From 2d54f0f57968d49f755f2e1d4ae14a33353b11c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 10 Dec 2024 15:01:27 +0100 Subject: [PATCH 1/7] feat: Split `sample_bipartite()` into two functions for the G(n,m) and G(n,p) case --- NAMESPACE | 2 + R/games.R | 158 ++++++++++++------ man/closeness.Rd | 2 +- man/sample_bipartite.Rd | 25 +-- man/sample_bipartite_gnm.Rd | 73 ++++++++ .../testthat/_snaps/bipartite.random.game.md | 18 ++ tests/testthat/test-bipartite.projection.R | 2 +- tests/testthat/test-bipartite.random.game.R | 64 ++++++- 8 files changed, 269 insertions(+), 75 deletions(-) create mode 100644 man/sample_bipartite_gnm.Rd create mode 100644 tests/testthat/_snaps/bipartite.random.game.md diff --git a/NAMESPACE b/NAMESPACE index d1c40956c1..fdacc190e3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -746,6 +746,8 @@ export(running_mean) export(sample_) export(sample_asym_pref) export(sample_bipartite) +export(sample_bipartite_gnm) +export(sample_bipartite_gnp) export(sample_chung_lu) export(sample_cit_cit_types) export(sample_cit_types) diff --git a/R/games.R b/R/games.R index 27ddea4eb8..c8f24c4480 100644 --- a/R/games.R +++ b/R/games.R @@ -265,7 +265,10 @@ callaway.traits.game <- function(nodes, types, edge.per.step = 1, type.dist = re #' @keywords internal #' @export bipartite.random.game <- function(n1, n2, type = c("gnp", "gnm"), p, m, directed = FALSE, mode = c("out", "in", "all")) { # nocov start - lifecycle::deprecate_soft("2.0.0", "bipartite.random.game()", "sample_bipartite()") + lifecycle::deprecate_warn( + "2.0.0", "bipartite.random.game()", + details = "Use sample_bipartite_gnp() or sample_bipartite_gnm()" + ) sample_bipartite(n1 = n1, n2 = n2, type = type, p = p, m = m, directed = directed, mode = mode) } # nocov end @@ -1695,13 +1698,8 @@ cit_cit_types <- function(...) constructor_spec(sample_cit_cit_types, ...) #' Bipartite random graphs #' -#' Generate bipartite graphs using the Erdős-Rényi model -#' -#' Similarly to unipartite (one-mode) networks, we can define the \eqn{G(n,p)}, and -#' \eqn{G(n,m)} graph classes for bipartite graphs, via their generating process. -#' In \eqn{G(n,p)} every possible edge between top and bottom vertices is realized -#' with probability \eqn{p}, independently of the rest of the edges. In \eqn{G(n,m)}, we -#' uniformly choose \eqn{m} edges to realize. +#' `r lifecycle::badge("deprecated")` Generate bipartite graphs using the Erdős-Rényi model. +#' 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. @@ -1725,72 +1723,134 @@ cit_cit_types <- function(...) constructor_spec(sample_cit_cit_types, ...) #' @family games #' @export #' @keywords graphs +sample_bipartite <- function(n1, n2, type = c("gnp", "gnm"), p, m, + directed = FALSE, mode = c("out", "in", "all")) { + + type <- igraph.match.arg(type) + + if (type == "gnp") { + lifecycle::deprecate_soft( + "2.1.3", + "sample_bipartite()", + "sample_gnp()" + ) + sample_bipartite_gnp(n1, n2, p, directed = directed, mode = mode) + } else if (type == "gnm") { + lifecycle::deprecate_soft( + "2.1.3", + "sample_bipartite()", + "sample_gnm()" + ) + sample_bipartite_gnm(n1, n2, m, directed = directed, mode = mode) + } +} + +#' @rdname sample_bipartite +#' @param ... Passed to `sample_bipartite()`. +#' @export +bipartite <- function(...) constructor_spec(sample_bipartite, ...) + +#' Bipartite random graphs +#' +#' Generate bipartite graphs using the Erdős-Rényi model +#' +#' Similarly to unipartite (one-mode) networks, we can define the \eqn{G(n,p)}, and +#' \eqn{G(n,m)} graph classes for bipartite graphs, via their generating process. +#' In \eqn{G(n,p)} every possible edge between top and bottom vertices is realized +#' with probability \eqn{p}, independently of the rest of the edges. In \eqn{G(n,m)}, we +#' uniformly choose \eqn{m} edges to realize. +#' +#' +#' @param n1 Integer scalar, the number of bottom vertices. +#' @param n2 Integer scalar, the number of top vertices. +#' @param type Character scalar, the type of the graph, \sQuote{gnp} creates a +#' \eqn{G(n,p)} graph, \sQuote{gnm} creates a \eqn{G(n,m)} graph. See details below. +#' @param p Real scalar, connection probability for \eqn{G(n,p)} graphs. +#' @param m Integer scalar, the number of edges for \eqn{G(n,m)} graphs. +#' @param directed Logical scalar, whether to create a directed graph. See also +#' the `mode` argument. +#' @param mode Character scalar, specifies how to direct the edges in directed +#' graphs. If it is \sQuote{out}, then directed edges point from bottom +#' vertices to top vertices. If it is \sQuote{in}, edges point from top +#' vertices to bottom vertices. \sQuote{out} and \sQuote{in} do not generate +#' mutual edges. If this argument is \sQuote{all}, then each edge direction is +#' considered independently and mutual edges might be generated. This argument +#' is ignored for undirected graphs. #' @examples #' #' ## empty graph -#' sample_bipartite(10, 5, p = 0) +#' sample_bipartite_gnp(10, 5, p = 0) #' #' ## full graph -#' sample_bipartite(10, 5, p = 1) +#' sample_bipartite_gnp(10, 5, p = 1) #' #' ## random bipartite graph -#' sample_bipartite(10, 5, p = .1) +#' sample_bipartite_gnp(10, 5, p = .1) #' #' ## directed bipartite graph, G(n,m) -#' sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") +#' sample_bipartite_gnm(10, 5, m = 20, directed = TRUE, mode = "all") #' -sample_bipartite <- function(n1, n2, type = c("gnp", "gnm"), p, m, - directed = FALSE, mode = c("out", "in", "all")) { +#' @export +sample_bipartite_gnm <- function(n1, n2, m, + ..., + directed = FALSE, + mode = c("out", "in", "all")) { + check_dots_empty() + n1 <- as.numeric(n1) n2 <- as.numeric(n2) - type <- igraph.match.arg(type) - if (!missing(p)) { - p <- as.numeric(p) - } - if (!missing(m)) { - m <- as.numeric(m) - } + + m <- as.numeric(m) + directed <- as.logical(directed) + mode <- switch(igraph.match.arg(mode), "out" = 1, "in" = 2, "all" = 3 ) - if (type == "gnp" && missing(p)) { - stop("Connection probability `p' is not given for Gnp graph") - } - if (type == "gnp" && !missing(m)) { - cli::cli_warn("Number of edges {.arg m} is ignored for Gnp graph.") - } - if (type == "gnm" && missing(m)) { - stop("Number of edges `m' is not given for Gnm graph") - } - if (type == "gnm" && !missing(p)) { - cli::cli_warn("Connection probability {.arg p} is ignored for Gnp graph.") - } - on.exit(.Call(R_igraph_finalizer)) - if (type == "gnp") { - res <- .Call(R_igraph_bipartite_game_gnp, n1, n2, p, directed, mode) - res <- set_vertex_attr(res$graph, "type", value = res$types) - res$name <- "Bipartite Gnp random graph" - res$p <- p - } else if (type == "gnm") { - res <- .Call(R_igraph_bipartite_game_gnm, n1, n2, m, directed, mode) - res <- set_vertex_attr(res$graph, "type", value = res$types) - res$name <- "Bipartite Gnm random graph" - res$m <- m - } + + res <- .Call(R_igraph_bipartite_game_gnm, n1, n2, m, directed, mode) + res <- set_vertex_attr(res$graph, "type", value = res$types) + res$name <- "Bipartite Gnm random graph" + res$m <- m res -} -#' @rdname sample_bipartite -#' @param ... Passed to `sample_bipartite()`. +} +#' @rdname sample_bipartite_gnm #' @export -bipartite <- function(...) constructor_spec(sample_bipartite, ...) +sample_bipartite_gnp <- function(n1, n2, p, + ..., + directed = FALSE, + mode = c("out", "in", "all")) { + check_dots_empty() + + n1 <- as.numeric(n1) + n2 <- as.numeric(n2) + + p <- as.numeric(p) + directed <- as.logical(directed) + + mode <- switch(igraph.match.arg(mode), + "out" = 1, + "in" = 2, + "all" = 3 + ) + + on.exit(.Call(R_igraph_finalizer)) + + res <- .Call(R_igraph_bipartite_game_gnp, n1, n2, p, directed, mode) + res <- set_vertex_attr(res$graph, "type", value = res$types) + res$name <- "Bipartite Gnp random graph" + res$p <- p + + res + +} #' Sample stochastic block model #' diff --git a/man/closeness.Rd b/man/closeness.Rd index 0502a7f28f..dc860d003e 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -43,7 +43,7 @@ Numeric vector with the closeness values of all the vertices in \code{v}. } \description{ -Closeness centrality measures how many steps is required to access every other +Closeness centrality measures how many steps are required to access every other vertex from a given vertex. } \details{ diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index 313bc7b16a..c55c057fbb 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -48,29 +48,8 @@ is ignored for undirected graphs.} A bipartite igraph graph. } \description{ -Generate bipartite graphs using the Erdős-Rényi model -} -\details{ -Similarly to unipartite (one-mode) networks, we can define the \eqn{G(n,p)}, and -\eqn{G(n,m)} graph classes for bipartite graphs, via their generating process. -In \eqn{G(n,p)} every possible edge between top and bottom vertices is realized -with probability \eqn{p}, independently of the rest of the edges. In \eqn{G(n,m)}, we -uniformly choose \eqn{m} edges to realize. -} -\examples{ - -## empty graph -sample_bipartite(10, 5, p = 0) - -## full graph -sample_bipartite(10, 5, p = 1) - -## random bipartite graph -sample_bipartite(10, 5, p = .1) - -## directed bipartite graph, G(n,m) -sample_bipartite(10, 5, type = "Gnm", m = 20, directed = TRUE, mode = "all") - +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Generate