From 29ccf8a6e2f6ff1d5ff1488786da222e351103fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 23 Jun 2026 11:59:02 +0200 Subject: [PATCH] docs: describe logical params more consistently Fix #2487 --- R/adjacency.R | 2 +- R/assortativity.R | 4 +-- R/bipartite.R | 2 +- R/centrality.R | 22 ++++++------ R/centralization.R | 14 ++++---- R/cohesive.blocks.R | 4 +-- R/community.R | 34 +++++++++--------- R/conversion.R | 22 ++++++------ R/decomposition.R | 6 ++-- R/efficiency.R | 2 +- R/embedding.R | 8 ++--- R/epi.R | 2 +- R/fit.R | 4 +-- R/flow.R | 10 +++--- R/foreign.R | 4 +-- R/games.R | 40 ++++++++++----------- R/incidence.R | 4 +-- R/indexing.R | 8 ++--- R/interface.R | 6 ++-- R/layout.R | 6 ++-- R/make.R | 20 +++++------ R/operators.R | 12 +++---- R/plot.R | 2 +- R/print.R | 10 +++--- R/rewire.R | 4 +-- R/scan.R | 4 +-- R/sir.R | 4 +-- R/stochastic_matrix.R | 6 ++-- R/structural-properties.R | 48 +++++++++++++------------- man/aging.ba.game.Rd | 4 +-- man/aging.barabasi.game.Rd | 4 +-- man/aging.prefatt.game.Rd | 4 +-- man/alpha.centrality.Rd | 2 +- man/alpha_centrality.Rd | 2 +- man/arpack.Rd | 2 +- man/as_adj.Rd | 6 ++-- man/as_adj_list.Rd | 2 +- man/as_adjacency_matrix.Rd | 6 ++-- man/as_biadjacency_matrix.Rd | 4 +-- man/assortativity.Rd | 4 +-- man/assortativity.degree.Rd | 2 +- man/assortativity.nominal.Rd | 4 +-- man/asymmetric.preference.game.Rd | 2 +- man/authority.score.Rd | 2 +- man/betweenness.Rd | 2 +- man/bfs.Rd | 14 ++++---- man/bipartite.projection.Rd | 2 +- man/bipartite.random.game.Rd | 2 +- man/bipartite_projection.Rd | 2 +- man/bonpow.Rd | 4 +-- man/callaway.traits.game.Rd | 2 +- man/centr_betw.Rd | 4 +-- man/centr_betw_tmax.Rd | 2 +- man/centr_clo.Rd | 2 +- man/centr_degree.Rd | 4 +-- man/centr_degree_tmax.Rd | 2 +- man/centr_eigen.Rd | 4 +-- man/centr_eigen_tmax.Rd | 2 +- man/centralization.betweenness.Rd | 4 +-- man/centralization.betweenness.tmax.Rd | 2 +- man/centralization.closeness.Rd | 2 +- man/centralization.degree.Rd | 4 +-- man/centralization.degree.tmax.Rd | 2 +- man/centralization.evcent.Rd | 4 +-- man/centralization.evcent.tmax.Rd | 2 +- man/centralize.Rd | 2 +- man/centralize.scores.Rd | 2 +- man/cited.type.game.Rd | 4 +-- man/citing.cited.type.game.Rd | 4 +-- man/closeness.Rd | 2 +- man/cluster_edge_betweenness.Rd | 12 +++---- man/cluster_fast_greedy.Rd | 6 ++-- man/cluster_infomap.Rd | 2 +- man/cluster_spinglass.Rd | 2 +- man/cluster_walktrap.Rd | 6 ++-- man/cohesive.blocks.Rd | 2 +- man/cohesive_blocks.Rd | 4 +-- man/communities.Rd | 4 +-- man/complementer.Rd | 2 +- man/components.Rd | 2 +- man/compose.Rd | 2 +- man/degree.Rd | 2 +- man/dfs.Rd | 10 +++--- man/difference.igraph.Rd | 2 +- man/distances.Rd | 4 +-- man/each_edge.Rd | 4 +-- man/edge.betweenness.community.Rd | 12 +++---- man/edge.connectivity.Rd | 2 +- man/edge.disjoint.paths.Rd | 2 +- man/edge_connectivity.Rd | 2 +- man/edge_density.Rd | 2 +- man/eigen_centrality.Rd | 2 +- man/embed_adjacency_matrix.Rd | 2 +- man/embed_laplacian_matrix.Rd | 2 +- man/establishment.game.Rd | 2 +- man/estimate_closeness.Rd | 2 +- man/evcent.Rd | 2 +- man/exportPajek.Rd | 2 +- man/fastgreedy.community.Rd | 6 ++-- man/fit_power_law.Rd | 4 +-- man/forest.fire.game.Rd | 2 +- man/get.adjacency.Rd | 6 ++-- man/get.adjlist.Rd | 2 +- man/get.edge.ids.Rd | 4 +-- man/get.incidence.Rd | 4 +-- man/get.shortest.paths.Rd | 4 +-- man/get.stochastic.Rd | 2 +- man/get_edge_ids.Rd | 4 +-- man/girth.Rd | 2 +- man/global_efficiency.Rd | 2 +- man/graph.adhesion.Rd | 2 +- man/graph.adjacency.Rd | 2 +- man/graph.adjlist.Rd | 2 +- man/graph.bfs.Rd | 14 ++++---- man/graph.bipartite.Rd | 2 +- man/graph.complementer.Rd | 2 +- man/graph.compose.Rd | 2 +- man/graph.data.frame.Rd | 2 +- man/graph.density.Rd | 2 +- man/graph.dfs.Rd | 10 +++--- man/graph.extended.chordal.ring.Rd | 2 +- man/graph.formula.Rd | 2 +- man/graph.full.bipartite.Rd | 2 +- man/graph.graphdb.Rd | 4 +-- man/graph.incidence.Rd | 4 +-- man/graph.laplacian.Rd | 2 +- man/graph.lattice.Rd | 6 ++-- man/graph.mincut.Rd | 2 +- man/graph.union.Rd | 2 +- man/graph_from_adj_list.Rd | 2 +- man/graph_from_adjacency_matrix.Rd | 2 +- man/graph_from_biadjacency_matrix.Rd | 4 +-- man/graph_from_data_frame.Rd | 2 +- man/graph_from_graphdb.Rd | 4 +-- man/graph_from_graphnel.Rd | 6 ++-- man/graph_from_literal.Rd | 2 +- man/grg.game.Rd | 4 +-- man/harmonic_centrality.Rd | 2 +- man/hits_scores.Rd | 2 +- man/hub.score.Rd | 2 +- man/hub_score.Rd | 2 +- man/igraph.from.graphNEL.Rd | 6 ++-- man/infomap.community.Rd | 2 +- man/intersection.igraph.Rd | 4 +-- man/is.chordal.Rd | 4 +-- man/is_chordal.Rd | 6 ++-- man/is_directed.Rd | 2 +- man/is_min_separator.Rd | 2 +- man/is_separator.Rd | 2 +- man/k.regular.game.Rd | 4 +-- man/laplacian_matrix.Rd | 2 +- man/lastcit.game.Rd | 2 +- man/layout.drl.Rd | 2 +- man/layout_as_tree.Rd | 4 +-- man/layout_with_drl.Rd | 2 +- man/local_scan.Rd | 2 +- man/make_bipartite_graph.Rd | 4 +-- man/make_chordal_ring.Rd | 2 +- man/make_circulant.Rd | 2 +- man/make_full_bipartite_graph.Rd | 2 +- man/make_full_multipartite.Rd | 2 +- man/make_lattice.Rd | 6 ++-- man/min_cut.Rd | 2 +- man/plot.igraph.Rd | 2 +- man/plot.sir.Rd | 2 +- man/plot_dendrogram.communities.Rd | 2 +- man/power.law.fit.Rd | 2 +- man/power_centrality.Rd | 4 +-- man/preference.game.Rd | 4 +-- man/print.igraph.Rd | 10 +++--- man/reciprocity.Rd | 2 +- man/sample_bipartite.Rd | 2 +- man/sample_bipartite_gnm.Rd | 2 +- man/sample_correlated_gnp_pair.Rd | 2 +- man/sample_dot_product.Rd | 2 +- man/sample_fitness.Rd | 4 +-- man/sample_fitness_pl.Rd | 6 ++-- man/sample_forestfire.Rd | 2 +- man/sample_grg.Rd | 4 +-- man/sample_k_regular.Rd | 4 +-- man/sample_last_cit.Rd | 4 +-- man/sample_pa_age.Rd | 4 +-- man/sample_pref.Rd | 4 +-- man/sample_sbm.Rd | 4 +-- man/sample_smallworld.Rd | 4 +-- man/sample_sphere_surface.Rd | 2 +- man/sample_sphere_volume.Rd | 2 +- man/sample_traits_callaway.Rd | 2 +- man/sbm.game.Rd | 4 +-- man/sir.Rd | 4 +-- man/spinglass.community.Rd | 2 +- man/static.fitness.game.Rd | 4 +-- man/static.power.law.game.Rd | 6 ++-- man/stochastic_matrix.Rd | 2 +- man/sub-.igraph.Rd | 4 +-- man/sub-sub-.igraph.Rd | 4 +-- man/subgraph.Rd | 2 +- man/subgraph.centrality.Rd | 2 +- man/subgraph.edges.Rd | 2 +- man/subgraph_centrality.Rd | 2 +- man/union.igraph.Rd | 2 +- man/vertex.connectivity.Rd | 2 +- man/vertex_connectivity.Rd | 2 +- man/walktrap.community.Rd | 6 ++-- man/watts.strogatz.game.Rd | 4 +-- man/which_multiple.Rd | 2 +- src/cpp11.cpp | 4 --- 207 files changed, 446 insertions(+), 450 deletions(-) diff --git a/R/adjacency.R b/R/adjacency.R index 3eaf74a2d27..5f3985a97ba 100644 --- a/R/adjacency.R +++ b/R/adjacency.R @@ -149,7 +149,7 @@ graph.adjacency <- function( #' edge attribute named by the `weighted` argument. If it is `TRUE` #' then a weighted graph is created and the name of the edge attribute will be #' `weight`. See also details below. -#' @param diag Logical scalar, whether to include the diagonal of the matrix in +#' @param diag Logical, whether to include the diagonal of the matrix in #' the calculation. If this is `FALSE` then the diagonal is zerod out #' first. #' @param add.colnames Character scalar, whether to add the column names as diff --git a/R/assortativity.R b/R/assortativity.R index 074fa421b35..8c8e95d0876 100644 --- a/R/assortativity.R +++ b/R/assortativity.R @@ -130,14 +130,14 @@ assortativity.degree <- function(graph, directed = TRUE) { #' This #' argument is ignored (with a warning) if it is not `NULL` and undirected #' assortativity coefficient is being calculated. -#' @param directed Logical scalar, whether to consider edge directions for +#' @param directed Logical, whether to consider edge directions for #' directed graphs. #' This argument is ignored for undirected graphs. #' Supply #' `TRUE` here to do the natural thing, i.e. use directed version of the #' measure for directed graphs and the undirected version for undirected #' graphs. -#' @param normalized Boolean, whether to compute the normalized assortativity. +#' @param normalized Logical, whether to compute the normalized assortativity. #' The non-normalized nominal assortativity is identical to modularity. #' The non-normalized value-based assortativity is simply the covariance of the #' values at the two ends of edges. diff --git a/R/bipartite.R b/R/bipartite.R index 92c0a5ee7b9..5174b6ce07b 100644 --- a/R/bipartite.R +++ b/R/bipartite.R @@ -129,7 +129,7 @@ bipartite.mapping <- function(graph) { #' one projection is requested in argument `which`. #' @param which A character scalar to specify which projection(s) to calculate. #' The default is to calculate both. -#' @param remove.type Logical scalar, whether to remove the `type` vertex +#' @param remove.type Logical, whether to remove the `type` vertex #' attribute from the projections. This makes sense because these graphs are #' not bipartite any more. However if you want to combine them with each other #' (or other bipartite graphs), then it is worth keeping this attribute. By diff --git a/R/centrality.R b/R/centrality.R index 2726612659d..55316c0682a 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -388,7 +388,7 @@ betweenness.estimate <- estimate_betweenness #' betweenness. If the graph has a `weight` edge attribute, then this is #' used by default. Weights are used to calculate weighted shortest paths, #' so they are interpreted as distances. -#' @param normalized Logical scalar, whether to normalize the betweenness +#' @param normalized Logical, whether to normalize the betweenness #' scores. If `TRUE`, then the results are normalized by the number of ordered #' or unordered vertex pairs in directed and undirected graphs, respectively. #' In an undirected graph, @@ -540,7 +540,7 @@ edge.betweenness.estimate <- estimate_edge_betweenness #' *to* a vertex, \dQuote{out} measures paths *from* a vertex, #' *all* uses undirected paths. This argument is ignored for undirected #' graphs. -#' @param normalized Logical scalar, whether to calculate the normalized +#' @param normalized Logical, whether to calculate the normalized #' closeness, i.e. the inverse average distance to all reachable vertices. #' The non-normalized closeness is the inverse of the sum of distances to #' all reachable vertices. @@ -854,7 +854,7 @@ arpack_defaults <- function() { #' \dQuote{input matrix}. (The input matrix is never given explicitly.) The #' second argument is `extra`. #' @param extra Extra argument to supply to `func`. -#' @param sym Logical scalar, whether the input matrix is symmetric. Always +#' @param sym Logical, whether the input matrix is symmetric. Always #' supply `TRUE` here if it is, since it can speed up the computation. #' @param options Options to ARPACK, a named list to overwrite some of the #' default option values. See details below. @@ -1041,7 +1041,7 @@ arpack.unpack.complex <- function(vectors, values, nev) { #' effectively means that the measure can only be calculated for small graphs. #' #' @param graph The input graph. It will be treated as undirected. -#' @param diag Boolean scalar, whether to include the diagonal of the adjacency +#' @param diag Logical, whether to include the diagonal of the adjacency #' matrix in the analysis. Giving `FALSE` here effectively eliminates the #' loops edges from the graph before the calculation. #' @return A numeric vector, the subgraph centrality scores of the vertices. @@ -1239,7 +1239,7 @@ eigen_defaults <- function() { #' computation, see [arpack()] for more about ARPACK in igraph. #' #' @param graph Graph to be analyzed. -#' @param directed Logical scalar, whether to consider direction of the edges +#' @param directed Logical, whether to consider direction of the edges #' in directed graphs. It is ignored for undirected graphs. #' @param scale `r lifecycle::badge("deprecated")` Normalization will always take #' place. @@ -1441,7 +1441,7 @@ diversity <- function(graph, weights = NULL, vids = V(graph)) { #' scores are the same as authority scores. #' #' @param graph The input graph. -#' @param scale Logical scalar, whether to scale the result to have a maximum +#' @param scale Logical, whether to scale the result to have a maximum #' score of one. If no scaling is used then the result vector has unit length #' in the Euclidean norm. #' @param weights Optional positive weight vector for calculating weighted @@ -1539,7 +1539,7 @@ authority_score <- function( #' @title Kleinberg's hub centrality scores. #' @rdname hub_score #' @param graph The input graph. -#' @param scale Logical scalar, whether to scale the result to have a maximum +#' @param scale Logical, whether to scale the result to have a maximum #' score of one. If no scaling is used then the result vector has unit length #' in the Euclidean norm. #' @param weights Optional positive weight vector for calculating weighted @@ -1707,7 +1707,7 @@ page_rank <- function( #' the edge directions only, \dQuote{in} traverses the edges in reverse, while #' \dQuote{all} ignores edge directions. This argument is ignored for undirected #' graphs. -#' @param normalized Logical scalar, whether to calculate the normalized +#' @param normalized Logical, whether to calculate the normalized #' harmonic centrality. If true, the result is the mean inverse path length to #' other vertices, i.e. it is normalized by the number of vertices minus one. #' If false, the result is the sum of inverse path lengths to other vertices. @@ -1874,7 +1874,7 @@ bonpow.sparse <- function( #' @param graph the input graph. #' @param nodes vertex sequence indicating which vertices are to be included in #' the calculation. By default, all vertices are included. -#' @param loops boolean indicating whether or not the diagonal should be +#' @param loops Logical indicating whether or not the diagonal should be #' treated as valid data. Set this true if and only if the data can contain #' loops. `loops` is `FALSE` by default. #' @param exponent exponent (decay rate) for the Bonacich power centrality @@ -1883,7 +1883,7 @@ bonpow.sparse <- function( #' 1. #' @param tol tolerance for near-singularities during matrix inversion (see #' [solve()]) -#' @param sparse Logical scalar, whether to use sparse matrices for the +#' @param sparse Logical, whether to use sparse matrices for the #' calculation. The \sQuote{Matrix} package is required for sparse matrix #' support #' @inheritParams as_adjacency_matrix @@ -2069,7 +2069,7 @@ alpha.centrality.sparse <- function( #' @inheritParams as_adjacency_matrix #' @param tol Tolerance for near-singularities during matrix inversion, see #' [solve()]. -#' @param sparse Logical scalar, whether to use sparse matrices for the +#' @param sparse Logical, whether to use sparse matrices for the #' calculation. The \sQuote{Matrix} package is required for sparse matrix #' support #' @return A numeric vector contaning the centrality scores for the selected diff --git a/R/centralization.R b/R/centralization.R index 54eda626476..f2c3b090149 100644 --- a/R/centralization.R +++ b/R/centralization.R @@ -282,7 +282,7 @@ NULL #' the most centralized graph with the same number of vertices as the graph #' under study. This is only used if the `normalized` argument is set #' to `TRUE`. -#' @param normalized Logical scalar. Whether to normalize the graph level +#' @param normalized Logical. Whether to normalize the graph level #' centrality score by dividing by the supplied theoretical maximum. #' @return A real scalar, the centralization of the graph from which #' `scores` were derived. @@ -329,9 +329,9 @@ centralize <- function(scores, theoretical.max = 0, normalized = TRUE) { #' @param graph The input graph. #' @param mode This is the same as the `mode` argument of #' `degree()`. -#' @param loops Logical scalar, whether to consider loops edges when +#' @param loops Logical, whether to consider loops edges when #' calculating the degree. -#' @param normalized Logical scalar. Whether to normalize the graph level +#' @param normalized Logical. Whether to normalize the graph level #' centrality score by dividing by the theoretical maximum. #' @return A named list with the following components: #' \describe{ @@ -435,7 +435,7 @@ centr_degree_tmax <- function( #' See [centralize()] for a summary of graph centralization. #' #' @param graph The input graph. -#' @param directed logical scalar, whether to use directed shortest paths for +#' @param directed Logical, whether to use directed shortest paths for #' calculating betweenness. #' @inheritParams centr_degree #' @return A named list with the following components: @@ -491,7 +491,7 @@ centr_betw <- function(graph, directed = TRUE, normalized = TRUE) { #' `nodes` and `directed` are both given. #' @param nodes The number of vertices. This is ignored if the graph is #' given. -#' @param directed Logical scalar, whether to use directed shortest paths +#' @param directed Logical, whether to use directed shortest paths #' for calculating betweenness. Ignored if an undirected graph was #' given. #' @return Real scalar, the theoretical maximum (unnormalized) graph @@ -605,7 +605,7 @@ centr_clo_tmax <- function( #' See [centralize()] for a summary of graph centralization. #' #' @param graph The input graph. -#' @param directed logical scalar, whether to use directed shortest paths for +#' @param directed Logical, whether to use directed shortest paths for #' calculating eigenvector centrality. #' @param scale `r lifecycle::badge("deprecated")` Ignored. Computing #' eigenvector centralization requires normalized eigenvector centrality scores. @@ -682,7 +682,7 @@ centr_eigen <- function( #' `nodes` is given. #' @param nodes The number of vertices. This is ignored if the graph is #' given. -#' @param directed logical scalar, whether to consider edge directions +#' @param directed Logical, whether to consider edge directions #' during the calculation. Ignored in undirected graphs. #' @param scale `r lifecycle::badge("deprecated")` Ignored. Computing #' eigenvector centralization requires normalized eigenvector centrality scores. diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R index b969a8fee76..e1c4f488a91 100644 --- a/R/cohesive.blocks.R +++ b/R/cohesive.blocks.R @@ -224,7 +224,7 @@ blockGraphs <- function(blocks, graph) { #' For `graphs_from_cohesive_blocks()` and `export_pajek()` the same graph must be #' supplied whose cohesive block structure is given in the `blocks()` #' argument. -#' @param labels Logical scalar, whether to add the vertex labels to the result +#' @param labels Logical, whether to add the vertex labels to the result #' object. These labels can be then used when reporting and plotting the #' cohesive blocks. #' @param blocks,x,object A `cohesiveBlocks` object, created with the @@ -240,7 +240,7 @@ blockGraphs <- function(blocks, graph) { #' of the files, without extension. (But it can contain the path to the files.) #' #' See also details below. -#' @param project.file Logical scalar, whether to create a single Pajek project +#' @param project.file Logical, whether to create a single Pajek project #' file containing all the data, or to create separated files for each item. #' See details below. #' @param y The graph whose cohesive blocks are supplied in the `x` diff --git a/R/community.R b/R/community.R index 65889c3c3e9..8923f72da61 100644 --- a/R/community.R +++ b/R/community.R @@ -584,7 +584,7 @@ code.length <- function(communities) { #' communities are colored green and other edges are red. #' @param hang Numeric scalar indicating how the height of leaves should be #' computed from the heights of their parents; see [plot.hclust()]. -#' @param use.modularity Logical scalar, whether to use the modularity values +#' @param use.modularity Logical, whether to use the modularity values #' to define the height of the branches. #' @param \dots Additional arguments. `plot.communities` passes these to #' [plot.igraph()]. The other functions silently ignore @@ -617,7 +617,7 @@ code.length <- function(communities) { #' #' `crossing()` returns a logical vector. #' -#' `is_hierarchical()` returns a logical scalar. +#' `is_hierarchical()` returns a Logical. #' #' `merges()` returns a two-column numeric matrix. #' @@ -1391,7 +1391,7 @@ community.to.membership2 <- function(merges, vcount, steps) { #' limit for the number of communities. It is not a problem to supply a #' (reasonably) big number here, in which case some spin states will be #' unpopulated. -#' @param parupdate Logical constant, whether to update the spins of the +#' @param parupdate Logical, whether to update the spins of the #' vertices in parallel (synchronously) or not. This argument is ignored if the #' second form of the function is used (i.e. the \sQuote{`vertex`} argument #' is present). It is also not implemented in the \dQuote{neg} implementation. @@ -1835,12 +1835,12 @@ cluster_fluid_communities <- function(graph, no.of.communities) { #' weights increase the probability that an edge is selected by the random #' walker. In other words, larger edge weights correspond to stronger connections. #' @param steps The length of the random walks to perform. -#' @param merges Logical scalar, whether to include the merge matrix in the +#' @param merges Logical, whether to include the merge matrix in the #' result. -#' @param modularity Logical scalar, whether to include the vector of the +#' @param modularity Logical, whether to include the vector of the #' modularity scores in the result. If the `membership` argument is true, #' then it will always be calculated. -#' @param membership Logical scalar, whether to calculate the membership vector +#' @param membership Logical, whether to calculate the membership vector #' for the split corresponding to the highest modularity value. #' @return `cluster_walktrap()` returns a [communities()] #' object, please see the [communities()] manual page for details. @@ -1946,11 +1946,11 @@ cluster_walktrap <- function( #' attribute, but you don't want to use it for community detection. Edge weights #' are used to calculate weighted edge betweenness. This means that edges are #' interpreted as distances, not as connection strengths. -#' @param directed Logical constant, whether to calculate directed edge +#' @param directed Logical, whether to calculate directed edge #' betweenness for directed graphs. It is ignored for undirected graphs. -#' @param edge.betweenness Logical constant, whether to return the edge +#' @param edge.betweenness Logical, whether to return the edge #' betweenness of the edges at the time of their removal. -#' @param merges Logical constant, whether to return the merge matrix +#' @param merges Logical, whether to return the merge matrix #' representing the hierarchical community structure of the network. This #' argument is called `merges`, even if the community structure algorithm #' itself is divisive and not agglomerative: it builds the tree from top to @@ -1962,12 +1962,12 @@ cluster_walktrap <- function( #' communities numbered from one to \eqn{N}. The first merge, the first line of #' the matrix creates community \eqn{N+1}, the second merge creates community #' \eqn{N+2}, etc. -#' @param bridges Logical constant, whether to return a list the edge removals +#' @param bridges Logical, whether to return a list the edge removals #' which actually splitted a component of the graph. -#' @param modularity Logical constant, whether to calculate the maximum +#' @param modularity Logical, whether to calculate the maximum #' modularity score, considering all possibly community structures along the #' edge-betweenness based edge removals. -#' @param membership Logical constant, whether to calculate the membership +#' @param membership Logical, whether to calculate the membership #' vector corresponding to the highest possible modularity score. #' @return `cluster_edge_betweenness()` returns a #' [communities()] object, please see the [communities()] @@ -2054,10 +2054,10 @@ cluster_edge_betweenness <- function( #' #' @param graph The input graph. It must be undirected and must not have #' multi-edges. -#' @param merges Logical scalar, whether to return the merge matrix. -#' @param modularity Logical scalar, whether to return a vector containing the +#' @param merges Logical, whether to return the merge matrix. +#' @param modularity Logical, whether to return a vector containing the #' modularity after each merge. -#' @param membership Logical scalar, whether to calculate the membership vector +#' @param membership Logical, whether to calculate the membership vector #' corresponding to the maximum modularity score, considering all possible #' community structures along the merges. #' @param weights The weights of the edges. It must be a positive numeric vector, @@ -2660,7 +2660,7 @@ cluster_optimal <- function(graph, weights = NULL) { #' jumps to that vertex. #' @param nb.trials The number of attempts to partition the network (can be any #' integer value equal or larger than 1). -#' @param modularity Logical scalar, whether to calculate the modularity score +#' @param modularity Logical, whether to calculate the modularity score #' of the detected community structure. #' @return `cluster_infomap()` returns a [communities()] object, #' please see the [communities()] manual page for details. @@ -2807,7 +2807,7 @@ plot_dendrogram <- function(x, mode = igraph_opt("dend.plot.type"), ...) { #' @param mode Which dendrogram plotting function to use. See details below. #' @param \dots Additional arguments to supply to the dendrogram plotting #' function. -#' @param use.modularity Logical scalar, whether to use the modularity values +#' @param use.modularity Logical, whether to use the modularity values #' to define the height of the branches. #' @param palette The color palette to use for colored plots. #' @return Returns whatever the return value was from the plotting function, diff --git a/R/conversion.R b/R/conversion.R index c978a051e50..a1ccb77f8a1 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -415,12 +415,12 @@ get.adjacency.sparse <- function( #' @param attr `r lifecycle::badge("deprecated")` Use `weights` instead. If #' supplied, the value is forwarded to `weights` as a character edge #' attribute name. -#' @param edges `r lifecycle::badge("deprecated")` Logical scalar, whether to return the edge IDs in the matrix. +#' @param edges `r lifecycle::badge("deprecated")` Logical, whether to return the edge IDs in the matrix. #' For non-existant edges zero is returned. -#' @param names Logical constant, whether to assign row and column names +#' @param names Logical, whether to assign row and column names #' to the matrix. These are only assigned if the `name` vertex attribute #' is present in the graph. -#' @param sparse Logical scalar, whether to create a sparse matrix. The +#' @param sparse Logical, whether to create a sparse matrix. The #' \sQuote{`Matrix`} package must be installed for creating sparse #' matrices. #' @return A `vcount(graph)` by `vcount(graph)` (usually) numeric @@ -732,7 +732,7 @@ as_undirected <- function( #' @param loops Character scalar, one of `"ignore"` (to omit loops), `"twice"` #' (to include loop edges twice) and `"once"` (to include them once). `"twice"` #' is not allowed for directed graphs and will be replaced with `"once"`. -#' @param multiple Logical scalar, set to `FALSE` to use only one representative +#' @param multiple Logical, set to `FALSE` to use only one representative #' of each set of parallel edges. #' @return A list of `igraph.vs` or a list of numeric vectors depending on #' the value of `igraph_opt("return.vs.es")`, see details for performance @@ -823,12 +823,12 @@ as_adj_edge_list <- function( #' attributes of the first of the multiple edges. #' #' @param graphNEL The graphNEL graph. -#' @param name Logical scalar, whether to add graphNEL vertex names as an +#' @param name Logical, whether to add graphNEL vertex names as an #' igraph vertex attribute called \sQuote{`name`}. -#' @param weight Logical scalar, whether to add graphNEL edge weights as an +#' @param weight Logical, whether to add graphNEL edge weights as an #' igraph edge attribute called \sQuote{`weight`}. (graphNEL graphs are #' always weighted.) -#' @param unlist.attrs Logical scalar. graphNEL attribute query functions +#' @param unlist.attrs Logical. graphNEL attribute query functions #' return the values of the attributes in R lists, if this argument is #' `TRUE` (the default) these will be converted to atomic vectors, #' whenever possible, before adding them to the igraph graph. @@ -1150,11 +1150,11 @@ get.incidence.sparse <- function( #' `type` vertex attribute. You must supply this argument if the graph has #' no `type` vertex attribute. #' @inheritParams as_adjacency_matrix -#' @param names Logical scalar, if `TRUE` and the vertices in the graph +#' @param names Logical, if `TRUE` and the vertices in the graph #' are named (i.e. the graph has a vertex attribute called `name`), then #' vertex names will be added to the result as row and column names. Otherwise #' the IDs of the vertices are used as row and column names. -#' @param sparse Logical scalar, if it is `TRUE` then a sparse matrix is +#' @param sparse Logical, if it is `TRUE` then a sparse matrix is #' created, you will need the `Matrix` package for this. #' @return A sparse or dense matrix. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} @@ -1327,7 +1327,7 @@ as_data_frame <- function(x, what = c("edges", "vertices", "both")) { #' undirected (\sQuote{all} or \sQuote{total}) or directed; and in the latter #' case, whether it contains the outgoing (\sQuote{out}) or the incoming #' (\sQuote{in}) neighbors of the vertices. -#' @param duplicate Logical scalar. For undirected graphs it gives whether +#' @param duplicate Logical. For undirected graphs it gives whether #' edges are included in the list twice. E.g. if it is `TRUE` then for an #' undirected \code{{A,B}} edge `graph_from_adj_list()` expects `A` #' included in the neighbors of `B` and `B` to be included in the @@ -1628,7 +1628,7 @@ graph.data.frame <- function(d, directed = TRUE, vertices = NULL) { #' columns. Additional columns are considered as edge attributes. Since #' version 0.7 this argument is coerced to a data frame with #' `as.data.frame`. -#' @param directed Logical scalar, whether or not to create a directed graph. +#' @param directed Logical, whether or not to create a directed graph. #' @param vertices A data frame with vertex metadata, or `NULL`. See #' details below. Since version 0.7 this argument is coerced to a data frame #' with `as.data.frame`, if not `NULL`. diff --git a/R/decomposition.R b/R/decomposition.R index 47df101955e..cdfce737fc1 100644 --- a/R/decomposition.R +++ b/R/decomposition.R @@ -74,12 +74,12 @@ is.chordal <- function( #' @param alpham1 Numeric vector, the inverse of `alpha`. If it is #' `NULL`, then it is automatically calculated by calling #' [max_cardinality()], or from `alpha`. -#' @param fillin Logical scalar, whether to calculate the fill-in edges. -#' @param newgraph Logical scalar, whether to calculate the triangulated graph. +#' @param fillin Logical, whether to calculate the fill-in edges. +#' @param newgraph Logical, whether to calculate the triangulated graph. #' @return A list with three members: #' \describe{ #' \item{chordal}{ -#' Logical scalar, it is `TRUE` iff the input graph is chordal. +#' Logical, it is `TRUE` iff the input graph is chordal. #' } #' \item{fillin}{ #' If requested, then a numeric vector giving the fill-in edges. `NULL` otherwise. diff --git a/R/efficiency.R b/R/efficiency.R index 1879a223461..fd628c45d90 100644 --- a/R/efficiency.R +++ b/R/efficiency.R @@ -42,7 +42,7 @@ #' and the graph has a `weight` edge attribute, then it is used automatically. #' @param vids The vertex IDs of the vertices for which the calculation will be done. #' Applies to the local efficiency calculation only. -#' @param directed Logical scalar, whether to consider directed paths. Ignored +#' @param directed Logical, whether to consider directed paths. Ignored #' for undirected graphs. #' @param mode Specifies how to define the local neighborhood of a vertex in #' directed graphs. \dQuote{out} considers out-neighbors only, \dQuote{in} diff --git a/R/embedding.R b/R/embedding.R index b5cc24831ed..8524f70eb4d 100644 --- a/R/embedding.R +++ b/R/embedding.R @@ -58,7 +58,7 @@ #' eigenvalues. The default is \sQuote{lm}. Note that for directed graphs #' \sQuote{la} and \sQuote{lm} are the equivalent, because the singular values #' are used for the ordering. -#' @param scaled Logical scalar, if `FALSE`, then \eqn{U} and \eqn{V} are +#' @param scaled Logical, if `FALSE`, then \eqn{U} and \eqn{V} are #' returned instead of \eqn{X} and \eqn{Y}. #' @param cvec A numeric vector, its length is the number vertices in the #' graph. This vector is added to the diagonal of the adjacency matrix. @@ -232,7 +232,7 @@ dim_select <- function(sv) { #' #' The default (i.e. type `default`) is to use `D-A` for undirected #' graphs and `OAP` for directed graphs. -#' @param scaled Logical scalar, if `FALSE`, then \eqn{U} and \eqn{V} are +#' @param scaled Logical, if `FALSE`, then \eqn{U} and \eqn{V} are #' returned instead of \eqn{X} and \eqn{Y}. #' @param options A named list containing the parameters for the SVD #' computation algorithm in ARPACK. By default, the list of values is assigned @@ -308,7 +308,7 @@ embed_laplacian_matrix <- function( #' @param dim Integer scalar, the dimension of the random vectors. #' @param n Integer scalar, the sample size. #' @param radius Numeric scalar, the radius of the sphere to sample. -#' @param positive Logical scalar, whether to sample from the positive orthant +#' @param positive Logical, whether to sample from the positive orthant #' of the sphere. #' @return A `dim` (length of the `alpha` vector for #' `sample_dirichlet()`) times `n` matrix, whose columns are the sample @@ -346,7 +346,7 @@ sample_sphere_surface <- function(dim, n = 1, radius = 1, positive = TRUE) { #' @param dim Integer scalar, the dimension of the random vectors. #' @param n Integer scalar, the sample size. #' @param radius Numeric scalar, the radius of the sphere to sample. -#' @param positive Logical scalar, whether to sample from the positive orthant +#' @param positive Logical, whether to sample from the positive orthant #' of the sphere. #' @return A `dim` (length of the `alpha` vector for #' `sample_dirichlet()`) times `n` matrix, whose columns are the sample diff --git a/R/epi.R b/R/epi.R index 92bf3d3041f..ea195d0a1b5 100644 --- a/R/epi.R +++ b/R/epi.R @@ -105,7 +105,7 @@ quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) { #' function. #' @param comp Character scalar, which component to plot. Either \sQuote{NI} #' (infected, default), \sQuote{NS} (susceptible) or \sQuote{NR} (recovered). -#' @param median Logical scalar, whether to plot the (binned) median. +#' @param median Logical, whether to plot the (binned) median. #' @param quantiles A vector of (binned) quantiles to plot. #' @param color Color of the individual simulation curves. #' @param median_color Color of the median curve. diff --git a/R/fit.R b/R/fit.R index 4993d32bc4e..1fc974f4ee7 100644 --- a/R/fit.R +++ b/R/fit.R @@ -100,7 +100,7 @@ power.law.fit <- function( #' @param start Numeric scalar. The initial value of the exponent for the #' minimizing function, for the \sQuote{`R.mle`} implementation. Usually #' it is safe to leave this untouched. -#' @param force.continuous Logical scalar. Whether to force a continuous +#' @param force.continuous Logical. Whether to force a continuous #' distribution for the \sQuote{`plfit`} implementation, even if the #' sample vector contains integer values only (by chance). If this argument is #' false, igraph will assume a continuous distribution if at least one sample @@ -130,7 +130,7 @@ power.law.fit <- function( #' named list with entries: #' \describe{ #' \item{continuous}{ -#' Logical scalar, whether the +#' Logical, whether the #' fitted power-law distribution was continuous or discrete. #' } #' \item{alpha}{ diff --git a/R/flow.R b/R/flow.R index d57da32db44..79d6eb11161 100644 --- a/R/flow.R +++ b/R/flow.R @@ -345,7 +345,7 @@ dominator.tree <- function(graph, root, mode = c("out", "in", "all", "total")) { #' @param target The ID of the target vertex (sometimes also called sink). #' @param capacity Vector giving the capacity of the edges. If this is #' `NULL` (the default) then the `capacity` edge attribute is used. -#' @param value.only Logical scalar, if `TRUE` only the minimum cut value +#' @param value.only Logical, if `TRUE` only the minimum cut value #' is returned, if `FALSE` the edges in the cut and a the two (or more) #' partitions are also returned. #' @return