644 --- a/man/is.maximal.matching.Rd +++ b/man/is.maximal.matching.Rd @@ -20,7 +20,7 @@ are taken from the \sQuote{\code{type}} vertex attribute, if present.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.maximal.matching()} was renamed to \code{is_max_matching()} to create a more +\code{is.maximal.matching()} was renamed to \code{\link[=is_max_matching]{is_max_matching()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.minimal.separator.Rd b/man/is.minimal.separator.Rd index 7dd2ab7f1b..3c86bfaaa7 100644 --- a/man/is.minimal.separator.Rd +++ b/man/is.minimal.separator.Rd @@ -16,7 +16,7 @@ separator.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.minimal.separator()} was renamed to \code{is_min_separator()} to create a more +\code{is.minimal.separator()} was renamed to \code{\link[=is_min_separator]{is_min_separator()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.multiple.Rd b/man/is.multiple.Rd index 94d5bddb84..cc062a2582 100644 --- a/man/is.multiple.Rd +++ b/man/is.multiple.Rd @@ -15,7 +15,7 @@ all edges in the graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.multiple()} was renamed to \code{which_multiple()} to create a more +\code{is.multiple()} was renamed to \code{\link[=which_multiple]{which_multiple()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.mutual.Rd b/man/is.mutual.Rd index 1c77ca435f..923bd67edf 100644 --- a/man/is.mutual.Rd +++ b/man/is.mutual.Rd @@ -17,7 +17,7 @@ includes all edges in the order of their ids.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.mutual()} was renamed to \code{which_mutual()} to create a more +\code{is.mutual()} was renamed to \code{\link[=which_mutual]{which_mutual()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.named.Rd b/man/is.named.Rd index f46cbcac02..f55f452ab7 100644 --- a/man/is.named.Rd +++ b/man/is.named.Rd @@ -12,7 +12,7 @@ is.named(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.named()} was renamed to \code{is_named()} to create a more +\code{is.named()} was renamed to \code{\link[=is_named]{is_named()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.separator.Rd b/man/is.separator.Rd index 3e5daeb31e..08bb7b55a1 100644 --- a/man/is.separator.Rd +++ b/man/is.separator.Rd @@ -16,7 +16,7 @@ separator.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.separator()} was renamed to \code{is_separator()} to create a more +\code{is.separator()} was renamed to \code{\link[=is_separator]{is_separator()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.simple.Rd b/man/is.simple.Rd index 2d4ecb434e..1629caa51d 100644 --- a/man/is.simple.Rd +++ b/man/is.simple.Rd @@ -12,7 +12,7 @@ is.simple(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.simple()} was renamed to \code{is_simple()} to create a more +\code{is.simple()} was renamed to \code{\link[=is_simple]{is_simple()}} to create a more consistent API. } \keyword{internal} diff --git a/man/is.weighted.Rd b/man/is.weighted.Rd index 28099ed6ce..d1263895bc 100644 --- a/man/is.weighted.Rd +++ b/man/is.weighted.Rd @@ -12,7 +12,7 @@ is.weighted(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{is.weighted()} was renamed to \code{is_weighted()} to create a more +\code{is.weighted()} was renamed to \code{\link[=is_weighted]{is_weighted()}} to create a more consistent API. } \keyword{internal} diff --git a/man/k.regular.game.Rd b/man/k.regular.game.Rd index f0fd01b0b5..6dde63c85f 100644 --- a/man/k.regular.game.Rd +++ b/man/k.regular.game.Rd @@ -20,7 +20,7 @@ out-degree and in-degree in a directed graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{k.regular.game()} was renamed to \code{sample_k_regular()} to create a more +\code{k.regular.game()} was renamed to \code{\link[=sample_k_regular]{sample_k_regular()}} to create a more consistent API. } \keyword{internal} diff --git a/man/label.propagation.community.Rd b/man/label.propagation.community.Rd index 72b63cf090..1f17fd8c98 100644 --- a/man/label.propagation.community.Rd +++ b/man/label.propagation.community.Rd @@ -47,7 +47,7 @@ will be ignored. Also note that vertices without labels cannot be fixed.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{label.propagation.community()} was renamed to \code{cluster_label_prop()} to create a more +\code{label.propagation.community()} was renamed to \code{\link[=cluster_label_prop]{cluster_label_prop()}} to create a more consistent API. } \keyword{internal} diff --git a/man/largest.cliques.Rd b/man/largest.cliques.Rd index 7ad65f633f..66bc925bc2 100644 --- a/man/largest.cliques.Rd +++ b/man/largest.cliques.Rd @@ -12,7 +12,7 @@ largest.cliques(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{largest.cliques()} was renamed to \code{largest_cliques()} to create a more +\code{largest.cliques()} was renamed to \code{\link[=largest_cliques]{largest_cliques()}} to create a more consistent API. } \keyword{internal} diff --git a/man/largest.independent.vertex.sets.Rd b/man/largest.independent.vertex.sets.Rd index 0e57e435b7..90baaf9022 100644 --- a/man/largest.independent.vertex.sets.Rd +++ b/man/largest.independent.vertex.sets.Rd @@ -12,7 +12,7 @@ largest.independent.vertex.sets(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{largest.independent.vertex.sets()} was renamed to \code{largest_ivs()} to create a more +\code{largest.independent.vertex.sets()} was renamed to \code{\link[=largest_ivs]{largest_ivs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/lastcit.game.Rd b/man/lastcit.game.Rd index eb3964a0aa..3cc3232c1f 100644 --- a/man/lastcit.game.Rd +++ b/man/lastcit.game.Rd @@ -28,7 +28,7 @@ probabilities for the different vertex types.