bipartite graphs using the Erdős-Rényi model. +Use \code{\link[=sample_bipartite_gnm]{sample_bipartite_gnm()}} and \code{\link[=sample_bipartite_gnp]{sample_bipartite_gnp()}} instead. } \seealso{ Random graph models (games) diff --git a/man/sample_bipartite_gnm.Rd b/man/sample_bipartite_gnm.Rd new file mode 100644 index 0000000000..eee1ad50d4 --- /dev/null +++ b/man/sample_bipartite_gnm.Rd @@ -0,0 +1,73 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/games.R +\name{sample_bipartite_gnm} +\alias{sample_bipartite_gnm} +\alias{sample_bipartite_gnp} +\title{Bipartite random graphs} +\usage{ +sample_bipartite_gnm( + n1, + n2, + m, + ..., + directed = FALSE, + mode = c("out", "in", "all") +) + +sample_bipartite_gnp( + n1, + n2, + p, + ..., + directed = FALSE, + mode = c("out", "in", "all") +) +} +\arguments{ +\item{n1}{Integer scalar, the number of bottom vertices.} + +\item{n2}{Integer scalar, the number of top vertices.} + +\item{m}{Integer scalar, the number of edges for \eqn{G(n,m)} graphs.} + +\item{directed}{Logical scalar, whether to create a directed graph. See also +the \code{mode} argument.} + +\item{mode}{Character scalar, specifies how to direct the edges in directed +graphs. If it is \sQuote{out}, then directed edges point from bottom +vertices to top vertices. If it is \sQuote{in}, edges point from top +vertices to bottom vertices. \sQuote{out} and \sQuote{in} do not generate +mutual edges. If this argument is \sQuote{all}, then each edge direction is +considered independently and mutual edges might be generated. This argument +is ignored for undirected graphs.} + +\item{p}{Real scalar, connection probability for \eqn{G(n,p)} graphs.} + +\item{type}{Character scalar, the type of the graph, \sQuote{gnp} creates a +\eqn{G(n,p)} graph, \sQuote{gnm} creates a \eqn{G(n,m)} graph. See details below.} +} +\description{ +Generate bipartite graphs using the Erdős-Rényi model +} +\details{ +Similarly to unipartite (one-mode) networks, we can define the \eqn{G(n,p)}, and +\eqn{G(n,m)} graph classes for bipartite graphs, via their generating process. +In \eqn{G(n,p)} every possible edge between top and bottom vertices is realized +with probability \eqn{p}, independently of the rest of the edges. In \eqn{G(n,m)}, we +uniformly choose \eqn{m} edges to realize. +} +\examples{ + +## empty graph +sample_bipartite_gnp(10, 5, p = 0) + +## full graph +sample_bipartite_gnp(10, 5, p = 1) + +## random bipartite graph +sample_bipartite_gnp(10, 5, p = .1) + +## directed bipartite graph, G(n,m) +sample_bipartite_gnm(10, 5, m = 20, directed = TRUE, mode = "all") + +} diff --git a/tests/testthat/_snaps/bipartite.random.game.md b/tests/testthat/_snaps/bipartite.random.game.md new file mode 100644 index 0000000000..74df74d86c --- /dev/null +++ b/tests/testthat/_snaps/bipartite.random.game.md @@ -0,0 +1,18 @@ +# sample_bipartite() deprecation + + Code + s <- sample_bipartite(10, 5, type = "gnp", p = 0) + Condition + Warning: + `sample_bipartite()` was deprecated in igraph 2.1.3. + i Please use `sample_gnp()` instead. + +--- + + Code + s <- sample_bipartite(10, 5, type = "gnm", m = 0) + Condition + Warning: + `sample_bipartite()` was deprecated in igraph 2.1.3. + i Please use `sample_gnm()` instead. + diff --git a/tests/testthat/test-bipartite.projection.R b/tests/testthat/test-bipartite.projection.R index 24a82b879d..fed5648794 100644 --- a/tests/testthat/test-bipartite.projection.R +++ b/tests/testthat/test-bipartite.projection.R @@ -40,7 +40,7 @@ test_that("bipartite_projection works", { test_that("bipartite_projection can calculate only one projection", { withr::local_seed(42) - g <- sample_bipartite(5, 10, p = .3) + g <- sample_bipartite_gnp(5, 10, p = .3) proj <- bipartite_projection(g) proj1 <- bipartite_projection(g, which = "false") proj2 <- bipartite_projection(g, which = "true") diff --git a/tests/testthat/test-bipartite.random.game.R b/tests/testthat/test-bipartite.random.game.R index 9d2df975e3..203ddb3f26 100644 --- a/tests/testthat/test-bipartite.random.game.R +++ b/tests/testthat/test-bipartite.random.game.R @@ -1,4 +1,5 @@ -test_that("sample_bipartite works", { +test_that("sample_bipartite() works", { + rlang::local_options(lifecycle_verbosity = "quiet") withr::local_seed(42) g1 <- sample_bipartite(10, 5, type = "gnp", p = .1) expect_equal(g1$name, "Bipartite Gnp random graph") @@ -51,3 +52,64 @@ test_that("sample_bipartite works", { ) expect_equal(ecount(g8), 99) }) + +test_that("sample_bipartite() deprecation", { + expect_snapshot(s <- sample_bipartite(10, 5, type = "gnp", p = 0)) + expect_snapshot(s <- sample_bipartite(10, 5, type = "gnm", m = 0)) +}) + +test_that("sample_bipartite_gnp() works", { + withr::local_seed(42) + g1 <- sample_bipartite_gnp(10, 5, p = .1) + expect_equal(g1$name, "Bipartite Gnp random graph") + expect_equal(vcount(g1), 15) + expect_equal(ecount(g1), 7) + expect_true(bipartite_mapping(g1)$res) + expect_false(is_directed(g1)) + + g2 <- sample_bipartite_gnp(10, 5, p = .1, directed = TRUE) + expect_equal(vcount(g2), 15) + expect_equal(ecount(g2), 6) + expect_true(bipartite_mapping(g2)$res) + expect_true(is_directed(g2)) + expect_output(print_all(g2), "5->11") + + g3 <- sample_bipartite_gnp(10, 5, p = .1, directed = TRUE, mode = "in") + expect_output(print_all(g3), "11->3") + + g7 <- sample_bipartite_gnp(10, 5, + p = 0.9999, directed = TRUE, + mode = "all" + ) + expect_equal(ecount(g7), 100) + +}) +test_that("sample_bipartite_gnm() works", { + withr::local_seed(42) + + g4 <- sample_bipartite_gnm(10, 5, m = 8) + expect_equal(vcount(g4), 15) + expect_equal(ecount(g4), 8) + expect_true(bipartite_mapping(g4)$res) + expect_false(is_directed(g4)) + + g5 <- sample_bipartite_gnm(10, 5, m = 8, directed = TRUE) + expect_equal(vcount(g5), 15) + expect_equal(ecount(g5), 8) + expect_true(bipartite_mapping(g5)$res) + expect_true(is_directed(g5)) + expect_output(print_all(g5), "5->11 7->11 8->11 8->12 4->13 5->13 6->13 9->13") + + g6 <- sample_bipartite_gnm(10, 5, m = 8, directed = TRUE, mode = "in") + expect_equal(vcount(g6), 15) + expect_equal(ecount(g6), 8) + expect_true(bipartite_mapping(g6)$res) + expect_true(is_directed(g6)) + expect_output(print_all(g6), "11-> 4 11-> 5 12-> 7 12-> 8 12-> 9 14-> 6 14->10 15-> 4") + + g8 <- sample_bipartite_gnm(10, 5, + m = 99, directed = TRUE, + mode = "all" + ) + expect_equal(ecount(g8), 99) +}) From 6d924e133ec6446d369f443398d77884592fba82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 10 Dec 2024 15:17:06 +0100 Subject: [PATCH 2/7] docs: fix manual page --- R/games.R | 3 +-- man/sample_bipartite_gnm.Rd | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/R/games.R b/R/games.R index c8f24c4480..8db82157c7 100644 --- a/R/games.R +++ b/R/games.R @@ -1763,8 +1763,6 @@ bipartite <- function(...) constructor_spec(sample_bipartite, ...) #' #' @param n1 Integer scalar, the number of bottom vertices. #' @param n2 Integer scalar, the number of top vertices. -#' @param type Character scalar, the type of the graph, \sQuote{gnp} creates a -#' \eqn{G(n,p)} graph, \sQuote{gnm} creates a \eqn{G(n,m)} graph. See details below. #' @param p Real scalar, connection probability for \eqn{G(n,p)} graphs. #' @param m Integer scalar, the number of edges for \eqn{G(n,m)} graphs. #' @param directed Logical scalar, whether to create a directed graph. See also @@ -1776,6 +1774,7 @@ bipartite <- function(...) constructor_spec(sample_bipartite, ...) #' mutual edges. If this argument is \sQuote{all}, then each edge direction is #' considered independently and mutual edges might be generated. This argument #' is ignored for undirected graphs. +#' @inheritParams rlang::args_dots_empty #' @examples #' #' ## empty graph diff --git a/man/sample_bipartite_gnm.Rd b/man/sample_bipartite_gnm.Rd index eee1ad50d4..13a3e0ab85 100644 --- a/man/sample_bipartite_gnm.Rd +++ b/man/sample_bipartite_gnm.Rd @@ -30,6 +30,8 @@ sample_bipartite_gnp( \item{m}{Integer scalar, the number of edges for \eqn{G(n,m)} graphs.} +\item{...}{These dots are for future extensions and must be empty.} + \item{directed}{Logical scalar, whether to create a directed graph. See also the \code{mode} argument.} @@ -42,9 +44,6 @@ considered independently and mutual edges might be generated. This argument is ignored for undirected graphs.} \item{p}{Real scalar, connection probability for \eqn{G(n,p)} graphs.} - -\item{type}{Character scalar, the type of the graph, \sQuote{gnp} creates a -\eqn{G(n,p)} graph, \sQuote{gnm} creates a \eqn{G(n,m)} graph. See details below.} } \description{ Generate bipartite graphs using the Erdős-Rényi model From c11a0b4036acf08c5c737cd7c9b010e6d38f269d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 10 Dec 2024 15:43:13 +0100 Subject: [PATCH 3/7] docs: fix for pkgdown index --- R/games.R | 1 + man/erdos.renyi.game.Rd | 1 + man/sample_.Rd | 1 + man/sample_bipartite.Rd | 1 + man/sample_bipartite_gnm.Rd | 30 ++++++++++++++++++++++++++++++ man/sample_chung_lu.Rd | 1 + man/sample_correlated_gnp.Rd | 1 + man/sample_correlated_gnp_pair.Rd | 1 + man/sample_degseq.Rd | 1 + man/sample_dot_product.Rd | 1 + man/sample_fitness.Rd | 1 + man/sample_fitness_pl.Rd | 1 + man/sample_forestfire.Rd | 1 + man/sample_gnm.Rd | 1 + man/sample_gnp.Rd | 1 + man/sample_grg.Rd | 1 + man/sample_growing.Rd | 1 + man/sample_hierarchical_sbm.Rd | 1 + man/sample_islands.Rd | 1 + man/sample_k_regular.Rd | 1 + man/sample_last_cit.Rd | 1 + man/sample_pa.Rd | 1 + man/sample_pa_age.Rd | 1 + man/sample_pref.Rd | 1 + man/sample_sbm.Rd | 1 + man/sample_smallworld.Rd | 1 + man/sample_traits_callaway.Rd | 1 + man/sample_tree.Rd | 1 + 28 files changed, 57 insertions(+) diff --git a/R/games.R b/R/games.R index 8db82157c7..8ac0133c99 100644 --- a/R/games.R +++ b/R/games.R @@ -1789,6 +1789,7 @@ bipartite <- function(...) constructor_spec(sample_bipartite, ...) #' ## directed bipartite graph, G(n,m) #' sample_bipartite_gnm(10, 5, m = 20, directed = TRUE, mode = "all") #' +#' @family games #' @export sample_bipartite_gnm <- function(n1, n2, m, ..., diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 3390cd3c4d..30d2367039 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -54,6 +54,7 @@ Mathematicae} 6, 290--297 (1959). Random graph models (games) \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_.Rd b/man/sample_.Rd index ebea0a7d2d..9d38f13a48 100644 --- a/man/sample_.Rd +++ b/man/sample_.Rd @@ -48,6 +48,7 @@ blocky3 <- pref_matrix \%>\% Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index c55c057fbb..53b5d3c4b6 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -55,6 +55,7 @@ Use \code{\link[=sample_bipartite_gnm]{sample_bipartite_gnm()}} and \code{\link[ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_bipartite_gnm.Rd b/man/sample_bipartite_gnm.Rd index 13a3e0ab85..f5e6302845 100644 --- a/man/sample_bipartite_gnm.Rd +++ b/man/sample_bipartite_gnm.Rd @@ -70,3 +70,33 @@ sample_bipartite_gnp(10, 5, p = .1) sample_bipartite_gnm(10, 5, m = 20, directed = TRUE, mode = "all") } +\seealso{ +Random graph models (games) +\code{\link{erdos.renyi.game}()}, +\code{\link{sample_}()}, +\code{\link{sample_bipartite}()}, +\code{\link{sample_chung_lu}()}, +\code{\link{sample_correlated_gnp}()}, +\code{\link{sample_correlated_gnp_pair}()}, +\code{\link{sample_degseq}()}, +\code{\link{sample_dot_product}()}, +\code{\link{sample_fitness}()}, +\code{\link{sample_fitness_pl}()}, +\code{\link{sample_forestfire}()}, +\code{\link{sample_gnm}()}, +\code{\link{sample_gnp}()}, +\code{\link{sample_grg}()}, +\code{\link{sample_growing}()}, +\code{\link{sample_hierarchical_sbm}()}, +\code{\link{sample_islands}()}, +\code{\link{sample_k_regular}()}, +\code{\link{sample_last_cit}()}, +\code{\link{sample_pa}()}, +\code{\link{sample_pa_age}()}, +\code{\link{sample_pref}()}, +\code{\link{sample_sbm}()}, +\code{\link{sample_smallworld}()}, +\code{\link{sample_traits_callaway}()}, +\code{\link{sample_tree}()} +} +\concept{games} diff --git a/man/sample_chung_lu.Rd b/man/sample_chung_lu.Rd index 529bd7fa22..7cb555faad 100644 --- a/man/sample_chung_lu.Rd +++ b/man/sample_chung_lu.Rd @@ -171,6 +171,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_correlated_gnp.Rd b/man/sample_correlated_gnp.Rd index c180df2459..cace3e64c4 100644 --- a/man/sample_correlated_gnp.Rd +++ b/man/sample_correlated_gnp.Rd @@ -59,6 +59,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index 473733336a..ba5d0693ad 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -52,6 +52,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index 8000211b9d..267d46eff0 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -198,6 +198,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index e84b56a390..f34fc48a23 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -60,6 +60,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index f6ab1840d9..ccc108b3a6 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -82,6 +82,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index 3e092097d3..82ae57a933 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -91,6 +91,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index 6d44e99b1e..131f7ece49 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -80,6 +80,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 5f71695a37..2b1f90778c 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -46,6 +46,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index 698f159aa8..18b48f5f37 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -57,6 +57,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index e891532cc9..1d68b0e1d5 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -48,6 +48,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index 7621ede2b1..cfed0a8be7 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -45,6 +45,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index fe5aebc0bb..be3b7ace50 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -60,6 +60,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 913e15b40f..3c2bf61818 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -39,6 +39,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 66f2df1876..22d6c7591e 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -51,6 +51,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index ac9b9dc09d..aded4bec8b 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -83,6 +83,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index d50f175ff6..47291e6f87 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -130,6 +130,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index dc7a0b45ae..0de557f4be 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -139,6 +139,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index 2b1140ec00..bd97f9f46d 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -102,6 +102,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index 9985a7f18a..40ff2ecf6d 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -56,6 +56,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 8bd2e7a815..d1a69d2cbd 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -68,6 +68,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index 4a5e65ffa0..363c3325e5 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -82,6 +82,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_tree.Rd b/man/sample_tree.Rd index 046ca29e35..74c82b37d6 100644 --- a/man/sample_tree.Rd +++ b/man/sample_tree.Rd @@ -40,6 +40,7 @@ Random graph models (games) \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, +\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, From c4739244ea825aafb6cb41e02603957de4999c59 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 12 Dec 2024 10:15:27 +0100 Subject: [PATCH 4/7] chore: also deprecate `bipartite()` --- NAMESPACE | 2 ++ R/games.R | 28 +++++++++++++++++++++++++++- 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/NAMESPACE b/NAMESPACE index fdacc190e3..62529efb22 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -186,6 +186,8 @@ export(bipartite.mapping) export(bipartite.projection) export(bipartite.projection.size) export(bipartite.random.game) +export(bipartite_gnm) +export(bipartite_gnp) export(bipartite_graph) export(bipartite_mapping) export(bipartite_projection) diff --git a/R/games.R b/R/games.R index 8ac0133c99..64658532db 100644 --- a/R/games.R +++ b/R/games.R @@ -1748,7 +1748,33 @@ sample_bipartite <- function(n1, n2, type = c("gnp", "gnm"), p, m, #' @rdname sample_bipartite #' @param ... Passed to `sample_bipartite()`. #' @export -bipartite <- function(...) constructor_spec(sample_bipartite, ...) +bipartite <- function(...) { + if (type == "gnp") { + lifecycle::deprecate_soft( + "2.1.3", + "bipartite()", + "bipartite_gnp()" + ) + bipartite_gnp(n1, n2, p, directed = directed, mode = mode) + } else if (type == "gnm") { + lifecycle::deprecate_soft( + "2.1.3", + "bipartite()", + "bipartite_gnm()" + ) + bipartite_gnm(n1, n2, m, directed = directed, mode = mode) + } + +} +#' @rdname sample_bipartite_gnm +#' @param ... Passed to `sample_bipartite_gnm()`. +#' @export +bipartite_gnm <- function(...) constructor_spec(sample_bipartite_gnm, ...) + +#' @rdname sample_bipartite_gnp +#' @param ... Passed to `sample_bipartite_gnp()`. +#' @export +bipartite_gnp <- function(...) constructor_spec(sample_bipartite_gnp, ...) #' Bipartite random graphs #' From 734593a4ca81b7d52eef1cf7efc366c868bef227 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 12 Dec 2024 10:16:30 +0100 Subject: [PATCH 5/7] fix: fix deprecation message --- R/games.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/games.R b/R/games.R index 64658532db..33a5b5344c 100644 --- a/R/games.R +++ b/R/games.R @@ -1732,14 +1732,14 @@ sample_bipartite <- function(n1, n2, type = c("gnp", "gnm"), p, m, lifecycle::deprecate_soft( "2.1.3", "sample_bipartite()", - "sample_gnp()" + "sample_bipartite_gnp()" ) sample_bipartite_gnp(n1, n2, p, directed = directed, mode = mode) } else if (type == "gnm") { lifecycle::deprecate_soft( "2.1.3", "sample_bipartite()", - "sample_gnm()" + "sample_bipartite_gnm()" ) sample_bipartite_gnm(n1, n2, m, directed = directed, mode = mode) } From af3bfa8d4a7d6692e543eb8b56459e3b9347d5bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 12 Dec 2024 10:20:14 +0100 Subject: [PATCH 6/7] docs: run `document()` --- R/games.R | 1 + man/erdos.renyi.game.Rd | 2 +- man/sample_.Rd | 2 +- man/sample_bipartite.Rd | 2 +- man/sample_bipartite_gnm.Rd | 9 ++++++--- man/sample_chung_lu.Rd | 2 +- man/sample_correlated_gnp.Rd | 2 +- man/sample_correlated_gnp_pair.Rd | 2 +- man/sample_degseq.Rd | 2 +- man/sample_dot_product.Rd | 2 +- man/sample_fitness.Rd | 2 +- man/sample_fitness_pl.Rd | 2 +- man/sample_forestfire.Rd | 2 +- man/sample_gnm.Rd | 2 +- man/sample_gnp.Rd | 2 +- man/sample_grg.Rd | 2 +- man/sample_growing.Rd | 2 +- man/sample_hierarchical_sbm.Rd | 2 +- man/sample_islands.Rd | 2 +- man/sample_k_regular.Rd | 2 +- man/sample_last_cit.Rd | 2 +- man/sample_pa.Rd | 2 +- man/sample_pa_age.Rd | 2 +- man/sample_pref.Rd | 2 +- man/sample_sbm.Rd | 2 +- man/sample_smallworld.Rd | 2 +- man/sample_traits_callaway.Rd | 2 +- man/sample_tree.Rd | 2 +- 28 files changed, 33 insertions(+), 29 deletions(-) diff --git a/R/games.R b/R/games.R index 33a5b5344c..fc4bb7a19e 100644 --- a/R/games.R +++ b/R/games.R @@ -1766,6 +1766,7 @@ bipartite <- function(...) { } } + #' @rdname sample_bipartite_gnm #' @param ... Passed to `sample_bipartite_gnm()`. #' @export diff --git a/man/erdos.renyi.game.Rd b/man/erdos.renyi.game.Rd index 30d2367039..caa0e0f924 100644 --- a/man/erdos.renyi.game.Rd +++ b/man/erdos.renyi.game.Rd @@ -52,9 +52,9 @@ Mathematicae} 6, 290--297 (1959). } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_.Rd b/man/sample_.Rd index 9d38f13a48..212a9fe71b 100644 --- a/man/sample_.Rd +++ b/man/sample_.Rd @@ -46,9 +46,9 @@ blocky3 <- pref_matrix \%>\% } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index 53b5d3c4b6..767047d151 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -53,9 +53,9 @@ Use \code{\link[=sample_bipartite_gnm]{sample_bipartite_gnm()}} and \code{\link[ } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_bipartite_gnm.Rd b/man/sample_bipartite_gnm.Rd index f5e6302845..be8939864a 100644 --- a/man/sample_bipartite_gnm.Rd +++ b/man/sample_bipartite_gnm.Rd @@ -1,10 +1,13 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/games.R -\name{sample_bipartite_gnm} +\name{bipartite_gnm} +\alias{bipartite_gnm} \alias{sample_bipartite_gnm} \alias{sample_bipartite_gnp} \title{Bipartite random graphs} \usage{ +bipartite_gnm(...) + sample_bipartite_gnm( n1, n2, @@ -24,14 +27,14 @@ sample_bipartite_gnp( ) } \arguments{ +\item{...}{Passed to \code{sample_bipartite_gnm()}.} + \item{n1}{Integer scalar, the number of bottom vertices.} \item{n2}{Integer scalar, the number of top vertices.} \item{m}{Integer scalar, the number of edges for \eqn{G(n,m)} graphs.} -\item{...}{These dots are for future extensions and must be empty.} - \item{directed}{Logical scalar, whether to create a directed graph. See also the \code{mode} argument.} diff --git a/man/sample_chung_lu.Rd b/man/sample_chung_lu.Rd index 7cb555faad..d636643229 100644 --- a/man/sample_chung_lu.Rd +++ b/man/sample_chung_lu.Rd @@ -168,10 +168,10 @@ with sharply specified degrees. \code{\link[=sample_gnp]{sample_gnp()}} creates fixed connection probability \eqn{p} between all vertex pairs. Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_correlated_gnp.Rd b/man/sample_correlated_gnp.Rd index cace3e64c4..563730a349 100644 --- a/man/sample_correlated_gnp.Rd +++ b/man/sample_correlated_gnp.Rd @@ -56,10 +56,10 @@ graph matching for correlated Erdős-Rényi graphs. } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp_pair}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index ba5d0693ad..f6ba5cfd95 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -49,10 +49,10 @@ graph matching for correlated Erdős-Rényi graphs. } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_degseq}()}, diff --git a/man/sample_degseq.Rd b/man/sample_degseq.Rd index 267d46eff0..0f381f59d6 100644 --- a/man/sample_degseq.Rd +++ b/man/sample_degseq.Rd @@ -195,10 +195,10 @@ all(degree(powerlaw_vl_graph) == powerlaw_degrees) \code{\link[=realize_degseq]{realize_degseq()}} for a deterministic variant. Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index f34fc48a23..f658f4e08b 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -57,10 +57,10 @@ for social networks. Dissertation, Johns Hopkins University, Maryland, USA, and \code{\link[=sample_sphere_volume]{sample_sphere_volume()}} for sampling position vectors. Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index ccc108b3a6..6b8c34bf65 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -79,10 +79,10 @@ distribution in scale-free networks. \emph{Phys Rev Lett} 87(27):278701, } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index 82ae57a933..18e547e3f7 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -88,10 +88,10 @@ scale-free networks under the Achlioptas process. \emph{Phys Rev Lett} } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index 131f7ece49..1d6c6f9765 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -77,10 +77,10 @@ conference on Knowledge discovery in data mining}, 177--187, 2005. model. Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnm.Rd b/man/sample_gnm.Rd index 2b1f90778c..aaf6353a42 100644 --- a/man/sample_gnm.Rd +++ b/man/sample_gnm.Rd @@ -43,10 +43,10 @@ Mathematicae} 6, 290--297 (1959). } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_gnp.Rd b/man/sample_gnp.Rd index 18b48f5f37..77d1347526 100644 --- a/man/sample_gnp.Rd +++ b/man/sample_gnp.Rd @@ -54,10 +54,10 @@ Mathematicae} 6, 290--297 (1959). } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 1d68b0e1d5..335d91b29f 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -45,10 +45,10 @@ g2 <- sample_grg(1000, 0.05, torus = TRUE) } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_growing.Rd b/man/sample_growing.Rd index cfed0a8be7..ab7826d489 100644 --- a/man/sample_growing.Rd +++ b/man/sample_growing.Rd @@ -42,10 +42,10 @@ g2 <- sample_growing(500, citation = TRUE) } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_hierarchical_sbm.Rd b/man/sample_hierarchical_sbm.Rd index be3b7ace50..48c0ab53d1 100644 --- a/man/sample_hierarchical_sbm.Rd +++ b/man/sample_hierarchical_sbm.Rd @@ -57,10 +57,10 @@ if (require(Matrix)) { } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_islands.Rd b/man/sample_islands.Rd index 3c2bf61818..be031b3f02 100644 --- a/man/sample_islands.Rd +++ b/man/sample_islands.Rd @@ -36,10 +36,10 @@ oc \code{\link[=sample_gnp]{sample_gnp()}} Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index 22d6c7591e..8258329274 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -48,10 +48,10 @@ sapply(k10, plot, vertex.label = NA) sequence. Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index aded4bec8b..a5a55001a9 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -80,10 +80,10 @@ vertex only. } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa.Rd b/man/sample_pa.Rd index 47291e6f87..ec8c4f8ada 100644 --- a/man/sample_pa.Rd +++ b/man/sample_pa.Rd @@ -127,10 +127,10 @@ de Solla Price, D. J. 1965. Networks of Scientific Papers \emph{Science}, } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index 0de557f4be..598cb93af4 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -136,10 +136,10 @@ max(degree(g3)) } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index bd97f9f46d..43aadaa2fa 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -99,10 +99,10 @@ tkplot(g, layout = layout_in_circle) } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index 40ff2ecf6d..c771995ca8 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -53,10 +53,10 @@ and evaluation. \emph{Social Networks}, 14, 5--61. } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index d1a69d2cbd..28f9adc0b4 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -65,10 +65,10 @@ Duncan J Watts and Steven H Strogatz: Collective dynamics of \code{\link[=make_lattice]{make_lattice()}}, \code{\link[=rewire]{rewire()}} Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index 363c3325e5..7d7886783e 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -79,10 +79,10 @@ g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2 } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, diff --git a/man/sample_tree.Rd b/man/sample_tree.Rd index 74c82b37d6..a5c600ba8f 100644 --- a/man/sample_tree.Rd +++ b/man/sample_tree.Rd @@ -37,10 +37,10 @@ g <- sample_tree(100, method = "lerw") } \seealso{ Random graph models (games) +\code{\link{bipartite_gnm}()}, \code{\link{erdos.renyi.game}()}, \code{\link{sample_}()}, \code{\link{sample_bipartite}()}, -\code{\link{sample_bipartite_gnm}()}, \code{\link{sample_chung_lu}()}, \code{\link{sample_correlated_gnp}()}, \code{\link{sample_correlated_gnp_pair}()}, From d2e008e2ce935e9eb122061e2c24aeea16b07a75 Mon Sep 17 00:00:00 2001 From: maelle <8360597+maelle@users.noreply.github.com> Date: Thu, 12 Dec 2024 09:27:07 +0000 Subject: [PATCH 7/7] [create-pull-request] automated change --- tests/testthat/_snaps/bipartite.random.game.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/_snaps/bipartite.random.game.md b/tests/testthat/_snaps/bipartite.random.game.md index 74df74d86c..0e3bd4cffe 100644 --- a/tests/testthat/_snaps/bipartite.random.game.md +++ b/tests/testthat/_snaps/bipartite.random.game.md @@ -5,7 +5,7 @@ Condition Warning: `sample_bipartite()` was deprecated in igraph 2.1.3. - i Please use `sample_gnp()` instead. + i Please use `sample_bipartite_gnp()` instead. --- @@ -14,5 +14,5 @@ Condition Warning: `sample_bipartite()` was deprecated in igraph 2.1.3. - i Please use `sample_gnm()` instead. + i Please use `sample_bipartite_gnm()` instead.