For `min_cut()` a nuieric constant, the value of the minimum @@ -482,7 +482,7 @@ min_cut <- function( #' can be `NULL`, see details below. #' @param target The ID of the target vertex, for `vertex_connectivity()` it #' can be `NULL`, see details below. -#' @param checks Logical constant. Whether to check that the graph is connected +#' @param checks Logical. Whether to check that the graph is connected #' and also the degree of the vertices. If the graph is not (strongly) #' connected then the connectivity is obviously zero. Otherwise if the minimum #' degree is one then the vertex connectivity is also one. It is a good idea to @@ -589,7 +589,7 @@ vertex_connectivity <- function( #' can be `NULL`, see details below. #' @param target The ID of the target vertex, for `edge_connectivity()` it #' can be `NULL`, see details below. -#' @param checks Logical constant. Whether to check that the graph is connected +#' @param checks Logical. Whether to check that the graph is connected #' and also the degree of the vertices. If the graph is not (strongly) #' connected then the connectivity is obviously zero. Otherwise if the minimum #' degree is one then the edge connectivity is also one. It is a good idea to @@ -1036,7 +1036,7 @@ max_flow <- function(graph, source, target, capacity = NULL) { #' ignored. #' @param candidate A numeric vector giving the vertex IDs of the candidate #' separator. -#' @return A logical scalar, whether the supplied vertex set is a (minimal) +#' @return A Logical, whether the supplied vertex set is a (minimal) #' vertex separator or not. #' lists all vertex separator of minimum size. #' @family flow @@ -1069,7 +1069,7 @@ is_separator <- function(graph, candidate) { #' ignored. #' @param candidate A numeric vector giving the vertex IDs of the candidate #' separator. -#' @return A logical scalar, whether the supplied vertex set is a (minimal) +#' @return A Logical, whether the supplied vertex set is a (minimal) #' vertex separator or not. #' @examples #' # The graph from the Moody-White paper diff --git a/R/foreign.R b/R/foreign.R index d4a2e9c6d5c..9170cf888e8 100644 --- a/R/foreign.R +++ b/R/foreign.R @@ -810,10 +810,10 @@ write.graph.dot <- function(graph, file) { #' there are a number of actual graphs in the database. This argument specifies #' which one to read. #' @param base The base address of the database. See details below. -#' @param compressed Logical constant, if TRUE than the file is expected to be +#' @param compressed Logical, if TRUE than the file is expected to be #' compressed by gzip. If `url` is `NULL` then a \sQuote{`.gz`} #' suffix is added to the filename. -#' @param directed Logical constant, whether to create a directed graph. +#' @param directed Logical, whether to create a directed graph. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @seealso [read_graph()], [isomorphic()] diff --git a/R/games.R b/R/games.R index d1aacef499d..3033eaf1768 100644 --- a/R/games.R +++ b/R/games.R @@ -1552,9 +1552,9 @@ growing <- function(n, m = 1, ..., directed = TRUE, citation = FALSE) { #' add in each time step if `out.seq` is NULL. See details below. #' @param out.seq The number of edges to add in each time step, a vector #' containing as many elements as the number of vertices. See details below. -#' @param out.pref Logical constant, whether to include edges not initiated by +#' @param out.pref Logical, whether to include edges not initiated by #' the vertex as a basis of preferential attachment. See details below. -#' @param directed Logical constant, whether to generate a directed graph. See +#' @param directed Logical, whether to generate a directed graph. See #' details below. #' @param zero.deg.appeal The degree-dependent part of the #' \sQuote{attractiveness} of the vertices with no adjacent edges. See also @@ -1774,7 +1774,7 @@ pa_age <- function( #' stationary in time. #' @param pref.matrix A matrix giving the preferences of the given vertex #' types. These should be probabilities, i.e. numbers between zero and one. -#' @param directed Logical constant, whether to generate directed graphs. +#' @param directed Logical, whether to generate directed graphs. #' @param k The number of trials per time step, see details below. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} @@ -1902,8 +1902,8 @@ traits <- function( #' @param nodes The number of vertices in the graph. #' @param radius The radius within which the vertices will be connected by an #' edge. -#' @param torus Logical constant, whether to use a torus instead of a square. -#' @param coords Logical scalar, whether to add the positions of the vertices +#' @param torus Logical, whether to use a torus instead of a square. +#' @param coords Logical, whether to add the positions of the vertices #' as vertex attributes called \sQuote{`x`} and \sQuote{`y`}. #' @return A graph object. If `coords` is `TRUE` then with vertex #' attributes \sQuote{`x`} and \sQuote{`y`}. @@ -1987,8 +1987,8 @@ grg <- function(nodes, radius, torus = FALSE, coords = FALSE) { #' @param pref.matrix A square matrix giving the preferences of the vertex #' types. The matrix has \sQuote{types} rows and columns. When generating #' an undirected graph, it must be symmetric. -#' @param directed Logical scalar, whether to create a directed graph. -#' @param loops Logical scalar, whether self-loops are allowed in the graph. +#' @param directed Logical, whether to create a directed graph. +#' @param loops Logical, whether self-loops are allowed in the graph. #' @return An igraph graph. #' @author Tamas Nepusz \email{ntamas@@gmail.com} and Gabor Csardi #' \email{csardi.gabor@@gmail.com} for the R interface @@ -2176,9 +2176,9 @@ connect <- function(graph, order, mode = c("all", "out", "in", "total")) { #' @param nei Integer constant, the neighborhood within which the vertices of #' the lattice will be connected. #' @param p Real constant between zero and one, the rewiring probability. -#' @param loops Logical scalar, whether loops edges are allowed in the +#' @param loops Logical, whether loops edges are allowed in the #' generated graph. -#' @param multiple Logical scalar, whether multiple edges are allowed int the +#' @param multiple Logical, whether multiple edges are allowed int the #' generated graph. #' @return A graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} @@ -2257,10 +2257,10 @@ smallworld <- function(dim, size, nei, p, loops = FALSE, multiple = FALSE) { #' @param pref Vector (`sample_last_cit()` and `sample_cit_types()` or #' matrix (`sample_cit_cit_types()`) giving the (unnormalized) citation #' probabilities for the different vertex types. -#' @param directed Logical scalar, whether to generate directed networks. +#' @param directed Logical, whether to generate directed networks. #' @param types Vector of length \sQuote{`n`}, the types of the vertices. #' Types are numbered from zero. -#' @param attr Logical scalar, whether to add the vertex types to the generated +#' @param attr Logical, whether to add the vertex types to the generated #' graph as a vertex attribute called \sQuote{`type`}. #' @return A new graph. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} @@ -2420,7 +2420,7 @@ cit_cit_types <- function( #' be given for \eqn{G(n,m)} graphs. #' @param m Integer scalar, the number of edges for \eqn{G(n,m)} graphs. Should not #' be given for \eqn{G(n,p)} graphs. -#' @param directed Logical scalar, whether to create a directed graph. See also +#' @param directed Logical, 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 @@ -2563,7 +2563,7 @@ bipartite_gnp <- function( #' @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. #' @inheritParams rlang::args_dots_empty -#' @param directed Logical scalar, whether to create a directed graph. See also +#' @param directed Logical, 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 @@ -2817,7 +2817,7 @@ hierarchical_sbm <- function(n, m, rho, C, p) { #' #' @param vecs A numeric matrix in which each latent position vector is a #' column. -#' @param directed A logical scalar, TRUE if the generated graph should be +#' @param directed A Logical, TRUE if the generated graph should be #' directed. #' @return An igraph graph object which is the generated random dot product #' graph. @@ -2916,8 +2916,8 @@ sample_islands <- function(islands.n, islands.size, islands.pin, n.inter) { #' graph. #' @param k Integer scalar, the degree of each vertex in the graph, or the #' out-degree and in-degree in a directed graph. -#' @param directed Logical scalar, whether to create a directed graph. -#' @param multiple Logical scalar, whether multiple edges are allowed. +#' @param directed Logical, whether to create a directed graph. +#' @param multiple Logical, whether multiple edges are allowed. #' @return An igraph graph. #' @author Tamas Nepusz \email{ntamas@@gmail.com} #' @seealso [sample_degseq()] for a generator with prescribed degree @@ -3173,8 +3173,8 @@ chung_lu <- function( #' #' If this argument is not `NULL`, then a directed graph is generated, #' otherwise an undirected one. -#' @param loops Logical scalar, whether to allow loop edges in the graph. -#' @param multiple Logical scalar, whether to allow multiple edges in the +#' @param loops Logical, whether to allow loop edges in the graph. +#' @param multiple Logical, whether to allow multiple edges in the #' graph. #' @return An igraph graph, directed or undirected. #' @author Tamas Nepusz \email{ntamas@@gmail.com} @@ -3246,7 +3246,7 @@ sample_fitness <- function( #' exponent of the in-degree distribution. If non-negative but less than 2, an #' error will be generated. #' @inheritParams sample_fitness -#' @param finite.size.correction Logical scalar, whether to use the proposed +#' @param finite.size.correction Logical, whether to use the proposed #' finite size correction of Cho et al., see references below. #' @return An igraph graph, directed or undirected. #' @author Tamas Nepusz \email{ntamas@@gmail.com} @@ -3445,7 +3445,7 @@ sample_correlated_gnp <- function( #' adjacency matrix being used as a vector). #' @param p A numeric scalar, the probability of an edge between two vertices, #' it must in the open (0,1) interval. -#' @param directed Logical scalar, whether to generate directed graphs. +#' @param directed Logical, whether to generate directed graphs. #' @param permutation A numeric vector, a permutation vector that is applied on #' the vertices of the first graph, to get the second graph. If `NULL`, #' the vertices are not permuted. diff --git a/R/incidence.R b/R/incidence.R index 886aa1a9f8c..77e301d6ac1 100644 --- a/R/incidence.R +++ b/R/incidence.R @@ -140,14 +140,14 @@ graph_incidence_build <- function( #' #' @param incidence The input bipartite adjacency matrix. It can also be a sparse matrix #' from the `Matrix` package. -#' @param directed Logical scalar, whether to create a directed graph. +#' @param directed Logical, whether to create a directed graph. #' @param mode A character constant, defines the direction of the edges in #' directed graphs, ignored for undirected graphs. If \sQuote{`out`}, then #' edges go from vertices of the first kind (corresponding to rows in the #' bipartite adjacency matrix) to vertices of the second kind (columns in the incidence #' matrix). If \sQuote{`in`}, then the opposite direction is used. If #' \sQuote{`all`} or \sQuote{`total`}, then mutual edges are created. -#' @param multiple Logical scalar, specifies how to interpret the matrix +#' @param multiple Logical, specifies how to interpret the matrix #' elements. See details below. #' @param weighted This argument specifies whether to create a weighted graph #' from the bipartite adjacency matrix. If it is `NULL` then an unweighted graph is diff --git a/R/indexing.R b/R/indexing.R index 6329bd5d5c7..fc53f10c42d 100644 --- a/R/indexing.R +++ b/R/indexing.R @@ -194,8 +194,8 @@ get_adjacency_submatrix <- function(x, i, j, attr = NULL) { #' be present together with any of the `i` and `j` arguments #' and if it is present, then the `from` argument must be present as #' well. -#' @param sparse Logical scalar, whether to return sparse matrices. -#' @param edges Logical scalar, whether to return edge IDs. +#' @param sparse Logical, whether to return sparse matrices. +#' @param edges Logical, whether to return edge IDs. #' @param drop Ignored. #' @param attr If not `NULL`, then it should be the name of an edge #' attribute. This attribute is queried and returned. @@ -360,9 +360,9 @@ get_adjacency_submatrix <- function(x, i, j, attr = NULL) { #' and if it is present, then the `from` argument must be present as #' well. #' @param ... Additional arguments are not used currently. -#' @param directed Logical scalar, whether to consider edge directions +#' @param directed Logical, whether to consider edge directions #' in directed graphs. It is ignored for undirected graphs. -#' @param edges Logical scalar, whether to return edge IDs. +#' @param edges Logical, whether to return edge IDs. #' @param exact Ignored. #' #' @family structural queries diff --git a/R/interface.R b/R/interface.R index bc528bf78d0..5f816421e8d 100644 --- a/R/interface.R +++ b/R/interface.R @@ -397,7 +397,7 @@ incident <- function(graph, v, mode = c("all", "out", "in", "total")) { #' Check whether a graph is directed #' #' @param graph The input graph -#' @return Logical scalar, whether the graph is directed. +#' @return Logical, whether the graph is directed. #' #' @family structural queries #' @@ -515,9 +515,9 @@ el_to_vec <- function(x, call = rlang::caller_env()) { #' or vector of vertex IDs or symbolic vertex names. #' For a vector, the values are interpreted pairwise, i.e. the first and second are used for #' the first edge, the third and fourth for the second, etc. -#' @param directed Logical scalar, whether to consider edge directions in +#' @param directed Logical, whether to consider edge directions in #' directed graphs. This argument is ignored for undirected graphs. -#' @param error Logical scalar, whether to report an error if an edge is not +#' @param error Logical, whether to report an error if an edge is not #' found in the graph. If `FALSE`, then no error is reported, and zero is #' returned for the non-existant edge(s). #' @return A numeric vector of edge IDs, one for each pair of input vertices. diff --git a/R/layout.R b/R/layout.R index e265c953279..d4d0b0a17bb 100644 --- a/R/layout.R +++ b/R/layout.R @@ -800,7 +800,7 @@ as_star <- function(...) layout_spec(layout_as_star, ...) #' topological sorting, performed with the opposite mode than the `mode` #' argument. After the vertices have been sorted, one is selected from each #' component. -#' @param circular Logical scalar, whether to plot the tree in a circular +#' @param circular Logical, whether to plot the tree in a circular #' fashion. Defaults to `FALSE`, so the tree branches are going bottom-up #' (or top-down, see the `flip.y` argument. #' @param rootlevel This argument can be useful when drawing forests which are @@ -813,7 +813,7 @@ as_star <- function(...) layout_spec(layout_as_star, ...) #' edges are used (this was the behavior in igraph 0.5 and before). This #' parameter also influences how the root vertices are calculated, if they are #' not given. See the `roots` parameter. -#' @param flip.y Logical scalar, whether to flip the \sQuote{y} coordinates. +#' @param flip.y Logical, whether to flip the \sQuote{y} coordinates. #' The default is flipping because that puts the root vertex on the top. #' @return A numeric matrix with two columns, and one row for each vertex. #' @author Tamas Nepusz \email{ntamas@@gmail.com} and Gabor Csardi @@ -2811,7 +2811,7 @@ layout.drl <- function( #' @aliases drl_defaults igraph.drl.coarsen #' @aliases igraph.drl.coarsest igraph.drl.default igraph.drl.final igraph.drl.refine #' @param graph The input graph, in can be directed or undirected. -#' @param use.seed Logical scalar, whether to use the coordinates given in the +#' @param use.seed Logical, whether to use the coordinates given in the #' `seed` argument as a starting point. #' @param seed A matrix with two columns, the starting coordinates for the #' vertices is `use.seed` is `TRUE`. It is ignored otherwise. diff --git a/R/make.R b/R/make.R index 8e70a149812..a51905fb72d 100644 --- a/R/make.R +++ b/R/make.R @@ -1696,7 +1696,7 @@ empty_graph <- function(n = 0, directed = TRUE) { #' @param ... For `graph_from_literal()` the formulae giving the #' structure of the graph, see details below. For `from_literal()` #' all arguments are passed to `graph_from_literal()`. -#' @param simplify Logical scalar, whether to call [simplify()] +#' @param simplify Logical, whether to call [simplify()] #' on the created graph. By default the graph is simplified, loop and #' multiple edges are removed. [simplify()] is only called when the #' created graph is not already simple, so the edge order from the @@ -1956,9 +1956,9 @@ full_graph <- function(n, directed = FALSE, loops = FALSE) { #' @param directed Whether to create a directed lattice. #' @param mutual Logical, if `TRUE` directed lattices will be #' mutually connected. -#' @param periodic Logical vector, Boolean vector, defines whether the generated lattice is -#' periodic along each dimension. This parameter may also be scalar boolen value which will -#' be extended to boolean vector with dimvector length. +#' @param periodic Logical vector, defines whether the generated lattice is +#' periodic along each dimension. This parameter may also be a single logical which will +#' be extended to a logical vector of `dimvector`` length. #' @param circular Deprecated, use `periodic` instead. #' @return An igraph graph. #' @@ -2342,7 +2342,7 @@ atlas <- function(n) { #' @param n The number of vertices. #' @param w A matrix which specifies the extended chordal ring. See #' details below. -#' @param directed Logical scalar, whether or not to create a directed graph. +#' @param directed Logical, whether or not to create a directed graph. #' @return An igraph graph. #' #' @family deterministic constructors @@ -2384,7 +2384,7 @@ chordal_ring <- function(n, w, directed = FALSE) { #' #' @param n Integer, the number of vertices in the circulant graph. #' @param shifts Integer vector, a list of the offsets within the circulant graph. -#' @param directed Boolean, whether to create a directed graph. +#' @param directed Logical, whether to create a directed graph. #' @return An igraph graph. #' #' @family deterministic constructors @@ -2573,7 +2573,7 @@ kautz_graph <- function(m, n) { #' #' @param n1 The number of vertices of the first kind. #' @param n2 The number of vertices of the second kind. -#' @param directed Logical scalar, whether the graphs is directed. +#' @param directed Logical, whether the graphs is directed. #' @param mode Scalar giving the kind of edges to create for directed graphs. #' If this is \sQuote{`out`} then all vertices of the first kind are #' connected to the others; \sQuote{`in`} specifies the opposite @@ -2666,13 +2666,13 @@ full_bipartite_graph <- function( #' regular [make_graph()] function. It is checked that the edges indeed #' connect vertices of different kind, according to the supplied `types` #' vector. The vector may be a string vector if `types` is a named vector. -#' @param directed Whether to create a directed graph, boolean constant. Note +#' @param directed Logical, whether to create a directed graph. Note #' that by default undirected graphs are created, as this is more common for #' bipartite graphs. #' @return `make_bipartite_graph()` returns a bipartite igraph graph. In other #' words, an igraph graph that has a vertex attribute named `type`. #' -#' `is_bipartite()` returns a logical scalar. +#' `is_bipartite()` returns a Logical. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @seealso [make_graph()] to create one-mode networks #' @keywords graphs @@ -2739,7 +2739,7 @@ bipartite_graph <- function(types, edges, directed = FALSE) { #' different partitions are present. #' #' @param n A numeric vector giving the number of vertices in each partition. -#' @param directed Logical scalar, whether to create a directed graph. +#' @param directed Logical, whether to create a directed graph. #' @param mode Character scalar, the type of connections for directed graphs. #' If `"out"`, then edges point from vertices of partitions with lower #' indices to partitions with higher indices; if `"in"`, then the opposite diff --git a/R/operators.R b/R/operators.R index 8782cfb0612..13020fe695c 100644 --- a/R/operators.R +++ b/R/operators.R @@ -472,7 +472,7 @@ union.default <- function(...) { #' #' @aliases %u% #' @param \dots Graph objects or lists of graph objects. -#' @param byname A logical scalar, or the character scalar `auto`. Whether +#' @param byname A Logical, or the character scalar `auto`. Whether #' to perform the operation based on symbolic vertex names. If it is #' `auto`, that means `TRUE` if all graphs are named and `FALSE` #' otherwise. A warning is generated if `auto` and some (but not all) @@ -553,12 +553,12 @@ intersection <- function(...) { #' #' @aliases %s% #' @param \dots Graph objects or lists of graph objects. -#' @param byname A logical scalar, or the character scalar `auto`. Whether +#' @param byname A Logical, or the character scalar `auto`. Whether #' to perform the operation based on symbolic vertex names. If it is #' `auto`, that means `TRUE` if all graphs are named and `FALSE` #' otherwise. A warning is generated if `auto` and some (but not all) #' graphs are named. -#' @param keep.all.vertices Logical scalar, whether to keep vertices that only +#' @param keep.all.vertices Logical, whether to keep vertices that only #' appear in a subset of the input graphs. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} @@ -637,7 +637,7 @@ difference <- function(...) { #' undirected graph. #' @param small The right hand side argument of the minus operator. A directed #' ot undirected graph. -#' @param byname A logical scalar, or the character scalar `auto`. Whether +#' @param byname A Logical, or the character scalar `auto`. Whether #' to perform the operation based on symbolic vertex names. If it is #' `auto`, that means `TRUE` if both graphs are named and #' `FALSE` otherwise. A warning is generated if `auto` and one graph, @@ -722,7 +722,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) { #' attributes are lost. #' #' @param graph The input graph, can be directed or undirected. -#' @param loops Logical constant, whether to generate loop edges. +#' @param loops Logical, whether to generate loop edges. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @family functions for manipulating graph structure @@ -791,7 +791,7 @@ complementer <- function(graph, loops = FALSE) { #' @aliases %c% #' @param g1 The first input graph. #' @param g2 The second input graph. -#' @param byname A logical scalar, or the character scalar `auto`. Whether +#' @param byname A Logical, or the character scalar `auto`. Whether #' to perform the operation based on symbolic vertex names. If it is #' `auto`, that means `TRUE` if both graphs are named and #' `FALSE` otherwise. A warning is generated if `auto` and one graph, diff --git a/R/plot.R b/R/plot.R index 1b0f390e6c7..e93fb18ea31 100644 --- a/R/plot.R +++ b/R/plot.R @@ -32,7 +32,7 @@ #' @aliases plot.graph #' @param x The graph to plot. #' @param axes Logical, whether to plot axes, defaults to FALSE. -#' @param add Logical scalar, whether to add the plot to the current device, or +#' @param add Logical, whether to add the plot to the current device, or #' delete the device's current contents first. #' @param xlim The limits for the horizontal axis, it is unlikely that you want #' to modify this. diff --git a/R/print.R b/R/print.R index 1a424b01842..b9afd427cab 100644 --- a/R/print.R +++ b/R/print.R @@ -564,13 +564,13 @@ print_all <- function(object, ...) { #' #' @aliases print.igraph print_all summary.igraph str.igraph #' @param x The graph to print. -#' @param full Logical scalar, whether to print the graph structure itself as +#' @param full Logical, whether to print the graph structure itself as #' well. -#' @param graph.attributes Logical constant, whether to print graph attributes. -#' @param vertex.attributes Logical constant, whether to print vertex +#' @param graph.attributes Logical, whether to print graph attributes. +#' @param vertex.attributes Logical, whether to print vertex #' attributes. -#' @param edge.attributes Logical constant, whether to print edge attributes. -#' @param names Logical constant, whether to print symbolic vertex names (i.e. +#' @param edge.attributes Logical, whether to print edge attributes. +#' @param names Logical, whether to print symbolic vertex names (i.e. #' the `name` vertex attribute) or vertex IDs. #' @param max.lines The maximum number of lines to use. The rest of the #' output will be truncated. diff --git a/R/rewire.R b/R/rewire.R index 0ba1f17a474..f054bda7a65 100644 --- a/R/rewire.R +++ b/R/rewire.R @@ -102,9 +102,9 @@ rewire_keeping_degseq <- function(graph, loops, niter) { #' Note that this method might create graphs with multiple and/or loop edges. #' #' @param prob The rewiring probability, a real number between zero and one. -#' @param loops Logical scalar, whether loop edges are allowed in the rewired +#' @param loops Logical, whether loop edges are allowed in the rewired #' graph. -#' @param multiple Logical scalar, whether multiple edges are allowed in the +#' @param multiple Logical, whether multiple edges are allowed in the #' generated graph. #' @param mode Character string, specifies which endpoint of the edges to rewire #' in directed graphs. \sQuote{all} rewires both endpoints, \sQuote{in} rewires diff --git a/R/scan.R b/R/scan.R index 004bcd38260..ea608e7ec9f 100644 --- a/R/scan.R +++ b/R/scan.R @@ -53,7 +53,7 @@ #' `weighted=FALSE`) and a function that computes the sum of edge #' weights is used for weighted graphs (if `weighted=TRUE`). This #' argument is ignored if `k` is zero. -#' @param weighted Logical scalar, TRUE if the edge weights should be used +#' @param weighted Logical, TRUE if the edge weights should be used #' for computation of the scan statistic. If TRUE, the graph should be #' weighted. Note that this argument is ignored if `FUN` is not #' `NULL`, `"ecount"` and `"sumweights"`. @@ -131,7 +131,7 @@ local_scan <- function( is.null(FUN) || is.function(FUN) || (is.character(FUN) && length(FUN) == 1) ) - ## Logical scalar + ## Logical stopifnot(is.logical(weighted), length(weighted) == 1) ## If weighted, then the graph(s) must be weighted diff --git a/R/sir.R b/R/sir.R index 67a4973b9e0..629a3a203b3 100644 --- a/R/sir.R +++ b/R/sir.R @@ -55,9 +55,9 @@ #' distribution. #' @param no.sim Integer scalar, the number simulation runs to perform. #' @param x A `sir` object, returned by the `sir()` function. -#' @param middle Logical scalar, whether to return the middle of the time bins, +#' @param middle Logical, whether to return the middle of the time bins, #' or the boundaries. -#' @param na.rm Logical scalar, whether to ignore `NA` values. `sir` +#' @param na.rm Logical, whether to ignore `NA` values. `sir` #' objects do not contain any `NA` values currently, so this argument is #' effectively ignored. #' @param comp Character scalar. The component to calculate the quantile of. diff --git a/R/stochastic_matrix.R b/R/stochastic_matrix.R index 01ece7ee3ca..800daffa7be 100644 --- a/R/stochastic_matrix.R +++ b/R/stochastic_matrix.R @@ -53,7 +53,7 @@ get.stochastic <- function( #' @param graph The input graph. Must be of class `igraph`. #' @param column.wise If `FALSE`, then the rows of the stochastic matrix #' sum up to one; otherwise it is the columns. -#' @param sparse Logical scalar, whether to return a sparse matrix. The +#' @param sparse Logical, whether to return a sparse matrix. The #' `Matrix` package is needed for sparse matrices. #' @return A regular matrix or a matrix of class `Matrix` if a #' `sparse` argument was `TRUE`. @@ -84,14 +84,14 @@ stochastic_matrix <- function( column.wise <- as.logical(column.wise) if (length(column.wise) != 1) { cli::cli_abort( - "{.arg column.wise} must be a logical scalar, not {.obj_type_friendly {column.wise}}." + "{.arg column.wise} must be a Logical, not {.obj_type_friendly {column.wise}}." ) } sparse <- as.logical(sparse) if (length(sparse) != 1) { cli::cli_abort( - "{.arg sparse} must be a logical scalar, not {.obj_type_friendly {sparse}}." + "{.arg sparse} must be a Logical, not {.obj_type_friendly {sparse}}." ) } diff --git a/R/structural-properties.R b/R/structural-properties.R index 9182950592e..2aa1e471ca2 100644 --- a/R/structural-properties.R +++ b/R/structural-properties.R @@ -445,7 +445,7 @@ graph.knn <- function( #' #' `graph.dfs()` was renamed to [dfs()] to create a more #' consistent API. -#' @param father Logical scalar, whether to return the father of the vertices. +#' @param father Logical, whether to return the father of the vertices. #' @inheritParams dfs #' @keywords internal #' @export @@ -523,7 +523,7 @@ graph.coreness <- function(graph, mode = c("all", "out", "in")) { #' `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. +#' @param father Logical, whether to return the father of the vertices. #' @keywords internal #' @export graph.bfs <- function( @@ -879,7 +879,7 @@ mean_distance <- function( #' in-degree or \dQuote{total} for the sum of the two. For undirected graphs #' this argument is ignored. \dQuote{all} is a synonym of \dQuote{total}. #' @param loops Logical; whether the loop edges are also counted. -#' @param normalized Logical scalar, whether to normalize the degree. If +#' @param normalized Logical, whether to normalize the degree. If #' `TRUE` then the result is divided by \eqn{n-1}, where \eqn{n} is the #' number of vertices in the graph. #' @inheritParams rlang::args_dots_empty @@ -1268,14 +1268,14 @@ distances <- function( #' form was used prior to igraph version 0.6. \dQuote{epath} means that the #' edges along the paths are reported. \dQuote{both} means that both forms are #' returned, in a named list with components \dQuote{vpath} and \dQuote{epath}. -#' @param predecessors Logical scalar, whether to return the predecessor vertex +#' @param predecessors Logical, whether to return the predecessor vertex #' for each vertex. The predecessor of vertex `i` in the tree is the #' vertex from which vertex `i` was reached. The predecessor of the start #' vertex (in the `from` argument) is itself by definition. If the #' predecessor is zero, it means that the given vertex was not reached from the #' source during the search. Note that the search terminates if all the #' vertices in `to` are reached. -#' @param inbound.edges Logical scalar, whether to return the inbound edge for +#' @param inbound.edges Logical, whether to return the inbound edge for #' each vertex. The inbound edge of vertex `i` in the tree is the edge via #' which vertex `i` was reached. The start vertex and vertices that were #' not reached during the search will have zero in the corresponding entry of @@ -1607,7 +1607,7 @@ induced_subgraph <- function( #' @rdname subgraph #' @param eids The edge IDs of the edges that will be kept in the result graph. -#' @param delete.vertices Logical scalar, whether to remove vertices that do +#' @param delete.vertices Logical, whether to remove vertices that do #' not have any adjacent edges in `eids`. #' @export subgraph_from_edges <- function(graph, eids, delete.vertices = TRUE) { @@ -1971,7 +1971,7 @@ constraint <- function(graph, nodes = V(graph), weights = NULL) { #' (2)+(3). This measure is calculated if `mode` is `ratio`. #' #' @param graph The graph object. -#' @param ignore.loops Logical constant, whether to ignore loop edges. +#' @param ignore.loops Logical, whether to ignore loop edges. #' @param mode See below. #' @return A numeric scalar between zero and one. #' @author Tamas Nepusz \email{ntamas@@gmail.com} and Gabor Csardi @@ -2008,7 +2008,7 @@ reciprocity <- function( #' results for such graphs. #' #' @param graph The input graph. -#' @param loops Logical constant, whether loop edges may exist in the graph. +#' @param loops Logical, whether loop edges may exist in the graph. #' This affects the calculation of the largest possible number of edges in the #' graph. If this parameter is set to FALSE yet the graph contains self-loops, #' the result will not be meaningful. @@ -2408,7 +2408,7 @@ feedback_vertex_set <- function(graph, weights = NULL, algo = c("exact_ip")) { #' #' @param graph The input graph. It may be directed, but the algorithm searches #' for undirected circles anyway. -#' @param circle Logical scalar, whether to return the shortest circle itself. +#' @param circle Logical, whether to return the shortest circle itself. #' @return A named list with two components: #' \describe{ #' \item{girth}{ @@ -2485,7 +2485,7 @@ girth <- function(graph, circle = TRUE) { #' @param graph The input graph. #' @param eids The edges to which the query is restricted. By default this is #' all edges in the graph. -#' @return `any_loop()` and `any_multiple()` return a logical scalar. +#' @return `any_loop()` and `any_multiple()` return a Logical. #' `which_loop()` and `which_multiple()` return a logical vector. #' `count_loops()` returns a numeric scalar with the total number of loop edges. #' `count_multiple()` returns a numeric vector. @@ -2604,22 +2604,22 @@ count_loops <- function(graph) { #' \sQuote{out} follows outgoing, \sQuote{in} incoming edges. \sQuote{all} #' ignores edge directions completely. \sQuote{total} is a synonym for #' \sQuote{all}. This argument is ignored for undirected graphs. -#' @param unreachable Logical scalar, whether the search should visit the +#' @param unreachable Logical, whether the search should visit the #' vertices that are unreachable from the given root vertex (or vertices). If #' `TRUE`, then additional searches are performed until all vertices are #' visited. #' @param restricted `NULL` (=no restriction), or a vector of vertices #' (IDs or symbolic names). In the latter case, the search is restricted to the #' given vertices. -#' @param order Logical scalar, whether to return the ordering of the vertices. -#' @param rank Logical scalar, whether to return the rank of the vertices. +#' @param order Logical, whether to return the ordering of the vertices. +#' @param rank Logical, whether to return the rank of the vertices. #' @param father `r lifecycle::badge("deprecated")` Use `parent` instead. -#' @param parent Logical scalar, whether to return the parent of the vertices. -#' @param pred Logical scalar, whether to return the predecessors of the +#' @param parent Logical, whether to return the parent of the vertices. +#' @param pred Logical, whether to return the predecessors of the #' vertices. -#' @param succ Logical scalar, whether to return the successors of the +#' @param succ Logical, whether to return the successors of the #' vertices. -#' @param dist Logical scalar, whether to return the distance from the root of +#' @param dist Logical, whether to return the distance from the root of #' the search tree. #' @param callback If not `NULL`, then it must be callback function. This #' is called whenever a vertex is visited. The callback function should @@ -2884,17 +2884,17 @@ bfs <- function( #' \sQuote{out} follows outgoing, \sQuote{in} incoming edges. \sQuote{all} #' ignores edge directions completely. \sQuote{total} is a synonym for #' \sQuote{all}. This argument is ignored for undirected graphs. -#' @param unreachable Logical scalar, whether the search should visit the +#' @param unreachable Logical, whether the search should visit the #' vertices that are unreachable from the given root vertex (or vertices). If #' `TRUE`, then additional searches are performed until all vertices are #' visited. -#' @param order Logical scalar, whether to return the DFS ordering of the +#' @param order Logical, whether to return the DFS ordering of the #' vertices. -#' @param order.out Logical scalar, whether to return the ordering based on +#' @param order.out Logical, whether to return the ordering based on #' leaving the subtree of the vertex. #' @param father `r lifecycle::badge("deprecated")`, use `parent` instead. -#' @param parent Logical scalar, whether to return the parent of the vertices. -#' @param dist Logical scalar, whether to return the distance from the root of +#' @param parent Logical, whether to return the parent of the vertices. +#' @param dist Logical, whether to return the distance from the root of #' the search tree. #' @param in.callback If not `NULL`, then it must be callback function. #' This is called whenever a vertex is visited. See details below. @@ -3114,7 +3114,7 @@ dfs <- function( #' connected components to search. It is ignored for undirected graphs. #' @param \dots Additional attributes to pass to `cluster`, right now only #' `mode` makes sense. -#' @return For `is_connected()` a logical constant. +#' @return For `is_connected()` a Logical. #' #' For `components()` a named list with three components: #' \describe{ @@ -3319,7 +3319,7 @@ unfold_tree <- function(graph, mode = c("all", "out", "in", "total"), roots) { #' `weight`, then it will be used automatically. Set this to `NA` if #' you want the unweighted Laplacian on a graph that has a `weight` edge #' attribute. -#' @param sparse Logical scalar, whether to return the result as a sparse +#' @param sparse Logical, whether to return the result as a sparse #' matrix. The `Matrix` package is required for sparse matrices. #' @return A numeric matrix. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} diff --git a/man/aging.ba.game.Rd b/man/aging.ba.game.Rd index dc615662e41..32bf32cc7fe 100644 --- a/man/aging.ba.game.Rd +++ b/man/aging.ba.game.Rd @@ -42,10 +42,10 @@ add in each time step if \code{out.seq} is NULL. See details below.} \item{out.seq}{The number of edges to add in each time step, a vector containing as many elements as the number of vertices. See details below.} -\item{out.pref}{Logical constant, whether to include edges not initiated by +\item{out.pref}{Logical, whether to include edges not initiated by the vertex as a basis of preferential attachment. See details below.} -\item{directed}{Logical constant, whether to generate a directed graph. See +\item{directed}{Logical, whether to generate a directed graph. See details below.} \item{zero.deg.appeal}{The degree-dependent part of the diff --git a/man/aging.barabasi.game.Rd b/man/aging.barabasi.game.Rd index c5dc471b881..3a1c36c7736 100644 --- a/man/aging.barabasi.game.Rd +++ b/man/aging.barabasi.game.Rd @@ -42,10 +42,10 @@ add in each time step if \code{out.seq} is NULL. See details below.} \item{out.seq}{The number of edges to add in each time step, a vector containing as many elements as the number of vertices. See details below.} -\item{out.pref}{Logical constant, whether to include edges not initiated by +\item{out.pref}{Logical, whether to include edges not initiated by the vertex as a basis of preferential attachment. See details below.} -\item{directed}{Logical constant, whether to generate a directed graph. See +\item{directed}{Logical, whether to generate a directed graph. See details below.} \item{zero.deg.appeal}{The degree-dependent part of the diff --git a/man/aging.prefatt.game.Rd b/man/aging.prefatt.game.Rd index 77e357d4b9d..e89d14fdb24 100644 --- a/man/aging.prefatt.game.Rd +++ b/man/aging.prefatt.game.Rd @@ -42,10 +42,10 @@ add in each time step if \code{out.seq} is NULL. See details below.} \item{out.seq}{The number of edges to add in each time step, a vector containing as many elements as the number of vertices. See details below.} -\item{out.pref}{Logical constant, whether to include edges not initiated by +\item{out.pref}{Logical, whether to include edges not initiated by the vertex as a basis of preferential attachment. See details below.} -\item{directed}{Logical constant, whether to generate a directed graph. See +\item{directed}{Logical, whether to generate a directed graph. See details below.} \item{zero.deg.appeal}{The degree-dependent part of the diff --git a/man/alpha.centrality.Rd b/man/alpha.centrality.Rd index 30b93c7b403..4cda7bcae53 100644 --- a/man/alpha.centrality.Rd +++ b/man/alpha.centrality.Rd @@ -51,7 +51,7 @@ is included in the matrix.} \item{tol}{Tolerance for near-singularities during matrix inversion, see \code{\link[=solve]{solve()}}.} -\item{sparse}{Logical scalar, whether to use sparse matrices for the +\item{sparse}{Logical, whether to use sparse matrices for the calculation. The \sQuote{Matrix} package is required for sparse matrix support} } diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index 6b7ee95740b..9052dc67537 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -51,7 +51,7 @@ is included in the matrix.} \item{tol}{Tolerance for near-singularities during matrix inversion, see \code{\link[=solve]{solve()}}.} -\item{sparse}{Logical scalar, whether to use sparse matrices for the +\item{sparse}{Logical, whether to use sparse matrices for the calculation. The \sQuote{Matrix} package is required for sparse matrix support} } diff --git a/man/arpack.Rd b/man/arpack.Rd index 180451e945a..45a21237d34 100644 --- a/man/arpack.Rd +++ b/man/arpack.Rd @@ -27,7 +27,7 @@ second argument is \code{extra}.} \item{extra}{Extra argument to supply to \code{func}.} -\item{sym}{Logical scalar, whether the input matrix is symmetric. Always +\item{sym}{Logical, whether the input matrix is symmetric. Always supply \code{TRUE} here if it is, since it can speed up the computation.} \item{options}{Options to ARPACK, a named list to overwrite some of the diff --git a/man/as_adj.Rd b/man/as_adj.Rd index fa0ff759b39..211d5c1b0dc 100644 --- a/man/as_adj.Rd +++ b/man/as_adj.Rd @@ -40,14 +40,14 @@ is included in the matrix.} supplied, the value is forwarded to \code{weights} as a character edge attribute name.} -\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical scalar, whether to return the edge IDs in the matrix. +\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical, whether to return the edge IDs in the matrix. For non-existant edges zero is returned.} -\item{names}{Logical constant, whether to assign row and column names +\item{names}{Logical, whether to assign row and column names to the matrix. These are only assigned if the \code{name} vertex attribute is present in the graph.} -\item{sparse}{Logical scalar, whether to create a sparse matrix. The +\item{sparse}{Logical, whether to create a sparse matrix. The \sQuote{\code{Matrix}} package must be installed for creating sparse matrices.} } diff --git a/man/as_adj_list.Rd b/man/as_adj_list.Rd index 258d8df1ea1..64d1a31f03a 100644 --- a/man/as_adj_list.Rd +++ b/man/as_adj_list.Rd @@ -30,7 +30,7 @@ for both. This argument is ignored for undirected graphs.} (to include loop edges twice) and \code{"once"} (to include them once). \code{"twice"} is not allowed for directed graphs and will be replaced with \code{"once"}.} -\item{multiple}{Logical scalar, set to \code{FALSE} to use only one representative +\item{multiple}{Logical, set to \code{FALSE} to use only one representative of each set of parallel edges.} } \value{ diff --git a/man/as_adjacency_matrix.Rd b/man/as_adjacency_matrix.Rd index f196c6c0d59..e89b439556e 100644 --- a/man/as_adjacency_matrix.Rd +++ b/man/as_adjacency_matrix.Rd @@ -39,15 +39,15 @@ used as weights. The attribute must be numeric or logical. If multiple edges share endpoints, the value of an arbitrarily chosen edge is included in the matrix.} -\item{names}{Logical constant, whether to assign row and column names +\item{names}{Logical, whether to assign row and column names to the matrix. These are only assigned if the \code{name} vertex attribute is present in the graph.} -\item{sparse}{Logical scalar, whether to create a sparse matrix. The +\item{sparse}{Logical, whether to create a sparse matrix. The \sQuote{\code{Matrix}} package must be installed for creating sparse matrices.} -\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical scalar, whether to return the edge IDs in the matrix. +\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical, whether to return the edge IDs in the matrix. For non-existant edges zero is returned.} \item{attr}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Use \code{weights} instead. If diff --git a/man/as_biadjacency_matrix.Rd b/man/as_biadjacency_matrix.Rd index c8e60a8616f..b3d97b8c8a8 100644 --- a/man/as_biadjacency_matrix.Rd +++ b/man/as_biadjacency_matrix.Rd @@ -37,12 +37,12 @@ used as weights. The attribute must be numeric or logical. If multiple edges share endpoints, the value of an arbitrarily chosen edge is included in the matrix.} -\item{names}{Logical scalar, if \code{TRUE} and the vertices in the graph +\item{names}{Logical, if \code{TRUE} and the vertices in the graph are named (i.e. the graph has a vertex attribute called \code{name}), then vertex names will be added to the result as row and column names. Otherwise the IDs of the vertices are used as row and column names.} -\item{sparse}{Logical scalar, if it is \code{TRUE} then a sparse matrix is +\item{sparse}{Logical, if it is \code{TRUE} then a sparse matrix is created, you will need the \code{Matrix} package for this.} \item{attr}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Use \code{weights} instead. If diff --git a/man/assortativity.Rd b/man/assortativity.Rd index 29dfc31907b..50eda0190ce 100644 --- a/man/assortativity.Rd +++ b/man/assortativity.Rd @@ -36,7 +36,7 @@ This argument is ignored (with a warning) if it is not \code{NULL} and undirected assortativity coefficient is being calculated.} -\item{directed}{Logical scalar, whether to consider edge directions for +\item{directed}{Logical, whether to consider edge directions for directed graphs. This argument is ignored for undirected graphs. Supply @@ -44,7 +44,7 @@ Supply measure for directed graphs and the undirected version for undirected graphs.} -\item{normalized}{Boolean, whether to compute the normalized assortativity. +\item{normalized}{Logical, whether to compute the normalized assortativity. The non-normalized nominal assortativity is identical to modularity. The non-normalized value-based assortativity is simply the covariance of the values at the two ends of edges.} diff --git a/man/assortativity.degree.Rd b/man/assortativity.degree.Rd index 74725be0a54..1c2be5594f9 100644 --- a/man/assortativity.degree.Rd +++ b/man/assortativity.degree.Rd @@ -9,7 +9,7 @@ assortativity.degree(graph, directed = TRUE) \arguments{ \item{graph}{The input graph, it can be directed or undirected.} -\item{directed}{Logical scalar, whether to consider edge directions for +\item{directed}{Logical, whether to consider edge directions for directed graphs. This argument is ignored for undirected graphs. Supply diff --git a/man/assortativity.nominal.Rd b/man/assortativity.nominal.Rd index a2236ceca3b..83d39e590ae 100644 --- a/man/assortativity.nominal.Rd +++ b/man/assortativity.nominal.Rd @@ -14,7 +14,7 @@ numbers, starting with one. Non-integer values are converted to integers with \code{\link[=as.integer]{as.integer()}}. Character vectors are converted to integers using \code{\link[=as.factor]{as.factor()}}.} -\item{directed}{Logical scalar, whether to consider edge directions for +\item{directed}{Logical, whether to consider edge directions for directed graphs. This argument is ignored for undirected graphs. Supply @@ -22,7 +22,7 @@ Supply measure for directed graphs and the undirected version for undirected graphs.} -\item{normalized}{Boolean, whether to compute the normalized assortativity. +\item{normalized}{Logical, whether to compute the normalized assortativity. The non-normalized nominal assortativity is identical to modularity. The non-normalized value-based assortativity is simply the covariance of the values at the two ends of edges.} diff --git a/man/asymmetric.preference.game.Rd b/man/asymmetric.preference.game.Rd index 533bc66fb53..41ed1342802 100644 --- a/man/asymmetric.preference.game.Rd +++ b/man/asymmetric.preference.game.Rd @@ -24,7 +24,7 @@ types.} types. The matrix has \sQuote{types} rows and columns. When generating an undirected graph, it must be symmetric.} -\item{loops}{Logical scalar, whether self-loops are allowed in the graph.} +\item{loops}{Logical, whether self-loops are allowed 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]}} diff --git a/man/authority.score.Rd b/man/authority.score.Rd index 814d1a19f36..2f2ba4666d5 100644 --- a/man/authority.score.Rd +++ b/man/authority.score.Rd @@ -14,7 +14,7 @@ authority.score( \arguments{ \item{graph}{The input graph.} -\item{scale}{Logical scalar, whether to scale the result to have a maximum +\item{scale}{Logical, whether to scale the result to have a maximum score of one. If no scaling is used then the result vector has unit length in the Euclidean norm.} diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 65100e4754e..35984e33f4f 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -37,7 +37,7 @@ betweenness. If the graph has a \code{weight} edge attribute, then this is used by default. Weights are used to calculate weighted shortest paths, so they are interpreted as distances.} -\item{normalized}{Logical scalar, whether to normalize the betweenness +\item{normalized}{Logical, whether to normalize the betweenness scores. If \code{TRUE}, then the results are normalized by the number of ordered or unordered vertex pairs in directed and undirected graphs, respectively. In an undirected graph, diff --git a/man/bfs.Rd b/man/bfs.Rd index c1395c33a81..f4a67ca80db 100644 --- a/man/bfs.Rd +++ b/man/bfs.Rd @@ -40,7 +40,7 @@ ignores edge directions completely. \sQuote{total} is a synonym for \item{...}{These dots are for future extensions and must be empty.} -\item{unreachable}{Logical scalar, whether the search should visit the +\item{unreachable}{Logical, whether the search should visit the vertices that are unreachable from the given root vertex (or vertices). If \code{TRUE}, then additional searches are performed until all vertices are visited.} @@ -49,19 +49,19 @@ visited.} (IDs or symbolic names). In the latter case, the search is restricted to the given vertices.} -\item{order}{Logical scalar, whether to return the ordering of the vertices.} +\item{order}{Logical, whether to return the ordering of the vertices.} -\item{rank}{Logical scalar, whether to return the rank of the vertices.} +\item{rank}{Logical, whether to return the rank of the vertices.} -\item{parent}{Logical scalar, whether to return the parent of the vertices.} +\item{parent}{Logical, whether to return the parent of the vertices.} -\item{pred}{Logical scalar, whether to return the predecessors of the +\item{pred}{Logical, whether to return the predecessors of the vertices.} -\item{succ}{Logical scalar, whether to return the successors of the +\item{succ}{Logical, whether to return the successors of the vertices.} -\item{dist}{Logical scalar, whether to return the distance from the root of +\item{dist}{Logical, whether to return the distance from the root of the search tree.} \item{callback}{If not \code{NULL}, then it must be callback function. This diff --git a/man/bipartite.projection.Rd b/man/bipartite.projection.Rd index 2893072d913..a841122f28d 100644 --- a/man/bipartite.projection.Rd +++ b/man/bipartite.projection.Rd @@ -36,7 +36,7 @@ one projection is requested in argument \code{which}.} \item{which}{A character scalar to specify which projection(s) to calculate. The default is to calculate both.} -\item{remove.type}{Logical scalar, whether to remove the \code{type} vertex +\item{remove.type}{Logical, whether to remove the \code{type} vertex attribute from the projections. This makes sense because these graphs are not bipartite any more. However if you want to combine them with each other (or other bipartite graphs), then it is worth keeping this attribute. By diff --git a/man/bipartite.random.game.Rd b/man/bipartite.random.game.Rd index 5568114c2aa..8610754eae3 100644 --- a/man/bipartite.random.game.Rd +++ b/man/bipartite.random.game.Rd @@ -28,7 +28,7 @@ be given for \eqn{G(n,m)} graphs.} \item{m}{Integer scalar, the number of edges for \eqn{G(n,m)} graphs. Should not be given for \eqn{G(n,p)} graphs.} -\item{directed}{Logical scalar, whether to create a directed graph. See also +\item{directed}{Logical, whether to create a directed graph. See also the \code{mode} argument.} \item{mode}{Character scalar, specifies how to direct the edges in directed diff --git a/man/bipartite_projection.Rd b/man/bipartite_projection.Rd index 11e097ef35b..961e0a4b812 100644 --- a/man/bipartite_projection.Rd +++ b/man/bipartite_projection.Rd @@ -39,7 +39,7 @@ one projection is requested in argument \code{which}.} \item{which}{A character scalar to specify which projection(s) to calculate. The default is to calculate both.} -\item{remove.type}{Logical scalar, whether to remove the \code{type} vertex +\item{remove.type}{Logical, whether to remove the \code{type} vertex attribute from the projections. This makes sense because these graphs are not bipartite any more. However if you want to combine them with each other (or other bipartite graphs), then it is worth keeping this attribute. By diff --git a/man/bonpow.Rd b/man/bonpow.Rd index 04c2cdf2b8d..33cb759d428 100644 --- a/man/bonpow.Rd +++ b/man/bonpow.Rd @@ -20,7 +20,7 @@ bonpow( \item{nodes}{vertex sequence indicating which vertices are to be included in the calculation. By default, all vertices are included.} -\item{loops}{boolean indicating whether or not the diagonal should be +\item{loops}{Logical indicating whether or not the diagonal should be treated as valid data. Set this true if and only if the data can contain loops. \code{loops} is \code{FALSE} by default.} @@ -33,7 +33,7 @@ score; can be negative} \item{tol}{tolerance for near-singularities during matrix inversion (see \code{\link[=solve]{solve()}})} -\item{sparse}{Logical scalar, whether to use sparse matrices for the +\item{sparse}{Logical, whether to use sparse matrices for the calculation. The \sQuote{Matrix} package is required for sparse matrix support} } diff --git a/man/callaway.traits.game.Rd b/man/callaway.traits.game.Rd index 1ae0913531e..b4abb173131 100644 --- a/man/callaway.traits.game.Rd +++ b/man/callaway.traits.game.Rd @@ -26,7 +26,7 @@ stationary in time.} \item{pref.matrix}{A matrix giving the preferences of the given vertex types. These should be probabilities, i.e. numbers between zero and one.} -\item{directed}{Logical constant, whether to generate directed graphs.} +\item{directed}{Logical, whether to generate directed graphs.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/centr_betw.Rd b/man/centr_betw.Rd index a413e11be56..72e1a570dbc 100644 --- a/man/centr_betw.Rd +++ b/man/centr_betw.Rd @@ -9,10 +9,10 @@ centr_betw(graph, directed = TRUE, normalized = TRUE) \arguments{ \item{graph}{The input graph.