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{lastcit.game()} was renamed to \code{sample_last_cit()} to create a more +\code{lastcit.game()} was renamed to \code{\link[=sample_last_cit]{sample_last_cit()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.auto.Rd b/man/layout.auto.Rd index a95c4e0b3b..918012af09 100644 --- a/man/layout.auto.Rd +++ b/man/layout.auto.Rd @@ -18,7 +18,7 @@ the real layout function. For \code{nicely()} all argument are passed to \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.auto()} was renamed to \code{layout_nicely()} to create a more +\code{layout.auto()} was renamed to \code{\link[=layout_nicely]{layout_nicely()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.bipartite.Rd b/man/layout.bipartite.Rd index ae9bc139b6..d4873e80f9 100644 --- a/man/layout.bipartite.Rd +++ b/man/layout.bipartite.Rd @@ -27,7 +27,7 @@ you have too many edge crossings, increase this.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.bipartite()} was renamed to \code{layout_as_bipartite()} to create a more +\code{layout.bipartite()} was renamed to \code{\link[=layout_as_bipartite]{layout_as_bipartite()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.circle.Rd b/man/layout.circle.Rd index 365f9a0369..411b4eedb2 100644 --- a/man/layout.circle.Rd +++ b/man/layout.circle.Rd @@ -14,7 +14,7 @@ layout.circle(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.circle()} was renamed to \code{layout_in_circle()} to create a more +\code{layout.circle()} was renamed to \code{\link[=layout_in_circle]{layout_in_circle()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.davidson.harel.Rd b/man/layout.davidson.harel.Rd index c961a4cd8d..693f209223 100644 --- a/man/layout.davidson.harel.Rd +++ b/man/layout.davidson.harel.Rd @@ -49,7 +49,7 @@ the energy function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.davidson.harel()} was renamed to \code{layout_with_dh()} to create a more +\code{layout.davidson.harel()} was renamed to \code{\link[=layout_with_dh]{layout_with_dh()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.drl.Rd b/man/layout.drl.Rd index 0457d084ea..8d95290403 100644 --- a/man/layout.drl.Rd +++ b/man/layout.drl.Rd @@ -41,7 +41,7 @@ significantly longer to compute.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.drl()} was renamed to \code{layout_with_drl()} to create a more +\code{layout.drl()} was renamed to \code{\link[=layout_with_drl]{layout_with_drl()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.fruchterman.reingold.Rd b/man/layout.fruchterman.reingold.Rd index 9a539e6bc0..960e60adb3 100644 --- a/man/layout.fruchterman.reingold.Rd +++ b/man/layout.fruchterman.reingold.Rd @@ -14,7 +14,7 @@ layout.fruchterman.reingold(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.fruchterman.reingold()} was renamed to \code{layout_with_fr()} to create a more +\code{layout.fruchterman.reingold()} was renamed to \code{\link[=layout_with_fr]{layout_with_fr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.gem.Rd b/man/layout.gem.Rd index a53adc0ca8..78a3b23cb0 100644 --- a/man/layout.gem.Rd +++ b/man/layout.gem.Rd @@ -38,7 +38,7 @@ default is the square root of the number of vertices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.gem()} was renamed to \code{layout_with_gem()} to create a more +\code{layout.gem()} was renamed to \code{\link[=layout_with_gem]{layout_with_gem()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.graphopt.Rd b/man/layout.graphopt.Rd index 05bd52f4bc..6ae8c116bd 100644 --- a/man/layout.graphopt.Rd +++ b/man/layout.graphopt.Rd @@ -46,7 +46,7 @@ movement allowed in a single step along a single axis. The default value is \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.graphopt()} was renamed to \code{layout_with_graphopt()} to create a more +\code{layout.graphopt()} was renamed to \code{\link[=layout_with_graphopt]{layout_with_graphopt()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.grid.Rd b/man/layout.grid.Rd index b964807d7f..d022e74396 100644 --- a/man/layout.grid.Rd +++ b/man/layout.grid.Rd @@ -23,7 +23,7 @@ determinted automatically.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.grid()} was renamed to \code{layout_on_grid()} to create a more +\code{layout.grid()} was renamed to \code{\link[=layout_on_grid]{layout_on_grid()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.kamada.kawai.Rd b/man/layout.kamada.kawai.Rd index c6a61a58a1..5b7652d09a 100644 --- a/man/layout.kamada.kawai.Rd +++ b/man/layout.kamada.kawai.Rd @@ -14,7 +14,7 @@ layout.kamada.kawai(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.kamada.kawai()} was renamed to \code{layout_with_kk()} to create a more +\code{layout.kamada.kawai()} was renamed to \code{\link[=layout_with_kk]{layout_with_kk()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.lgl.Rd b/man/layout.lgl.Rd index b99525f298..b641b81a5b 100644 --- a/man/layout.lgl.Rd +++ b/man/layout.lgl.Rd @@ -14,7 +14,7 @@ layout.lgl(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.lgl()} was renamed to \code{layout_with_lgl()} to create a more +\code{layout.lgl()} was renamed to \code{\link[=layout_with_lgl]{layout_with_lgl()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.mds.Rd b/man/layout.mds.Rd index bfc263b959..6514e3a1c4 100644 --- a/man/layout.mds.Rd +++ b/man/layout.mds.Rd @@ -23,7 +23,7 @@ solving the eigenproblem} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.mds()} was renamed to \code{layout_with_mds()} to create a more +\code{layout.mds()} was renamed to \code{\link[=layout_with_mds]{layout_with_mds()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.merge.Rd b/man/layout.merge.Rd index c8306f5e56..1430791832 100644 --- a/man/layout.merge.Rd +++ b/man/layout.merge.Rd @@ -17,7 +17,7 @@ layout.merge(graphs, layouts, method = "dla") \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.merge()} was renamed to \code{merge_coords()} to create a more +\code{layout.merge()} was renamed to \code{\link[=merge_coords]{merge_coords()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.norm.Rd b/man/layout.norm.Rd index 711b13ea28..4e67feccf5 100644 --- a/man/layout.norm.Rd +++ b/man/layout.norm.Rd @@ -30,7 +30,7 @@ are \code{NULL} then no normalization is performed along this direction.