} -\item{directed}{logical scalar, whether to use directed shortest paths for +\item{directed}{Logical, whether to use directed shortest paths for calculating betweenness.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \value{ diff --git a/man/centr_betw_tmax.Rd b/man/centr_betw_tmax.Rd index bdb5b470b8b..e46b82a1618 100644 --- a/man/centr_betw_tmax.Rd +++ b/man/centr_betw_tmax.Rd @@ -13,7 +13,7 @@ centr_betw_tmax(graph = NULL, nodes = 0, directed = TRUE) \item{nodes}{The number of vertices. This is ignored if the graph is given.} -\item{directed}{Logical scalar, whether to use directed shortest paths +\item{directed}{Logical, whether to use directed shortest paths for calculating betweenness. Ignored if an undirected graph was given.} } diff --git a/man/centr_clo.Rd b/man/centr_clo.Rd index a53b0ef8246..ff9845546a4 100644 --- a/man/centr_clo.Rd +++ b/man/centr_clo.Rd @@ -12,7 +12,7 @@ centr_clo(graph, mode = c("out", "in", "all", "total"), normalized = TRUE) \item{mode}{This is the same as the \code{mode} argument of \code{closeness()}.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \value{ diff --git a/man/centr_degree.Rd b/man/centr_degree.Rd index c6ec9c25775..a0c26a1e8f2 100644 --- a/man/centr_degree.Rd +++ b/man/centr_degree.Rd @@ -17,10 +17,10 @@ centr_degree( \item{mode}{This is the same as the \code{mode} argument of \code{degree()}.} -\item{loops}{Logical scalar, whether to consider loops edges when +\item{loops}{Logical, whether to consider loops edges when calculating the degree.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \value{ diff --git a/man/centr_degree_tmax.Rd b/man/centr_degree_tmax.Rd index 29d10b55e99..7a6f8cae489 100644 --- a/man/centr_degree_tmax.Rd +++ b/man/centr_degree_tmax.Rd @@ -19,7 +19,7 @@ centr_degree_tmax( \item{mode}{This is the same as the \code{mode} argument of \code{degree()}. Ignored if \code{graph} is given and the graph is undirected.} -\item{loops}{Logical scalar, whether to consider loops edges when +\item{loops}{Logical, whether to consider loops edges when calculating the degree.} } \value{ diff --git a/man/centr_eigen.Rd b/man/centr_eigen.Rd index be845de58ef..333a53501b5 100644 --- a/man/centr_eigen.Rd +++ b/man/centr_eigen.Rd @@ -15,7 +15,7 @@ centr_eigen( \arguments{ \item{graph}{The input graph.} -\item{directed}{logical scalar, whether to use directed shortest paths for +\item{directed}{Logical, whether to use directed shortest paths for calculating eigenvector centrality.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Ignored. Computing @@ -24,7 +24,7 @@ eigenvector centralization requires normalized eigenvector centrality scores.} \item{options}{This is passed to \code{\link[=eigen_centrality]{eigen_centrality()}}, the options for the ARPACK eigensolver.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \value{ diff --git a/man/centr_eigen_tmax.Rd b/man/centr_eigen_tmax.Rd index 068f9c3a9c8..86ce59f90da 100644 --- a/man/centr_eigen_tmax.Rd +++ b/man/centr_eigen_tmax.Rd @@ -18,7 +18,7 @@ centr_eigen_tmax( \item{nodes}{The number of vertices. This is ignored if the graph is given.} -\item{directed}{logical scalar, whether to consider edge directions +\item{directed}{Logical, whether to consider edge directions during the calculation. Ignored in undirected graphs.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Ignored. Computing diff --git a/man/centralization.betweenness.Rd b/man/centralization.betweenness.Rd index 1a0b36856d5..e9169ed9145 100644 --- a/man/centralization.betweenness.Rd +++ b/man/centralization.betweenness.Rd @@ -9,10 +9,10 @@ centralization.betweenness(graph, directed = TRUE, normalized = TRUE) \arguments{ \item{graph}{The input graph.} -\item{directed}{logical scalar, whether to use directed shortest paths for +\item{directed}{Logical, whether to use directed shortest paths for calculating betweenness.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \description{ diff --git a/man/centralization.betweenness.tmax.Rd b/man/centralization.betweenness.tmax.Rd index 23d77bc600b..fb9bbfd5864 100644 --- a/man/centralization.betweenness.tmax.Rd +++ b/man/centralization.betweenness.tmax.Rd @@ -13,7 +13,7 @@ centralization.betweenness.tmax(graph = NULL, nodes = 0, directed = TRUE) \item{nodes}{The number of vertices. This is ignored if the graph is given.} -\item{directed}{Logical scalar, whether to use directed shortest paths +\item{directed}{Logical, whether to use directed shortest paths for calculating betweenness. Ignored if an undirected graph was given.} } diff --git a/man/centralization.closeness.Rd b/man/centralization.closeness.Rd index 2a58c7164cf..caf53f309ae 100644 --- a/man/centralization.closeness.Rd +++ b/man/centralization.closeness.Rd @@ -16,7 +16,7 @@ centralization.closeness( \item{mode}{This is the same as the \code{mode} argument of \code{closeness()}.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \description{ diff --git a/man/centralization.degree.Rd b/man/centralization.degree.Rd index fcc7c29d4ea..f508c372e7b 100644 --- a/man/centralization.degree.Rd +++ b/man/centralization.degree.Rd @@ -17,10 +17,10 @@ centralization.degree( \item{mode}{This is the same as the \code{mode} argument of \code{degree()}.} -\item{loops}{Logical scalar, whether to consider loops edges when +\item{loops}{Logical, whether to consider loops edges when calculating the degree.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \description{ diff --git a/man/centralization.degree.tmax.Rd b/man/centralization.degree.tmax.Rd index a8ee59e781f..29d7b242e75 100644 --- a/man/centralization.degree.tmax.Rd +++ b/man/centralization.degree.tmax.Rd @@ -19,7 +19,7 @@ centralization.degree.tmax( \item{mode}{This is the same as the \code{mode} argument of \code{degree()}. Ignored if \code{graph} is given and the graph is undirected.} -\item{loops}{Logical scalar, whether to consider loops edges when +\item{loops}{Logical, whether to consider loops edges when calculating the degree.} } \description{ diff --git a/man/centralization.evcent.Rd b/man/centralization.evcent.Rd index 1592b68d728..dd83655867c 100644 --- a/man/centralization.evcent.Rd +++ b/man/centralization.evcent.Rd @@ -15,7 +15,7 @@ centralization.evcent( \arguments{ \item{graph}{The input graph.} -\item{directed}{logical scalar, whether to use directed shortest paths for +\item{directed}{Logical, whether to use directed shortest paths for calculating eigenvector centrality.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Ignored. Computing @@ -24,7 +24,7 @@ eigenvector centralization requires normalized eigenvector centrality scores.} \item{options}{This is passed to \code{\link[=eigen_centrality]{eigen_centrality()}}, the options for the ARPACK eigensolver.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the theoretical maximum.} } \description{ diff --git a/man/centralization.evcent.tmax.Rd b/man/centralization.evcent.tmax.Rd index 941bf2f1c47..7800a83252c 100644 --- a/man/centralization.evcent.tmax.Rd +++ b/man/centralization.evcent.tmax.Rd @@ -18,7 +18,7 @@ centralization.evcent.tmax( \item{nodes}{The number of vertices. This is ignored if the graph is given.} -\item{directed}{logical scalar, whether to consider edge directions +\item{directed}{Logical, whether to consider edge directions during the calculation. Ignored in undirected graphs.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Ignored. Computing diff --git a/man/centralize.Rd b/man/centralize.Rd index 5ab9241e2ed..5df23809675 100644 --- a/man/centralize.Rd +++ b/man/centralize.Rd @@ -15,7 +15,7 @@ the most centralized graph with the same number of vertices as the graph under study. This is only used if the \code{normalized} argument is set to \code{TRUE}.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the supplied theoretical maximum.} } \value{ diff --git a/man/centralize.scores.Rd b/man/centralize.scores.Rd index c8beb7003bb..35ed7653490 100644 --- a/man/centralize.scores.Rd +++ b/man/centralize.scores.Rd @@ -14,7 +14,7 @@ the most centralized graph with the same number of vertices as the graph under study. This is only used if the \code{normalized} argument is set to \code{TRUE}.} -\item{normalized}{Logical scalar. Whether to normalize the graph level +\item{normalized}{Logical. Whether to normalize the graph level centrality score by dividing by the supplied theoretical maximum.} } \description{ diff --git a/man/cited.type.game.Rd b/man/cited.type.game.Rd index 4ab76a878f8..8af960e4d8d 100644 --- a/man/cited.type.game.Rd +++ b/man/cited.type.game.Rd @@ -25,9 +25,9 @@ Types are numbered from zero.} matrix (\code{sample_cit_cit_types()}) giving the (unnormalized) citation probabilities for the different vertex types.} -\item{directed}{Logical scalar, whether to generate directed networks.} +\item{directed}{Logical, whether to generate directed networks.} -\item{attr}{Logical scalar, whether to add the vertex types to the generated +\item{attr}{Logical, whether to add the vertex types to the generated graph as a vertex attribute called \sQuote{\code{type}}.} } \description{ diff --git a/man/citing.cited.type.game.Rd b/man/citing.cited.type.game.Rd index 91e4aab00cc..34df098f145 100644 --- a/man/citing.cited.type.game.Rd +++ b/man/citing.cited.type.game.Rd @@ -25,9 +25,9 @@ Types are numbered from zero.} matrix (\code{sample_cit_cit_types()}) giving the (unnormalized) citation probabilities for the different vertex types.} -\item{directed}{Logical scalar, whether to generate directed networks.} +\item{directed}{Logical, whether to generate directed networks.} -\item{attr}{Logical scalar, whether to add the vertex types to the generated +\item{attr}{Logical, whether to add the vertex types to the generated graph as a vertex attribute called \sQuote{\code{type}}.} } \description{ diff --git a/man/closeness.Rd b/man/closeness.Rd index ce4b993a58e..db7f7f44bd9 100644 --- a/man/closeness.Rd +++ b/man/closeness.Rd @@ -30,7 +30,7 @@ closeness. If the graph has a \code{weight} edge attribute, then this is used by default. Weights are used for calculating weighted shortest paths, so they are interpreted as distances.} -\item{normalized}{Logical scalar, whether to calculate the normalized +\item{normalized}{Logical, whether to calculate the normalized closeness, i.e. the inverse average distance to all reachable vertices. The non-normalized closeness is the inverse of the sum of distances to all reachable vertices.} diff --git a/man/cluster_edge_betweenness.Rd b/man/cluster_edge_betweenness.Rd index 0542df67c0a..87d47143c25 100644 --- a/man/cluster_edge_betweenness.Rd +++ b/man/cluster_edge_betweenness.Rd @@ -27,13 +27,13 @@ attribute, but you don't want to use it for community detection. Edge weights are used to calculate weighted edge betweenness. This means that edges are interpreted as distances, not as connection strengths.} -\item{directed}{Logical constant, whether to calculate directed edge +\item{directed}{Logical, whether to calculate directed edge betweenness for directed graphs. It is ignored for undirected graphs.} -\item{edge.betweenness}{Logical constant, whether to return the edge +\item{edge.betweenness}{Logical, whether to return the edge betweenness of the edges at the time of their removal.} -\item{merges}{Logical constant, whether to return the merge matrix +\item{merges}{Logical, whether to return the merge matrix representing the hierarchical community structure of the network. This argument is called \code{merges}, even if the community structure algorithm itself is divisive and not agglomerative: it builds the tree from top to @@ -46,14 +46,14 @@ communities numbered from one to \eqn{N}. The first merge, the first line of the matrix creates community \eqn{N+1}, the second merge creates community \eqn{N+2}, etc.} -\item{bridges}{Logical constant, whether to return a list the edge removals +\item{bridges}{Logical, whether to return a list the edge removals which actually splitted a component of the graph.} -\item{modularity}{Logical constant, whether to calculate the maximum +\item{modularity}{Logical, whether to calculate the maximum modularity score, considering all possibly community structures along the edge-betweenness based edge removals.} -\item{membership}{Logical constant, whether to calculate the membership +\item{membership}{Logical, whether to calculate the membership vector corresponding to the highest possible modularity score.} } \value{ diff --git a/man/cluster_fast_greedy.Rd b/man/cluster_fast_greedy.Rd index bd5513efd27..a830b5cb2f2 100644 --- a/man/cluster_fast_greedy.Rd +++ b/man/cluster_fast_greedy.Rd @@ -16,12 +16,12 @@ cluster_fast_greedy( \item{graph}{The input graph. It must be undirected and must not have multi-edges.} -\item{merges}{Logical scalar, whether to return the merge matrix.} +\item{merges}{Logical, whether to return the merge matrix.} -\item{modularity}{Logical scalar, whether to return a vector containing the +\item{modularity}{Logical, whether to return a vector containing the modularity after each merge.} -\item{membership}{Logical scalar, whether to calculate the membership vector +\item{membership}{Logical, whether to calculate the membership vector corresponding to the maximum modularity score, considering all possible community structures along the merges.} diff --git a/man/cluster_infomap.Rd b/man/cluster_infomap.Rd index c876cc0624a..87fd01756fa 100644 --- a/man/cluster_infomap.Rd +++ b/man/cluster_infomap.Rd @@ -31,7 +31,7 @@ jumps to that vertex.} \item{nb.trials}{The number of attempts to partition the network (can be any integer value equal or larger than 1).} -\item{modularity}{Logical scalar, whether to calculate the modularity score +\item{modularity}{Logical, whether to calculate the modularity score of the detected community structure.} } \value{ diff --git a/man/cluster_spinglass.Rd b/man/cluster_spinglass.Rd index 1ab27b96c67..afcdfde5599 100644 --- a/man/cluster_spinglass.Rd +++ b/man/cluster_spinglass.Rd @@ -39,7 +39,7 @@ limit for the number of communities. It is not a problem to supply a (reasonably) big number here, in which case some spin states will be unpopulated.} -\item{parupdate}{Logical constant, whether to update the spins of the +\item{parupdate}{Logical, whether to update the spins of the vertices in parallel (synchronously) or not. This argument is ignored if the second form of the function is used (i.e. the \sQuote{\code{vertex}} argument is present). It is also not implemented in the \dQuote{neg} implementation.} diff --git a/man/cluster_walktrap.Rd b/man/cluster_walktrap.Rd index c4d3026ab37..af320c6500a 100644 --- a/man/cluster_walktrap.Rd +++ b/man/cluster_walktrap.Rd @@ -28,14 +28,14 @@ walker. In other words, larger edge weights correspond to stronger connections.} \item{steps}{The length of the random walks to perform.} -\item{merges}{Logical scalar, whether to include the merge matrix in the +\item{merges}{Logical, whether to include the merge matrix in the result.} -\item{modularity}{Logical scalar, whether to include the vector of the +\item{modularity}{Logical, whether to include the vector of the modularity scores in the result. If the \code{membership} argument is true, then it will always be calculated.} -\item{membership}{Logical scalar, whether to calculate the membership vector +\item{membership}{Logical, whether to calculate the membership vector for the split corresponding to the highest modularity value.} } \value{ diff --git a/man/cohesive.blocks.Rd b/man/cohesive.blocks.Rd index dc63ae7a51f..2bda8400d28 100644 --- a/man/cohesive.blocks.Rd +++ b/man/cohesive.blocks.Rd @@ -15,7 +15,7 @@ For \code{graphs_from_cohesive_blocks()} and \code{export_pajek()} the same grap supplied whose cohesive block structure is given in the \code{blocks()} argument.} -\item{labels}{Logical scalar, whether to add the vertex labels to the result +\item{labels}{Logical, whether to add the vertex labels to the result object. These labels can be then used when reporting and plotting the cohesive blocks.} } diff --git a/man/cohesive_blocks.Rd b/man/cohesive_blocks.Rd index 3b1ea50d337..6aa6f590330 100644 --- a/man/cohesive_blocks.Rd +++ b/man/cohesive_blocks.Rd @@ -63,7 +63,7 @@ For \code{graphs_from_cohesive_blocks()} and \code{export_pajek()} the same grap supplied whose cohesive block structure is given in the \code{blocks()} argument.} -\item{labels}{Logical scalar, whether to add the vertex labels to the result +\item{labels}{Logical, whether to add the vertex labels to the result object. These labels can be then used when reporting and plotting the cohesive blocks.} @@ -107,7 +107,7 @@ of the files, without extension. (But it can contain the path to the files.) See also details below.} -\item{project.file}{Logical scalar, whether to create a single Pajek project +\item{project.file}{Logical, whether to create a single Pajek project file containing all the data, or to create separated files for each item. See details below.} } diff --git a/man/communities.Rd b/man/communities.Rd index 8e6f0dd9111..711da26f037 100644 --- a/man/communities.Rd +++ b/man/communities.Rd @@ -71,7 +71,7 @@ them.} \item{hang}{Numeric scalar indicating how the height of leaves should be computed from the heights of their parents; see \code{\link[=plot.hclust]{plot.hclust()}}.} -\item{use.modularity}{Logical scalar, whether to use the modularity values +\item{use.modularity}{Logical, whether to use the modularity values to define the height of the branches.} \item{no}{Integer scalar, the desired number of communities. If too low or @@ -129,7 +129,7 @@ the graph that was the input of the community detection. \code{crossing()} returns a logical vector. -\code{is_hierarchical()} returns a logical scalar. +\code{is_hierarchical()} returns a Logical. \code{merges()} returns a two-column numeric matrix. diff --git a/man/complementer.Rd b/man/complementer.Rd index cca23ad7b0c..e296947d887 100644 --- a/man/complementer.Rd +++ b/man/complementer.Rd @@ -9,7 +9,7 @@ complementer(graph, loops = FALSE) \arguments{ \item{graph}{The input graph, can be directed or undirected.} -\item{loops}{Logical constant, whether to generate loop edges.} +\item{loops}{Logical, whether to generate loop edges.} } \value{ A new graph object. diff --git a/man/components.Rd b/man/components.Rd index c8cc7de3987..8d6dc61306e 100644 --- a/man/components.Rd +++ b/man/components.Rd @@ -35,7 +35,7 @@ directed graphs \dQuote{weak} implies weakly, \dQuote{strong} strongly connected components to search. It is ignored for undirected graphs.} } \value{ -For \code{is_connected()} a logical constant. +For \code{is_connected()} a Logical. For \code{components()} a named list with three components: \describe{ diff --git a/man/compose.Rd b/man/compose.Rd index f26ae5aad8f..02308050dfe 100644 --- a/man/compose.Rd +++ b/man/compose.Rd @@ -12,7 +12,7 @@ compose(g1, g2, byname = "auto") \item{g2}{The second input graph.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if both graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and one graph, diff --git a/man/degree.Rd b/man/degree.Rd index e68186fd7f3..51dab326a3b 100644 --- a/man/degree.Rd +++ b/man/degree.Rd @@ -38,7 +38,7 @@ this argument is ignored. \dQuote{all} is a synonym of \dQuote{total}.} \item{loops}{Logical; whether the loop edges are also counted.} -\item{normalized}{Logical scalar, whether to normalize the degree. If +\item{normalized}{Logical, whether to normalize the degree. If \code{TRUE} then the result is divided by \eqn{n-1}, where \eqn{n} is the number of vertices in the graph.} diff --git a/man/dfs.Rd b/man/dfs.Rd index 9815cc12ac7..1fc4efabf69 100644 --- a/man/dfs.Rd +++ b/man/dfs.Rd @@ -34,20 +34,20 @@ ignores edge directions completely. \sQuote{total} is a synonym for \item{...}{These dots are for future extensions and must be empty.} -\item{unreachable}{Logical scalar, whether the search should visit the +\item{unreachable}{Logical, whether the search should visit the vertices that are unreachable from the given root vertex (or vertices). If \code{TRUE}, then additional searches are performed until all vertices are visited.} -\item{order}{Logical scalar, whether to return the DFS ordering of the +\item{order}{Logical, whether to return the DFS ordering of the vertices.} -\item{order.out}{Logical scalar, whether to return the ordering based on +\item{order.out}{Logical, whether to return the ordering based on leaving the subtree of the vertex.} -\item{parent}{Logical scalar, whether to return the parent of the vertices.} +\item{parent}{Logical, whether to return the parent of the vertices.} -\item{dist}{Logical scalar, whether to return the distance from the root of +\item{dist}{Logical, whether to return the distance from the root of the search tree.} \item{in.callback}{If not \code{NULL}, then it must be callback function. diff --git a/man/difference.igraph.Rd b/man/difference.igraph.Rd index 45940d9ddd0..7bae49e61d5 100644 --- a/man/difference.igraph.Rd +++ b/man/difference.igraph.Rd @@ -14,7 +14,7 @@ undirected graph.} \item{small}{The right hand side argument of the minus operator. A directed ot undirected graph.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if both graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and one graph, diff --git a/man/distances.Rd b/man/distances.Rd index 1a7e8811000..60e0abdd8fb 100644 --- a/man/distances.Rd +++ b/man/distances.Rd @@ -107,7 +107,7 @@ form was used prior to igraph version 0.6. \dQuote{epath} means that the edges along the paths are reported. \dQuote{both} means that both forms are returned, in a named list with components \dQuote{vpath} and \dQuote{epath}.} -\item{predecessors}{Logical scalar, whether to return the predecessor vertex +\item{predecessors}{Logical, whether to return the predecessor vertex for each vertex. The predecessor of vertex \code{i} in the tree is the vertex from which vertex \code{i} was reached. The predecessor of the start vertex (in the \code{from} argument) is itself by definition. If the @@ -115,7 +115,7 @@ predecessor is zero, it means that the given vertex was not reached from the source during the search. Note that the search terminates if all the vertices in \code{to} are reached.} -\item{inbound.edges}{Logical scalar, whether to return the inbound edge for +\item{inbound.edges}{Logical, whether to return the inbound edge for each vertex. The inbound edge of vertex \code{i} in the tree is the edge via which vertex \code{i} was reached. The start vertex and vertices that were not reached during the search will have zero in the corresponding entry of diff --git a/man/each_edge.Rd b/man/each_edge.Rd index 5af92a88660..65bfc40e78a 100644 --- a/man/each_edge.Rd +++ b/man/each_edge.Rd @@ -14,10 +14,10 @@ each_edge( \arguments{ \item{prob}{The rewiring probability, a real number between zero and one.} -\item{loops}{Logical scalar, whether loop edges are allowed in the rewired +\item{loops}{Logical, whether loop edges are allowed in the rewired graph.} -\item{multiple}{Logical scalar, whether multiple edges are allowed in the +\item{multiple}{Logical, whether multiple edges are allowed in the generated graph.} \item{mode}{Character string, specifies which endpoint of the edges to rewire diff --git a/man/edge.betweenness.community.Rd b/man/edge.betweenness.community.Rd index 9edf27ea22f..6115b9ee9ed 100644 --- a/man/edge.betweenness.community.Rd +++ b/man/edge.betweenness.community.Rd @@ -27,13 +27,13 @@ attribute, but you don't want to use it for community detection. Edge weights are used to calculate weighted edge betweenness. This means that edges are interpreted as distances, not as connection strengths.} -\item{directed}{Logical constant, whether to calculate directed edge +\item{directed}{Logical, whether to calculate directed edge betweenness for directed graphs. It is ignored for undirected graphs.} -\item{edge.betweenness}{Logical constant, whether to return the edge +\item{edge.betweenness}{Logical, whether to return the edge betweenness of the edges at the time of their removal.} -\item{merges}{Logical constant, whether to return the merge matrix +\item{merges}{Logical, whether to return the merge matrix representing the hierarchical community structure of the network. This argument is called \code{merges}, even if the community structure algorithm itself is divisive and not agglomerative: it builds the tree from top to @@ -46,14 +46,14 @@ communities numbered from one to \eqn{N}. The first merge, the first line of the matrix creates community \eqn{N+1}, the second merge creates community \eqn{N+2}, etc.} -\item{bridges}{Logical constant, whether to return a list the edge removals +\item{bridges}{Logical, whether to return a list the edge removals which actually splitted a component of the graph.} -\item{modularity}{Logical constant, whether to calculate the maximum +\item{modularity}{Logical, whether to calculate the maximum modularity score, considering all possibly community structures along the edge-betweenness based edge removals.} -\item{membership}{Logical constant, whether to calculate the membership +\item{membership}{Logical, whether to calculate the membership vector corresponding to the highest possible modularity score.} } \description{ diff --git a/man/edge.connectivity.Rd b/man/edge.connectivity.Rd index b832a74cd08..5074e4b76f2 100644 --- a/man/edge.connectivity.Rd +++ b/man/edge.connectivity.Rd @@ -15,7 +15,7 @@ can be \code{NULL}, see details below.} \item{target}{The ID of the target vertex, for \code{edge_connectivity()} it can be \code{NULL}, see details below.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the edge connectivity is also one. It is a good idea to diff --git a/man/edge.disjoint.paths.Rd b/man/edge.disjoint.paths.Rd index a241f87606f..4cb344b96be 100644 --- a/man/edge.disjoint.paths.Rd +++ b/man/edge.disjoint.paths.Rd @@ -15,7 +15,7 @@ can be \code{NULL}, see details below.} \item{target}{The ID of the target vertex, for \code{edge_connectivity()} it can be \code{NULL}, see details below.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the edge connectivity is also one. It is a good idea to diff --git a/man/edge_connectivity.Rd b/man/edge_connectivity.Rd index f76d179acf2..e4c31aa3669 100644 --- a/man/edge_connectivity.Rd +++ b/man/edge_connectivity.Rd @@ -21,7 +21,7 @@ can be \code{NULL}, see details below.} \item{target}{The ID of the target vertex, for \code{edge_connectivity()} it can be \code{NULL}, see details below.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the edge connectivity is also one. It is a good idea to diff --git a/man/edge_density.Rd b/man/edge_density.Rd index eabb77f3ffe..4c654811d9c 100644 --- a/man/edge_density.Rd +++ b/man/edge_density.Rd @@ -9,7 +9,7 @@ edge_density(graph, loops = FALSE) \arguments{ \item{graph}{The input graph.} -\item{loops}{Logical constant, whether loop edges may exist in the graph. +\item{loops}{Logical, whether loop edges may exist in the graph. This affects the calculation of the largest possible number of edges in the graph. If this parameter is set to FALSE yet the graph contains self-loops, the result will not be meaningful.} diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd index 836a4c4e77b..287bfa656fa 100644 --- a/man/eigen_centrality.Rd +++ b/man/eigen_centrality.Rd @@ -15,7 +15,7 @@ eigen_centrality( \arguments{ \item{graph}{Graph to be analyzed.} -\item{directed}{Logical scalar, whether to consider direction of the edges +\item{directed}{Logical, whether to consider direction of the edges in directed graphs. It is ignored for undirected graphs.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Normalization will always take diff --git a/man/embed_adjacency_matrix.Rd b/man/embed_adjacency_matrix.Rd index 0b5deeb2fca..d7ec8e55b5b 100644 --- a/man/embed_adjacency_matrix.Rd +++ b/man/embed_adjacency_matrix.Rd @@ -34,7 +34,7 @@ eigenvalues. The default is \sQuote{lm}. Note that for directed graphs \sQuote{la} and \sQuote{lm} are the equivalent, because the singular values are used for the ordering.} -\item{scaled}{Logical scalar, if \code{FALSE}, then \eqn{U} and \eqn{V} are +\item{scaled}{Logical, if \code{FALSE}, then \eqn{U} and \eqn{V} are returned instead of \eqn{X} and \eqn{Y}.} \item{cvec}{A numeric vector, its length is the number vertices in the diff --git a/man/embed_laplacian_matrix.Rd b/man/embed_laplacian_matrix.Rd index 98d47a783f7..acefa7735e3 100644 --- a/man/embed_laplacian_matrix.Rd +++ b/man/embed_laplacian_matrix.Rd @@ -54,7 +54,7 @@ for directed graphs. The default (i.e. type \code{default}) is to use \code{D-A} for undirected graphs and \code{OAP} for directed graphs.} -\item{scaled}{Logical scalar, if \code{FALSE}, then \eqn{U} and \eqn{V} are +\item{scaled}{Logical, if \code{FALSE}, then \eqn{U} and \eqn{V} are returned instead of \eqn{X} and \eqn{Y}.} \item{options}{A named list containing the parameters for the SVD diff --git a/man/establishment.game.Rd b/man/establishment.game.Rd index 35c226542df..fab6da8bb31 100644 --- a/man/establishment.game.Rd +++ b/man/establishment.game.Rd @@ -26,7 +26,7 @@ stationary in time.} \item{pref.matrix}{A matrix giving the preferences of the given vertex types. These should be probabilities, i.e. numbers between zero and one.} -\item{directed}{Logical constant, whether to generate directed graphs.} +\item{directed}{Logical, whether to generate directed graphs.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/estimate_closeness.Rd b/man/estimate_closeness.Rd index 0b6fb83b1a4..0f71008210a 100644 --- a/man/estimate_closeness.Rd +++ b/man/estimate_closeness.Rd @@ -32,7 +32,7 @@ closeness. If the graph has a \code{weight} edge attribute, then this is used by default. Weights are used for calculating weighted shortest paths, so they are interpreted as distances.} -\item{normalized}{Logical scalar, whether to calculate the normalized +\item{normalized}{Logical, whether to calculate the normalized closeness, i.e. the inverse average distance to all reachable vertices. The non-normalized closeness is the inverse of the sum of distances to all reachable vertices.} diff --git a/man/evcent.Rd b/man/evcent.Rd index 838f58d6ca8..a618c521979 100644 --- a/man/evcent.Rd +++ b/man/evcent.Rd @@ -15,7 +15,7 @@ evcent( \arguments{ \item{graph}{Graph to be analyzed.} -\item{directed}{Logical scalar, whether to consider direction of the edges +\item{directed}{Logical, whether to consider direction of the edges in directed graphs. It is ignored for undirected graphs.} \item{scale}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Normalization will always take diff --git a/man/exportPajek.Rd b/man/exportPajek.Rd index ccb5ef9fb61..d88573b6188 100644 --- a/man/exportPajek.Rd +++ b/man/exportPajek.Rd @@ -27,7 +27,7 @@ of the files, without extension. (But it can contain the path to the files.) See also details below.} -\item{project.file}{Logical scalar, whether to create a single Pajek project +\item{project.file}{Logical, whether to create a single Pajek project file containing all the data, or to create separated files for each item. See details below.} } diff --git a/man/fastgreedy.community.Rd b/man/fastgreedy.community.Rd index 957bf210ba7..ff1251fb379 100644 --- a/man/fastgreedy.community.Rd +++ b/man/fastgreedy.community.Rd @@ -16,12 +16,12 @@ fastgreedy.community( \item{graph}{The input graph. It must be undirected and must not have multi-edges.} -\item{merges}{Logical scalar, whether to return the merge matrix.} +\item{merges}{Logical, whether to return the merge matrix.} -\item{modularity}{Logical scalar, whether to return a vector containing the +\item{modularity}{Logical, whether to return a vector containing the modularity after each merge.} -\item{membership}{Logical scalar, whether to calculate the membership vector +\item{membership}{Logical, whether to calculate the membership vector corresponding to the maximum modularity score, considering all possible community structures along the merges.} diff --git a/man/fit_power_law.Rd b/man/fit_power_law.Rd index 01e474afb74..c35bb42001c 100644 --- a/man/fit_power_law.Rd +++ b/man/fit_power_law.Rd @@ -31,7 +31,7 @@ argument makes it possible to fit only the tail of the distribution.} minimizing function, for the \sQuote{\code{R.mle}} implementation. Usually it is safe to leave this untouched.} -\item{force.continuous}{Logical scalar. Whether to force a continuous +\item{force.continuous}{Logical. Whether to force a continuous distribution for the \sQuote{\code{plfit}} implementation, even if the sample vector contains integer values only (by chance). If this argument is false, igraph will assume a continuous distribution if at least one sample @@ -67,7 +67,7 @@ If \code{implementation} is \sQuote{\code{plfit}}, then the result is a named list with entries: \describe{ \item{continuous}{ -Logical scalar, whether the +Logical, whether the fitted power-law distribution was continuous or discrete. } \item{alpha}{ diff --git a/man/forest.fire.game.Rd b/man/forest.fire.game.Rd index 730a969ef54..28aa158ba63 100644 --- a/man/forest.fire.game.Rd +++ b/man/forest.fire.game.Rd @@ -16,7 +16,7 @@ probability is calculated as \code{bw.factor*fw.prob}.} \item{ambs}{The number of ambassador vertices.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create 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]}} diff --git a/man/get.adjacency.Rd b/man/get.adjacency.Rd index ef4a95bfc9b..3fa07e6a9e9 100644 --- a/man/get.adjacency.Rd +++ b/man/get.adjacency.Rd @@ -26,14 +26,14 @@ matrix is returned.} supplied, the value is forwarded to \code{weights} as a character edge attribute name.} -\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical scalar, whether to return the edge IDs in the matrix. +\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical, whether to return the edge IDs in the matrix. For non-existant edges zero is returned.} -\item{names}{Logical constant, whether to assign row and column names +\item{names}{Logical, whether to assign row and column names to the matrix. These are only assigned if the \code{name} vertex attribute is present in the graph.} -\item{sparse}{Logical scalar, whether to create a sparse matrix. The +\item{sparse}{Logical, whether to create a sparse matrix. The \sQuote{\code{Matrix}} package must be installed for creating sparse matrices.} } diff --git a/man/get.adjlist.Rd b/man/get.adjlist.Rd index e35c005240f..841feb1311f 100644 --- a/man/get.adjlist.Rd +++ b/man/get.adjlist.Rd @@ -23,7 +23,7 @@ for both. This argument is ignored for undirected graphs.} (to include loop edges twice) and \code{"once"} (to include them once). \code{"twice"} is not allowed for directed graphs and will be replaced with \code{"once"}.} -\item{multiple}{Logical scalar, set to \code{FALSE} to use only one representative +\item{multiple}{Logical, set to \code{FALSE} to use only one representative of each set of parallel edges.} } \description{ diff --git a/man/get.edge.ids.Rd b/man/get.edge.ids.Rd index e01a9a88f79..a78552ec802 100644 --- a/man/get.edge.ids.Rd +++ b/man/get.edge.ids.Rd @@ -14,10 +14,10 @@ or vector of vertex IDs or symbolic vertex names. For a vector, the values are interpreted pairwise, i.e. the first and second are used for the first edge, the third and fourth for the second, etc.} -\item{directed}{Logical scalar, whether to consider edge directions in +\item{directed}{Logical, whether to consider edge directions in directed graphs. This argument is ignored for undirected graphs.} -\item{error}{Logical scalar, whether to report an error if an edge is not +\item{error}{Logical, whether to report an error if an edge is not found in the graph. If \code{FALSE}, then no error is reported, and zero is returned for the non-existant edge(s).} diff --git a/man/get.incidence.Rd b/man/get.incidence.Rd index d0dc41eb710..669892978f7 100644 --- a/man/get.incidence.Rd +++ b/man/get.incidence.Rd @@ -18,12 +18,12 @@ no \code{type} vertex attribute.} supplied, the value is forwarded to \code{weights} as a character edge attribute name.} -\item{names}{Logical scalar, if \code{TRUE} and the vertices in the graph +\item{names}{Logical, if \code{TRUE} and the vertices in the graph are named (i.e. the graph has a vertex attribute called \code{name}), then vertex names will be added to the result as row and column names. Otherwise the IDs of the vertices are used as row and column names.} -\item{sparse}{Logical scalar, if it is \code{TRUE} then a sparse matrix is +\item{sparse}{Logical, if it is \code{TRUE} then a sparse matrix is created, you will need the \code{Matrix} package for this.