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.norm()} was renamed to \code{norm_coords()} to create a more +\code{layout.norm()} was renamed to \code{\link[=norm_coords]{norm_coords()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.random.Rd b/man/layout.random.Rd index 7e63a1c702..d7564f6484 100644 --- a/man/layout.random.Rd +++ b/man/layout.random.Rd @@ -14,7 +14,7 @@ layout.random(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.random()} was renamed to \code{layout_randomly()} to create a more +\code{layout.random()} was renamed to \code{\link[=layout_randomly]{layout_randomly()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.reingold.tilford.Rd b/man/layout.reingold.tilford.Rd index ef4c6cb8be..45e9a22fa8 100644 --- a/man/layout.reingold.tilford.Rd +++ b/man/layout.reingold.tilford.Rd @@ -14,7 +14,7 @@ layout.reingold.tilford(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.reingold.tilford()} was renamed to \code{layout_as_tree()} to create a more +\code{layout.reingold.tilford()} was renamed to \code{\link[=layout_as_tree]{layout_as_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.sphere.Rd b/man/layout.sphere.Rd index 248447aa8e..cf542f4419 100644 --- a/man/layout.sphere.Rd +++ b/man/layout.sphere.Rd @@ -14,7 +14,7 @@ layout.sphere(..., params = list()) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.sphere()} was renamed to \code{layout_on_sphere()} to create a more +\code{layout.sphere()} was renamed to \code{\link[=layout_on_sphere]{layout_on_sphere()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.star.Rd b/man/layout.star.Rd index 25364c9e18..1e0fd4fbad 100644 --- a/man/layout.star.Rd +++ b/man/layout.star.Rd @@ -18,7 +18,7 @@ The default ordering is given by the vertex ids.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.star()} was renamed to \code{layout_as_star()} to create a more +\code{layout.star()} was renamed to \code{\link[=layout_as_star]{layout_as_star()}} to create a more consistent API. } \keyword{internal} diff --git a/man/layout.sugiyama.Rd b/man/layout.sugiyama.Rd index fc92543145..3a87fe3359 100644 --- a/man/layout.sugiyama.Rd +++ b/man/layout.sugiyama.Rd @@ -46,7 +46,7 @@ them.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{layout.sugiyama()} was renamed to \code{layout_with_sugiyama()} to create a more +\code{layout.sugiyama()} was renamed to \code{\link[=layout_with_sugiyama]{layout_with_sugiyama()}} to create a more consistent API. } \keyword{internal} diff --git a/man/leading.eigenvector.community.Rd b/man/leading.eigenvector.community.Rd index c35aa58bd1..8665e80228 100644 --- a/man/leading.eigenvector.community.Rd +++ b/man/leading.eigenvector.community.Rd @@ -46,7 +46,7 @@ the modularity matrix. See details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{leading.eigenvector.community()} was renamed to \code{cluster_leading_eigen()} to create a more +\code{leading.eigenvector.community()} was renamed to \code{\link[=cluster_leading_eigen]{cluster_leading_eigen()}} to create a more consistent API. } \keyword{internal} diff --git a/man/line.graph.Rd b/man/line.graph.Rd index 90ecd45077..bd56ef4771 100644 --- a/man/line.graph.Rd +++ b/man/line.graph.Rd @@ -12,7 +12,7 @@ line.graph(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{line.graph()} was renamed to \code{make_line_graph()} to create a more +\code{line.graph()} was renamed to \code{\link[=make_line_graph]{make_line_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/list.edge.attributes.Rd b/man/list.edge.attributes.Rd index 7f34f59203..e6475c08d3 100644 --- a/man/list.edge.attributes.Rd +++ b/man/list.edge.attributes.Rd @@ -12,7 +12,7 @@ list.edge.attributes(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{list.edge.attributes()} was renamed to \code{edge_attr_names()} to create a more +\code{list.edge.attributes()} was renamed to \code{\link[=edge_attr_names]{edge_attr_names()}} to create a more consistent API. } \keyword{internal} diff --git a/man/list.graph.attributes.Rd b/man/list.graph.attributes.Rd index 4ed78a6592..d156cbadce 100644 --- a/man/list.graph.attributes.Rd +++ b/man/list.graph.attributes.Rd @@ -12,7 +12,7 @@ list.graph.attributes(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{list.graph.attributes()} was renamed to \code{graph_attr_names()} to create a more +\code{list.graph.attributes()} was renamed to \code{\link[=graph_attr_names]{graph_attr_names()}} to create a more consistent API. } \keyword{internal} diff --git a/man/list.vertex.attributes.Rd b/man/list.vertex.attributes.Rd index f30d3bb049..7c5bb9f613 100644 --- a/man/list.vertex.attributes.Rd +++ b/man/list.vertex.attributes.Rd @@ -12,7 +12,7 @@ list.vertex.attributes(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{list.vertex.attributes()} was renamed to \code{vertex_attr_names()} to create a more +\code{list.vertex.attributes()} was renamed to \code{\link[=vertex_attr_names]{vertex_attr_names()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maxcohesion.Rd b/man/maxcohesion.Rd index 909b4b50c7..c88f5d9b09 100644 --- a/man/maxcohesion.Rd +++ b/man/maxcohesion.Rd @@ -9,7 +9,7 @@ maxcohesion(blocks) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maxcohesion()} was renamed to \code{max_cohesion()} to create a more +\code{maxcohesion()} was renamed to \code{\link[=max_cohesion]{max_cohesion()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximal.cliques.Rd b/man/maximal.cliques.Rd index f00d9668cd..7212d6ecc5 100644 --- a/man/maximal.cliques.Rd +++ b/man/maximal.cliques.Rd @@ -30,7 +30,7 @@ whitespace.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximal.cliques()} was renamed to \code{max_cliques()} to create a more +\code{maximal.cliques()} was renamed to \code{\link[=max_cliques]{max_cliques()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximal.cliques.count.Rd b/man/maximal.cliques.count.Rd index 718282e0ae..6510c6c6fa 100644 --- a/man/maximal.cliques.count.Rd +++ b/man/maximal.cliques.count.Rd @@ -24,7 +24,7 @@ parallelize the finding of maximal cliques.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximal.cliques.count()} was renamed to \code{count_max_cliques()} to create a more +\code{maximal.cliques.count()} was renamed to \code{\link[=count_max_cliques]{count_max_cliques()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximal.independent.vertex.sets.Rd b/man/maximal.independent.vertex.sets.Rd index 8384d3a8c6..33a98687b4 100644 --- a/man/maximal.independent.vertex.sets.Rd +++ b/man/maximal.independent.vertex.sets.Rd @@ -12,7 +12,7 @@ maximal.independent.vertex.sets(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximal.independent.vertex.sets()} was renamed to \code{max_ivs()} to create a more +\code{maximal.independent.vertex.sets()} was renamed to \code{\link[=max_ivs]{max_ivs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximal_ivs.Rd b/man/maximal_ivs.Rd index f7cff3d19b..7bdaadef57 100644 --- a/man/maximal_ivs.Rd +++ b/man/maximal_ivs.Rd @@ -12,7 +12,7 @@ maximal_ivs(graph) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximal_ivs()} was renamed to \code{max_ivs()} to create a more +\code{maximal_ivs()} was renamed to \code{\link[=max_ivs]{max_ivs()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximum.bipartite.matching.Rd b/man/maximum.bipartite.matching.Rd index e9f32d6e80..432180b0a6 100644 --- a/man/maximum.bipartite.matching.Rd +++ b/man/maximum.bipartite.matching.Rd @@ -35,7 +35,7 @@ is ignored.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximum.bipartite.matching()} was renamed to \code{max_bipartite_match()} to create a more +\code{maximum.bipartite.matching()} was renamed to \code{\link[=max_bipartite_match]{max_bipartite_match()}} to create a more consistent API. } \keyword{internal} diff --git a/man/maximum.cardinality.search.Rd b/man/maximum.cardinality.search.Rd index 61824a991f..d1ccc74e20 100644 --- a/man/maximum.cardinality.search.Rd +++ b/man/maximum.cardinality.search.Rd @@ -13,7 +13,7 @@ ignored, as the algorithm is defined for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{maximum.cardinality.search()} was renamed to \code{max_cardinality()} to create a more +\code{maximum.cardinality.search()} was renamed to \code{\link[=max_cardinality]{max_cardinality()}} to create a more consistent API. } \keyword{internal} diff --git a/man/minimal.st.separators.Rd b/man/minimal.st.separators.Rd index fc5457b641..f318da5a8f 100644 --- a/man/minimal.st.separators.Rd +++ b/man/minimal.st.separators.Rd @@ -13,7 +13,7 @@ ignored.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{minimal.st.separators()} was renamed to \code{min_st_separators()} to create a more +\code{minimal.st.separators()} was renamed to \code{\link[=min_st_separators]{min_st_separators()}} to create a more consistent API. } \keyword{internal} diff --git a/man/minimum.size.separators.Rd b/man/minimum.size.separators.Rd index ae1afad982..39ebaa5881 100644 --- a/man/minimum.size.separators.Rd +++ b/man/minimum.size.separators.Rd @@ -13,7 +13,7 @@ ignored.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{minimum.size.separators()} was renamed to \code{min_separators()} to create a more +\code{minimum.size.separators()} was renamed to \code{\link[=min_separators]{min_separators()}} to create a more consistent API. } \keyword{internal} diff --git a/man/minimum.spanning.tree.Rd b/man/minimum.spanning.tree.Rd index 03961542ca..79dc14a82d 100644 --- a/man/minimum.spanning.tree.Rd +++ b/man/minimum.spanning.tree.Rd @@ -26,7 +26,7 @@ algorithm is chosen, otherwise the unweighted algorithm is used.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{minimum.spanning.tree()} was renamed to \code{mst()} to create a more +\code{minimum.spanning.tree()} was renamed to \code{\link[=mst]{mst()}} to create a more consistent API. } \keyword{internal} diff --git a/man/mod.matrix.Rd b/man/mod.matrix.Rd index 073cdaec47..c4da04d2a1 100644 --- a/man/mod.matrix.Rd +++ b/man/mod.matrix.Rd @@ -21,7 +21,7 @@ modularity. Ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{mod.matrix()} was renamed to \code{modularity_matrix()} to create a more +\code{mod.matrix()} was renamed to \code{\link[=modularity_matrix]{modularity_matrix()}} to create a more consistent API. } \keyword{internal} diff --git a/man/multilevel.community.Rd b/man/multilevel.community.Rd index bfd757a07a..e72f66f2c3 100644 --- a/man/multilevel.community.Rd +++ b/man/multilevel.community.Rd @@ -26,7 +26,7 @@ is set to 1.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{multilevel.community()} was renamed to \code{cluster_louvain()} to create a more +\code{multilevel.community()} was renamed to \code{\link[=cluster_louvain]{cluster_louvain()}} to create a more consistent API. } \keyword{internal} diff --git a/man/neighborhood.size.Rd b/man/neighborhood.size.Rd index 1c8f9fc09e..b52295c691 100644 --- a/man/neighborhood.size.Rd +++ b/man/neighborhood.size.Rd @@ -33,7 +33,7 @@ argument is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{neighborhood.size()} was renamed to \code{ego_size()} to create a more +\code{neighborhood.size()} was renamed to \code{\link[=ego_size]{ego_size()}} to create a more consistent API. } \keyword{internal} diff --git a/man/no.clusters.Rd b/man/no.clusters.Rd index 598b20de68..43a87f30cc 100644 --- a/man/no.clusters.Rd +++ b/man/no.clusters.Rd @@ -16,7 +16,7 @@ connected components to search. It is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{no.clusters()} was renamed to \code{count_components()} to create a more +\code{no.clusters()} was renamed to \code{\link[=count_components]{count_components()}} to create a more consistent API. } \keyword{internal} diff --git a/man/optimal.community.Rd b/man/optimal.community.Rd index f45b72f4aa..7bef05e310 100644 --- a/man/optimal.community.Rd +++ b/man/optimal.community.Rd @@ -20,7 +20,7 @@ edge weight means a stronger connection for this function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{optimal.community()} was renamed to \code{cluster_optimal()} to create a more +\code{optimal.community()} was renamed to \code{\link[=cluster_optimal]{cluster_optimal()}} to create a more consistent API. } \keyword{internal} diff --git a/man/page.rank.Rd b/man/page.rank.Rd index 6c57efa0a0..69075bee79 100644 --- a/man/page.rank.Rd +++ b/man/page.rank.Rd @@ -57,7 +57,7 @@ implementation is used.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{page.rank()} was renamed to \code{page_rank()} to create a more +\code{page.rank()} was renamed to \code{\link[=page_rank]{page_rank()}} to create a more consistent API. } \keyword{internal} diff --git a/man/path.length.hist.Rd b/man/path.length.hist.Rd index 96ecac0782..0a75217313 100644 --- a/man/path.length.hist.Rd +++ b/man/path.length.hist.Rd @@ -15,7 +15,7 @@ this argument is ignored for undirected graphs.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{path.length.hist()} was renamed to \code{distance_table()} to create a more +\code{path.length.hist()} was renamed to \code{\link[=distance_table]{distance_table()}} to create a more consistent API. } \keyword{internal} diff --git a/man/permute.vertices.Rd b/man/permute.vertices.Rd index 3c806fca4f..33be49ef11 100644 --- a/man/permute.vertices.Rd +++ b/man/permute.vertices.Rd @@ -16,7 +16,7 @@ first element is the new id of vertex 1, etc. Every number between one and \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{permute.vertices()} was renamed to \code{permute()} to create a more +\code{permute.vertices()} was renamed to \code{\link[=permute]{permute()}} to create a more consistent API. } \keyword{internal} diff --git a/man/piecewise.layout.Rd b/man/piecewise.layout.Rd index b65fc7c4d3..093943ac13 100644 --- a/man/piecewise.layout.Rd +++ b/man/piecewise.layout.Rd @@ -17,7 +17,7 @@ function.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{piecewise.layout()} was renamed to \code{layout_components()} to create a more +\code{piecewise.layout()} was renamed to \code{\link[=layout_components]{layout_components()}} to create a more consistent API. } \keyword{internal} diff --git a/man/plotHierarchy.Rd b/man/plotHierarchy.Rd index b14305576c..2973c4f939 100644 --- a/man/plotHierarchy.Rd +++ b/man/plotHierarchy.Rd @@ -21,7 +21,7 @@ them to \code{plot.igraph()}. \code{\link[=print]{print()}} and \code{\link[=su \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{plotHierarchy()} was renamed to \code{plot_hierarchy()} to create a more +\code{plotHierarchy()} was renamed to \code{\link[=plot_hierarchy]{plot_hierarchy()}} to create a more consistent API. } \keyword{internal} diff --git a/man/power.law.fit.Rd b/man/power.law.fit.Rd index b898a61d50..39dec611e1 100644 --- a/man/power.law.fit.Rd +++ b/man/power.law.fit.Rd @@ -46,7 +46,7 @@ implementation.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{power.law.fit()} was renamed to \code{fit_power_law()} to create a more +\code{power.law.fit()} was renamed to \code{\link[=fit_power_law]{fit_power_law()}} to create a more consistent API. } \keyword{internal} diff --git a/man/preference.game.Rd b/man/preference.game.Rd index c24b04fd7e..2cd83f95a8 100644 --- a/man/preference.game.Rd +++ b/man/preference.game.Rd @@ -38,7 +38,7 @@ an undirected graph, it must be symmetric.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{preference.game()} was renamed to \code{sample_pref()} to create a more +\code{preference.game()} was renamed to \code{\link[=sample_pref]{sample_pref()}} to create a more consistent API. } \keyword{internal} diff --git a/man/read.graph.Rd b/man/read.graph.Rd index 57e9fb642f..9c9bf90676 100644 --- a/man/read.graph.Rd +++ b/man/read.graph.Rd @@ -27,7 +27,7 @@ insensitive.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{read.graph()} was renamed to \code{read_graph()} to create a more +\code{read.graph()} was renamed to \code{\link[=read_graph]{read_graph()}} to create a more consistent API. } \keyword{internal} diff --git a/man/remove.edge.attribute.Rd b/man/remove.edge.attribute.Rd index 4f389a40df..fa1e894421 100644 --- a/man/remove.edge.attribute.Rd +++ b/man/remove.edge.attribute.Rd @@ -14,7 +14,7 @@ remove.edge.attribute(graph, name) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{remove.edge.attribute()} was renamed to \code{delete_edge_attr()} to create a more +\code{remove.edge.attribute()} was renamed to \code{\link[=delete_edge_attr]{delete_edge_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/remove.graph.attribute.Rd b/man/remove.graph.attribute.Rd index 3dda70b6f4..209df829e2 100644 --- a/man/remove.graph.attribute.Rd +++ b/man/remove.graph.attribute.Rd @@ -14,7 +14,7 @@ remove.graph.attribute(graph, name) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{remove.graph.attribute()} was renamed to \code{delete_graph_attr()} to create a more +\code{remove.graph.attribute()} was renamed to \code{\link[=delete_graph_attr]{delete_graph_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/remove.vertex.attribute.Rd b/man/remove.vertex.attribute.Rd index c59c10d948..d663f91e9c 100644 --- a/man/remove.vertex.attribute.Rd +++ b/man/remove.vertex.attribute.Rd @@ -14,7 +14,7 @@ remove.vertex.attribute(graph, name) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{remove.vertex.attribute()} was renamed to \code{delete_vertex_attr()} to create a more +\code{remove.vertex.attribute()} was renamed to \code{\link[=delete_vertex_attr]{delete_vertex_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/running.mean.Rd b/man/running.mean.Rd index 40030a0d38..d9bbfcd961 100644 --- a/man/running.mean.Rd +++ b/man/running.mean.Rd @@ -15,7 +15,7 @@ i.e. smaller than the length of \code{v}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{running.mean()} was renamed to \code{running_mean()} to create a more +\code{running.mean()} was renamed to \code{\link[=running_mean]{running_mean()}} to create a more consistent API. } \keyword{internal} diff --git a/man/sbm.game.Rd b/man/sbm.game.Rd index 21f8a4d1b1..1c162c0558 100644 --- a/man/sbm.game.Rd +++ b/man/sbm.game.Rd @@ -25,7 +25,7 @@ group. The sum of the vector must match the number of vertices.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{sbm.game()} was renamed to \code{sample_sbm()} to create a more +\code{sbm.game()} was renamed to \code{\link[=sample_sbm]{sample_sbm()}} to create a more consistent API. } \keyword{internal} diff --git a/man/set.edge.attribute.Rd b/man/set.edge.attribute.Rd index eb72afa005..1122bb1bd1 100644 --- a/man/set.edge.attribute.Rd +++ b/man/set.edge.attribute.Rd @@ -21,7 +21,7 @@ If \code{NULL}, the input is returned unchanged.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{set.edge.attribute()} was renamed to \code{set_edge_attr()} to create a more +\code{set.edge.attribute()} was renamed to \code{\link[=set_edge_attr]{set_edge_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/set.graph.attribute.Rd b/man/set.graph.attribute.Rd index 8493701bf4..191187c8b4 100644 --- a/man/set.graph.attribute.Rd +++ b/man/set.graph.attribute.Rd @@ -16,7 +16,7 @@ set.graph.attribute(graph, name, value) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{set.graph.attribute()} was renamed to \code{set_graph_attr()} to create a more +\code{set.graph.attribute()} was renamed to \code{\link[=set_graph_attr]{set_graph_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/set.vertex.attribute.Rd b/man/set.vertex.attribute.Rd index ecbac31373..2909519c57 100644 --- a/man/set.vertex.attribute.Rd +++ b/man/set.vertex.attribute.Rd @@ -21,7 +21,7 @@ If \code{NULL}, the input is returned unchanged.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{set.vertex.attribute()} was renamed to \code{set_vertex_attr()} to create a more +\code{set.vertex.attribute()} was renamed to \code{\link[=set_vertex_attr]{set_vertex_attr()}} to create a more consistent API. } \keyword{internal} diff --git a/man/shortest.paths.Rd b/man/shortest.paths.Rd index 5283b5c0b0..f1d4343de3 100644 --- a/man/shortest.paths.Rd +++ b/man/shortest.paths.Rd @@ -51,7 +51,7 @@ used, regardless of this argument.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{shortest.paths()} was renamed to \code{distances()} to create a more +\code{shortest.paths()} was renamed to \code{\link[=distances]{distances()}} to create a more consistent API. } \keyword{internal} diff --git a/man/showtrace.Rd b/man/showtrace.Rd index 7914691631..d03777315b 100644 --- a/man/showtrace.Rd +++ b/man/showtrace.Rd @@ -9,7 +9,7 @@ showtrace(communities) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{showtrace()} was renamed to \code{show_trace()} to create a more +\code{showtrace()} was renamed to \code{\link[=show_trace]{show_trace()}} to create a more consistent API. } \keyword{internal} diff --git a/man/spinglass.community.Rd b/man/spinglass.community.Rd index 2619b3fc8c..9be9060522 100644 --- a/man/spinglass.community.Rd +++ b/man/spinglass.community.Rd @@ -87,7 +87,7 @@ is ignored if the \sQuote{orig} implementation is chosen.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{spinglass.community()} was renamed to \code{cluster_spinglass()} to create a more +\code{spinglass.community()} was renamed to \code{\link[=cluster_spinglass]{cluster_spinglass()}} to create a more consistent API. } \keyword{internal} diff --git a/man/stCuts.Rd b/man/stCuts.Rd index 6dbf7b8165..04a64ea8ac 100644 --- a/man/stCuts.Rd +++ b/man/stCuts.Rd @@ -16,7 +16,7 @@ stCuts(graph, source, target) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{stCuts()} was renamed to \code{st_cuts()} to create a more +\code{stCuts()} was renamed to \code{\link[=st_cuts]{st_cuts()}} to create a more consistent API. } \keyword{internal} diff --git a/man/stMincuts.Rd b/man/stMincuts.Rd index 4300849e0c..d37c925e69 100644 --- a/man/stMincuts.Rd +++ b/man/stMincuts.Rd @@ -22,7 +22,7 @@ here.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{stMincuts()} was renamed to \code{st_min_cuts()} to create a more +\code{stMincuts()} was renamed to \code{\link[=st_min_cuts]{st_min_cuts()}} to create a more consistent API. } \keyword{internal} diff --git a/man/static.fitness.game.Rd b/man/static.fitness.game.Rd index c74c06399a..1135ef69e3 100644 --- a/man/static.fitness.game.Rd +++ b/man/static.fitness.game.Rd @@ -33,7 +33,7 @@ graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{static.fitness.game()} was renamed to \code{sample_fitness()} to create a more +\code{static.fitness.game()} was renamed to \code{\link[=sample_fitness]{sample_fitness()}} to create a more consistent API. } \keyword{internal} diff --git a/man/static.power.law.game.Rd b/man/static.power.law.game.Rd index 99d64735e0..e2ac83118a 100644 --- a/man/static.power.law.game.Rd +++ b/man/static.power.law.game.Rd @@ -41,7 +41,7 @@ finite size correction of Cho et al., see references below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{static.power.law.game()} was renamed to \code{sample_fitness_pl()} to create a more +\code{static.power.law.game()} was renamed to \code{\link[=sample_fitness_pl]{sample_fitness_pl()}} to create a more consistent API. } \keyword{internal} diff --git a/man/subgraph.centrality.Rd b/man/subgraph.centrality.Rd index 927df1f142..7b0d2395e9 100644 --- a/man/subgraph.centrality.Rd +++ b/man/subgraph.centrality.Rd @@ -16,7 +16,7 @@ loops edges from the graph before the calculation.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{subgraph.centrality()} was renamed to \code{subgraph_centrality()} to create a more +\code{subgraph.centrality()} was renamed to \code{\link[=subgraph_centrality]{subgraph_centrality()}} to create a more consistent API. } \keyword{internal} diff --git a/man/subgraph.edges.Rd b/man/subgraph.edges.Rd index f3ec54ade4..ccbf150d49 100644 --- a/man/subgraph.edges.Rd +++ b/man/subgraph.edges.Rd @@ -17,7 +17,7 @@ not have any adjacent edges in \code{eids}.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{subgraph.edges()} was renamed to \code{subgraph_from_edges()} to create a more +\code{subgraph.edges()} was renamed to \code{\link[=subgraph_from_edges]{subgraph_from_edges()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.canvas.Rd b/man/tkplot.canvas.Rd index f8b133b175..aff531edf8 100644 --- a/man/tkplot.canvas.Rd +++ b/man/tkplot.canvas.Rd @@ -12,7 +12,7 @@ tkplot.canvas(tkp.id) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.canvas()} was renamed to \code{tk_canvas()} to create a more +\code{tkplot.canvas()} was renamed to \code{\link[=tk_canvas]{tk_canvas()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.center.Rd b/man/tkplot.center.Rd index 65bed3a600..1aee681c18 100644 --- a/man/tkplot.center.Rd +++ b/man/tkplot.center.Rd @@ -12,7 +12,7 @@ tkplot.center(tkp.id) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.center()} was renamed to \code{tk_center()} to create a more +\code{tkplot.center()} was renamed to \code{\link[=tk_center]{tk_center()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.close.Rd b/man/tkplot.close.Rd index a8caffb03e..43f28061c0 100644 --- a/man/tkplot.close.Rd +++ b/man/tkplot.close.Rd @@ -14,7 +14,7 @@ tkplot.close(tkp.id, window.close = TRUE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.close()} was renamed to \code{tk_close()} to create a more +\code{tkplot.close()} was renamed to \code{\link[=tk_close]{tk_close()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.export.postscript.Rd b/man/tkplot.export.postscript.Rd index 7b507d049c..5d1c657e5f 100644 --- a/man/tkplot.export.postscript.Rd +++ b/man/tkplot.export.postscript.Rd @@ -12,7 +12,7 @@ tkplot.export.postscript(tkp.id) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.export.postscript()} was renamed to \code{tk_postscript()} to create a more +\code{tkplot.export.postscript()} was renamed to \code{\link[=tk_postscript]{tk_postscript()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.fit.to.screen.Rd b/man/tkplot.fit.to.screen.Rd index 890c21acac..b15a6c39eb 100644 --- a/man/tkplot.fit.to.screen.Rd +++ b/man/tkplot.fit.to.screen.Rd @@ -16,7 +16,7 @@ tkplot.fit.to.screen(tkp.id, width = NULL, height = NULL) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.fit.to.screen()} was renamed to \code{tk_fit()} to create a more +\code{tkplot.fit.to.screen()} was renamed to \code{\link[=tk_fit]{tk_fit()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.getcoords.Rd b/man/tkplot.getcoords.Rd index 764eaa3718..0f879e6a76 100644 --- a/man/tkplot.getcoords.Rd +++ b/man/tkplot.getcoords.Rd @@ -14,7 +14,7 @@ tkplot.getcoords(tkp.id, norm = FALSE) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.getcoords()} was renamed to \code{tk_coords()} to create a more +\code{tkplot.getcoords()} was renamed to \code{\link[=tk_coords]{tk_coords()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.off.Rd b/man/tkplot.off.Rd index af466411db..edfe4b355c 100644 --- a/man/tkplot.off.Rd +++ b/man/tkplot.off.Rd @@ -9,7 +9,7 @@ tkplot.off() \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.off()} was renamed to \code{tk_off()} to create a more +\code{tkplot.off()} was renamed to \code{\link[=tk_off]{tk_off()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.reshape.Rd b/man/tkplot.reshape.Rd index 00720067f4..4a57a32510 100644 --- a/man/tkplot.reshape.Rd +++ b/man/tkplot.reshape.Rd @@ -19,7 +19,7 @@ the complete list.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.reshape()} was renamed to \code{tk_reshape()} to create a more +\code{tkplot.reshape()} was renamed to \code{\link[=tk_reshape]{tk_reshape()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.rotate.Rd b/man/tkplot.rotate.Rd index 229bb59db4..982904597e 100644 --- a/man/tkplot.rotate.Rd +++ b/man/tkplot.rotate.Rd @@ -16,7 +16,7 @@ tkplot.rotate(tkp.id, degree = NULL, rad = NULL) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.rotate()} was renamed to \code{tk_rotate()} to create a more +\code{tkplot.rotate()} was renamed to \code{\link[=tk_rotate]{tk_rotate()}} to create a more consistent API. } \keyword{internal} diff --git a/man/tkplot.setcoords.Rd b/man/tkplot.setcoords.Rd index f3004ecf88..012beb47fc 100644 --- a/man/tkplot.setcoords.Rd +++ b/man/tkplot.setcoords.Rd @@ -15,7 +15,7 @@ vertices, in absolute coordinates.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{tkplot.setcoords()} was renamed to \code{tk_set_coords()} to create a more +\code{tkplot.setcoords()} was renamed to \code{\link[=tk_set_coords]{tk_set_coords()}} to create a more consistent API. } \keyword{internal} diff --git a/man/topological.sort.Rd b/man/topological.sort.Rd index 2de3ec2774..b3b4c2effd 100644 --- a/man/topological.sort.Rd +++ b/man/topological.sort.Rd @@ -18,7 +18,7 @@ nodes from which it receives edges. Nodes with no outgoing edges go first.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{topological.sort()} was renamed to \code{topo_sort()} to create a more +\code{topological.sort()} was renamed to \code{\link[=topo_sort]{topo_sort()}} to create a more consistent API. } \keyword{internal} diff --git a/man/triad.census.Rd b/man/triad.census.Rd index 81f27edcd4..111dbc34c7 100644 --- a/man/triad.census.Rd +++ b/man/triad.census.Rd @@ -13,7 +13,7 @@ results a warning, and undefined results.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{triad.census()} was renamed to \code{triad_census()} to create a more +\code{triad.census()} was renamed to \code{\link[=triad_census]{triad_census()}} to create a more consistent API. } \keyword{internal} diff --git a/man/unfold.tree.Rd b/man/unfold.tree.Rd index 386e74ca67..92e4f4533a 100644 --- a/man/unfold.tree.Rd +++ b/man/unfold.tree.Rd @@ -20,7 +20,7 @@ search is performed. Typically it contains one vertex per component.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{unfold.tree()} was renamed to \code{unfold_tree()} to create a more +\code{unfold.tree()} was renamed to \code{\link[=unfold_tree]{unfold_tree()}} to create a more consistent API. } \keyword{internal} diff --git a/man/vertex.connectivity.Rd b/man/vertex.connectivity.Rd index b4dd0a34a0..2746f2f5f8 100644 --- a/man/vertex.connectivity.Rd +++ b/man/vertex.connectivity.Rd @@ -24,7 +24,7 @@ thanks Peter.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{vertex.connectivity()} was renamed to \code{vertex_connectivity()} to create a more +\code{vertex.connectivity()} was renamed to \code{\link[=vertex_connectivity]{vertex_connectivity()}} to create a more consistent API. } \keyword{internal} diff --git a/man/vertex.disjoint.paths.Rd b/man/vertex.disjoint.paths.Rd index e3c6cf5f05..281fb3f879 100644 --- a/man/vertex.disjoint.paths.Rd +++ b/man/vertex.disjoint.paths.Rd @@ -16,7 +16,7 @@ can be \code{NULL}, see details below.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{vertex.disjoint.paths()} was renamed to \code{vertex_disjoint_paths()} to create a more +\code{vertex.disjoint.paths()} was renamed to \code{\link[=vertex_disjoint_paths]{vertex_disjoint_paths()}} to create a more consistent API. } \keyword{internal} diff --git a/man/vertex.shapes.Rd b/man/vertex.shapes.Rd index df20602a96..054c1b577f 100644 --- a/man/vertex.shapes.Rd +++ b/man/vertex.shapes.Rd @@ -14,7 +14,7 @@ vertex shapes are returned.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{vertex.shapes()} was renamed to \code{shapes()} to create a more +\code{vertex.shapes()} was renamed to \code{\link[=shapes]{shapes()}} to create a more consistent API. } \keyword{internal} diff --git a/man/walktrap.community.Rd b/man/walktrap.community.Rd index fe81576b7d..940aa1f396 100644 --- a/man/walktrap.community.Rd +++ b/man/walktrap.community.Rd @@ -41,7 +41,7 @@ for the split corresponding to the highest modularity value.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{walktrap.community()} was renamed to \code{cluster_walktrap()} to create a more +\code{walktrap.community()} was renamed to \code{\link[=cluster_walktrap]{cluster_walktrap()}} to create a more consistent API. } \keyword{internal} diff --git a/man/watts.strogatz.game.Rd b/man/watts.strogatz.game.Rd index 866efb74b2..1f436ffc91 100644 --- a/man/watts.strogatz.game.Rd +++ b/man/watts.strogatz.game.Rd @@ -25,7 +25,7 @@ generated graph.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{watts.strogatz.game()} was renamed to \code{sample_smallworld()} to create a more +\code{watts.strogatz.game()} was renamed to \code{\link[=sample_smallworld]{sample_smallworld()}} to create a more consistent API. } \keyword{internal} diff --git a/man/weighted_cliques.Rd b/man/weighted_cliques.Rd index cfa579448a..d3af9be317 100644 --- a/man/weighted_cliques.Rd +++ b/man/weighted_cliques.Rd @@ -34,7 +34,7 @@ or only the maximal ones (\code{TRUE}).} \value{ \code{weighted_cliques()} and \code{largest_weighted_cliques()} return a list containing numeric vectors of vertex IDs. Each list element is a weighted -clique, i.e. a vertex sequence of class \code{\link[=V]{igraph.vs()}}. +clique, i.e. a vertex sequence of class \link[=V]{igraph.vs}. \code{weighted_clique_num()} returns an integer scalar. } diff --git a/man/write.graph.Rd b/man/write.graph.Rd index c7376de875..42637c42a6 100644 --- a/man/write.graph.Rd +++ b/man/write.graph.Rd @@ -28,7 +28,7 @@ this argument is case insensitive.} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -\code{write.graph()} was renamed to \code{write_graph()} to create a more +\code{write.graph()} was renamed to \code{\link[=write_graph]{write_graph()}} to create a more consistent API. } \keyword{internal}