} } \description{ diff --git a/man/get.shortest.paths.Rd b/man/get.shortest.paths.Rd index c8edcc27313..f631dd02c8c 100644 --- a/man/get.shortest.paths.Rd +++ b/man/get.shortest.paths.Rd @@ -47,7 +47,7 @@ form was used prior to igraph version 0.6. \dQuote{epath} means that the edges along the paths are reported. \dQuote{both} means that both forms are returned, in a named list with components \dQuote{vpath} and \dQuote{epath}.} -\item{predecessors}{Logical scalar, whether to return the predecessor vertex +\item{predecessors}{Logical, whether to return the predecessor vertex for each vertex. The predecessor of vertex \code{i} in the tree is the vertex from which vertex \code{i} was reached. The predecessor of the start vertex (in the \code{from} argument) is itself by definition. If the @@ -55,7 +55,7 @@ predecessor is zero, it means that the given vertex was not reached from the source during the search. Note that the search terminates if all the vertices in \code{to} are reached.} -\item{inbound.edges}{Logical scalar, whether to return the inbound edge for +\item{inbound.edges}{Logical, whether to return the inbound edge for each vertex. The inbound edge of vertex \code{i} in the tree is the edge via which vertex \code{i} was reached. The start vertex and vertices that were not reached during the search will have zero in the corresponding entry of diff --git a/man/get.stochastic.Rd b/man/get.stochastic.Rd index df4c0d29b32..9a0c834553f 100644 --- a/man/get.stochastic.Rd +++ b/man/get.stochastic.Rd @@ -16,7 +16,7 @@ get.stochastic( \item{column.wise}{If \code{FALSE}, then the rows of the stochastic matrix sum up to one; otherwise it is the columns.} -\item{sparse}{Logical scalar, whether to return a sparse matrix. The +\item{sparse}{Logical, whether to return a sparse matrix. The \code{Matrix} package is needed for sparse matrices.} } \description{ diff --git a/man/get_edge_ids.Rd b/man/get_edge_ids.Rd index 9118a92436a..07ba9544181 100644 --- a/man/get_edge_ids.Rd +++ b/man/get_edge_ids.Rd @@ -14,10 +14,10 @@ or vector of vertex IDs or symbolic vertex names. For a vector, the values are interpreted pairwise, i.e. the first and second are used for the first edge, the third and fourth for the second, etc.} -\item{directed}{Logical scalar, whether to consider edge directions in +\item{directed}{Logical, whether to consider edge directions in directed graphs. This argument is ignored for undirected graphs.} -\item{error}{Logical scalar, whether to report an error if an edge is not +\item{error}{Logical, whether to report an error if an edge is not found in the graph. If \code{FALSE}, then no error is reported, and zero is returned for the non-existant edge(s).} } diff --git a/man/girth.Rd b/man/girth.Rd index e88d5a816fc..5ca83865603 100644 --- a/man/girth.Rd +++ b/man/girth.Rd @@ -10,7 +10,7 @@ girth(graph, circle = TRUE) \item{graph}{The input graph. It may be directed, but the algorithm searches for undirected circles anyway.} -\item{circle}{Logical scalar, whether to return the shortest circle itself.} +\item{circle}{Logical, whether to return the shortest circle itself.} } \value{ A named list with two components: diff --git a/man/global_efficiency.Rd b/man/global_efficiency.Rd index 7479423a667..9e7df3c6e35 100644 --- a/man/global_efficiency.Rd +++ b/man/global_efficiency.Rd @@ -30,7 +30,7 @@ average_local_efficiency( additionally, no edge weight may be NaN. If it is \code{NULL} (the default) and the graph has a \code{weight} edge attribute, then it is used automatically.} -\item{directed}{Logical scalar, whether to consider directed paths. Ignored +\item{directed}{Logical, whether to consider directed paths. Ignored for undirected graphs.} \item{vids}{The vertex IDs of the vertices for which the calculation will be done. diff --git a/man/graph.adhesion.Rd b/man/graph.adhesion.Rd index b5ef47f9a7e..56d7cfb3214 100644 --- a/man/graph.adhesion.Rd +++ b/man/graph.adhesion.Rd @@ -9,7 +9,7 @@ graph.adhesion(graph, checks = TRUE) \arguments{ \item{graph}{The input graph.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the edge connectivity is also one. It is a good idea to diff --git a/man/graph.adjacency.Rd b/man/graph.adjacency.Rd index 0ee561f3139..e03c982fc4f 100644 --- a/man/graph.adjacency.Rd +++ b/man/graph.adjacency.Rd @@ -32,7 +32,7 @@ edge attribute named by the \code{weighted} argument. If it is \code{TRUE} then a weighted graph is created and the name of the edge attribute will be \code{weight}. See also details below.} -\item{diag}{Logical scalar, whether to include the diagonal of the matrix in +\item{diag}{Logical, whether to include the diagonal of the matrix in the calculation. If this is \code{FALSE} then the diagonal is zerod out first.} diff --git a/man/graph.adjlist.Rd b/man/graph.adjlist.Rd index 8e2895891b2..601a9a6e650 100644 --- a/man/graph.adjlist.Rd +++ b/man/graph.adjlist.Rd @@ -16,7 +16,7 @@ undirected (\sQuote{all} or \sQuote{total}) or directed; and in the latter case, whether it contains the outgoing (\sQuote{out}) or the incoming (\sQuote{in}) neighbors of the vertices.} -\item{duplicate}{Logical scalar. For undirected graphs it gives whether +\item{duplicate}{Logical. For undirected graphs it gives whether edges are included in the list twice. E.g. if it is \code{TRUE} then for an undirected \code{{A,B}} edge \code{graph_from_adj_list()} expects \code{A} included in the neighbors of \code{B} and \code{B} to be included in the diff --git a/man/graph.bfs.Rd b/man/graph.bfs.Rd index 9a99cec931a..5959721ddf5 100644 --- a/man/graph.bfs.Rd +++ b/man/graph.bfs.Rd @@ -36,7 +36,7 @@ it, so it keeps the distance it was first found at rather than \code{0}.} ignores edge directions completely. \sQuote{total} is a synonym for \sQuote{all}. This argument is ignored for undirected graphs.} -\item{unreachable}{Logical scalar, whether the search should visit the +\item{unreachable}{Logical, whether the search should visit the vertices that are unreachable from the given root vertex (or vertices). If \code{TRUE}, then additional searches are performed until all vertices are visited.} @@ -45,19 +45,19 @@ visited.} (IDs or symbolic names). In the latter case, the search is restricted to the given vertices.} -\item{order}{Logical scalar, whether to return the ordering of the vertices.} +\item{order}{Logical, whether to return the ordering of the vertices.} -\item{rank}{Logical scalar, whether to return the rank of the vertices.} +\item{rank}{Logical, whether to return the rank of the vertices.} -\item{father}{Logical scalar, whether to return the father of the vertices.} +\item{father}{Logical, whether to return the father of the vertices.} -\item{pred}{Logical scalar, whether to return the predecessors of the +\item{pred}{Logical, whether to return the predecessors of the vertices.} -\item{succ}{Logical scalar, whether to return the successors of the +\item{succ}{Logical, whether to return the successors of the vertices.} -\item{dist}{Logical scalar, whether to return the distance from the root of +\item{dist}{Logical, whether to return the distance from the root of the search tree.} \item{callback}{If not \code{NULL}, then it must be callback function. This diff --git a/man/graph.bipartite.Rd b/man/graph.bipartite.Rd index ce32bf3e77b..3e95f20c385 100644 --- a/man/graph.bipartite.Rd +++ b/man/graph.bipartite.Rd @@ -17,7 +17,7 @@ regular \code{\link[=make_graph]{make_graph()}} function. It is checked that the connect vertices of different kind, according to the supplied \code{types} vector. The vector may be a string vector if \code{types} is a named vector.} -\item{directed}{Whether to create a directed graph, boolean constant. Note +\item{directed}{Logical, whether to create a directed graph. Note that by default undirected graphs are created, as this is more common for bipartite graphs.} } diff --git a/man/graph.complementer.Rd b/man/graph.complementer.Rd index 50b1be3a6fd..d11ae057ab4 100644 --- a/man/graph.complementer.Rd +++ b/man/graph.complementer.Rd @@ -9,7 +9,7 @@ graph.complementer(graph, loops = FALSE) \arguments{ \item{graph}{The input graph, can be directed or undirected.} -\item{loops}{Logical constant, whether to generate loop edges.} +\item{loops}{Logical, whether to generate loop edges.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/graph.compose.Rd b/man/graph.compose.Rd index 8cd2dd7d4fe..b033a85150f 100644 --- a/man/graph.compose.Rd +++ b/man/graph.compose.Rd @@ -11,7 +11,7 @@ graph.compose(g1, g2, byname = "auto") \item{g2}{The second input graph.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if both graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and one graph, diff --git a/man/graph.data.frame.Rd b/man/graph.data.frame.Rd index 7b87f3a650a..65b57fb2366 100644 --- a/man/graph.data.frame.Rd +++ b/man/graph.data.frame.Rd @@ -12,7 +12,7 @@ columns. Additional columns are considered as edge attributes. Since version 0.7 this argument is coerced to a data frame with \code{as.data.frame}.} -\item{directed}{Logical scalar, whether or not to create a directed graph.} +\item{directed}{Logical, whether or not to create a directed graph.} \item{vertices}{A data frame with vertex metadata, or \code{NULL}. See details below. Since version 0.7 this argument is coerced to a data frame diff --git a/man/graph.density.Rd b/man/graph.density.Rd index 704159818f9..e4ab75e651b 100644 --- a/man/graph.density.Rd +++ b/man/graph.density.Rd @@ -9,7 +9,7 @@ graph.density(graph, loops = FALSE) \arguments{ \item{graph}{The input graph.} -\item{loops}{Logical constant, whether loop edges may exist in the graph. +\item{loops}{Logical, whether loop edges may exist in the graph. This affects the calculation of the largest possible number of edges in the graph. If this parameter is set to FALSE yet the graph contains self-loops, the result will not be meaningful.} diff --git a/man/graph.dfs.Rd b/man/graph.dfs.Rd index 332e2674268..f382468f368 100644 --- a/man/graph.dfs.Rd +++ b/man/graph.dfs.Rd @@ -30,20 +30,20 @@ graph.dfs( ignores edge directions completely. \sQuote{total} is a synonym for \sQuote{all}. This argument is ignored for undirected graphs.} -\item{unreachable}{Logical scalar, whether the search should visit the +\item{unreachable}{Logical, whether the search should visit the vertices that are unreachable from the given root vertex (or vertices). If \code{TRUE}, then additional searches are performed until all vertices are visited.} -\item{order}{Logical scalar, whether to return the DFS ordering of the +\item{order}{Logical, whether to return the DFS ordering of the vertices.} -\item{order.out}{Logical scalar, whether to return the ordering based on +\item{order.out}{Logical, whether to return the ordering based on leaving the subtree of the vertex.} -\item{father}{Logical scalar, whether to return the father of the vertices.} +\item{father}{Logical, whether to return the father of the vertices.} -\item{dist}{Logical scalar, whether to return the distance from the root of +\item{dist}{Logical, whether to return the distance from the root of the search tree.} \item{in.callback}{If not \code{NULL}, then it must be callback function. diff --git a/man/graph.extended.chordal.ring.Rd b/man/graph.extended.chordal.ring.Rd index 6d1b0a83a04..e5baf01ddd5 100644 --- a/man/graph.extended.chordal.ring.Rd +++ b/man/graph.extended.chordal.ring.Rd @@ -12,7 +12,7 @@ graph.extended.chordal.ring(n, w, directed = FALSE) \item{w}{A matrix which specifies the extended chordal ring. See details below.} -\item{directed}{Logical scalar, whether or not to create a directed graph.} +\item{directed}{Logical, whether or not to create 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]}} diff --git a/man/graph.formula.Rd b/man/graph.formula.Rd index 55578421f35..fbd0145077a 100644 --- a/man/graph.formula.Rd +++ b/man/graph.formula.Rd @@ -11,7 +11,7 @@ graph.formula(..., simplify = TRUE) structure of the graph, see details below. For \code{from_literal()} all arguments are passed to \code{graph_from_literal()}.} -\item{simplify}{Logical scalar, whether to call \code{\link[=simplify]{simplify()}} +\item{simplify}{Logical, whether to call \code{\link[=simplify]{simplify()}} on the created graph. By default the graph is simplified, loop and multiple edges are removed. \code{\link[=simplify]{simplify()}} is only called when the created graph is not already simple, so the edge order from the diff --git a/man/graph.full.bipartite.Rd b/man/graph.full.bipartite.Rd index 2bc9cd007f5..25649b5e162 100644 --- a/man/graph.full.bipartite.Rd +++ b/man/graph.full.bipartite.Rd @@ -11,7 +11,7 @@ graph.full.bipartite(n1, n2, directed = FALSE, mode = c("all", "out", "in")) \item{n2}{The number of vertices of the second kind.} -\item{directed}{Logical scalar, whether the graphs is directed.} +\item{directed}{Logical, whether the graphs is directed.} \item{mode}{Scalar giving the kind of edges to create for directed graphs. If this is \sQuote{\code{out}} then all vertices of the first kind are diff --git a/man/graph.graphdb.Rd b/man/graph.graphdb.Rd index 7dc2debef6b..9a73ccf333f 100644 --- a/man/graph.graphdb.Rd +++ b/man/graph.graphdb.Rd @@ -41,11 +41,11 @@ which one to read.} \item{base}{The base address of the database. See details below.} -\item{compressed}{Logical constant, if TRUE than the file is expected to be +\item{compressed}{Logical, if TRUE than the file is expected to be compressed by gzip. If \code{url} is \code{NULL} then a \sQuote{\code{.gz}} suffix is added to the filename.} -\item{directed}{Logical constant, whether to create a directed graph.} +\item{directed}{Logical, whether to create 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]}} diff --git a/man/graph.incidence.Rd b/man/graph.incidence.Rd index 65afa2c20ef..ad16e6eaa84 100644 --- a/man/graph.incidence.Rd +++ b/man/graph.incidence.Rd @@ -17,7 +17,7 @@ graph.incidence( \item{incidence}{The input bipartite adjacency matrix. It can also be a sparse matrix from the \code{Matrix} package.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} \item{mode}{A character constant, defines the direction of the edges in directed graphs, ignored for undirected graphs. If \sQuote{\code{out}}, then @@ -26,7 +26,7 @@ bipartite adjacency matrix) to vertices of the second kind (columns in the incid matrix). If \sQuote{\verb{in}}, then the opposite direction is used. If \sQuote{\code{all}} or \sQuote{\code{total}}, then mutual edges are created.} -\item{multiple}{Logical scalar, specifies how to interpret the matrix +\item{multiple}{Logical, specifies how to interpret the matrix elements. See details below.} \item{weighted}{This argument specifies whether to create a weighted graph diff --git a/man/graph.laplacian.Rd b/man/graph.laplacian.Rd index 933197d4e2c..e0437326ac4 100644 --- a/man/graph.laplacian.Rd +++ b/man/graph.laplacian.Rd @@ -22,7 +22,7 @@ matrix. If this is \code{NULL} and the graph has an edge attribute called you want the unweighted Laplacian on a graph that has a \code{weight} edge attribute.} -\item{sparse}{Logical scalar, whether to return the result as a sparse +\item{sparse}{Logical, whether to return the result as a sparse matrix. The \code{Matrix} package is required for sparse matrices.} } \description{ diff --git a/man/graph.lattice.Rd b/man/graph.lattice.Rd index 790d06dbdc0..b51b3a01045 100644 --- a/man/graph.lattice.Rd +++ b/man/graph.lattice.Rd @@ -32,9 +32,9 @@ lattice will be connected. This parameter is not used right now.} \item{mutual}{Logical, if \code{TRUE} directed lattices will be mutually connected.} -\item{periodic}{Logical vector, Boolean vector, defines whether the generated lattice is -periodic along each dimension. This parameter may also be scalar boolen value which will -be extended to boolean vector with dimvector length.} +\item{periodic}{Logical vector, defines whether the generated lattice is +periodic along each dimension. This parameter may also be a single logical which will +be extended to a logical vector of `dimvector`` length.} \item{circular}{Deprecated, use \code{periodic} instead.} } diff --git a/man/graph.mincut.Rd b/man/graph.mincut.Rd index d553ac186ac..beb0f0e82eb 100644 --- a/man/graph.mincut.Rd +++ b/man/graph.mincut.Rd @@ -22,7 +22,7 @@ graph.mincut( \item{capacity}{Vector giving the capacity of the edges. If this is \code{NULL} (the default) then the \code{capacity} edge attribute is used.} -\item{value.only}{Logical scalar, if \code{TRUE} only the minimum cut value +\item{value.only}{Logical, if \code{TRUE} only the minimum cut value is returned, if \code{FALSE} the edges in the cut and a the two (or more) partitions are also returned.} } diff --git a/man/graph.union.Rd b/man/graph.union.Rd index 63d7e5f96d4..5598a09fa69 100644 --- a/man/graph.union.Rd +++ b/man/graph.union.Rd @@ -9,7 +9,7 @@ graph.union(..., byname = "auto") \arguments{ \item{...}{Graph objects or lists of graph objects.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if all graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and some (but not all) diff --git a/man/graph_from_adj_list.Rd b/man/graph_from_adj_list.Rd index 0744469c19b..7ebdbe8d139 100644 --- a/man/graph_from_adj_list.Rd +++ b/man/graph_from_adj_list.Rd @@ -20,7 +20,7 @@ undirected (\sQuote{all} or \sQuote{total}) or directed; and in the latter case, whether it contains the outgoing (\sQuote{out}) or the incoming (\sQuote{in}) neighbors of the vertices.} -\item{duplicate}{Logical scalar. For undirected graphs it gives whether +\item{duplicate}{Logical. For undirected graphs it gives whether edges are included in the list twice. E.g. if it is \code{TRUE} then for an undirected \code{{A,B}} edge \code{graph_from_adj_list()} expects \code{A} included in the neighbors of \code{B} and \code{B} to be included in the diff --git a/man/graph_from_adjacency_matrix.Rd b/man/graph_from_adjacency_matrix.Rd index d8d79206e79..3503fdb97be 100644 --- a/man/graph_from_adjacency_matrix.Rd +++ b/man/graph_from_adjacency_matrix.Rd @@ -42,7 +42,7 @@ edge attribute named by the \code{weighted} argument. If it is \code{TRUE} then a weighted graph is created and the name of the edge attribute will be \code{weight}. See also details below.} -\item{diag}{Logical scalar, whether to include the diagonal of the matrix in +\item{diag}{Logical, whether to include the diagonal of the matrix in the calculation. If this is \code{FALSE} then the diagonal is zerod out first.} diff --git a/man/graph_from_biadjacency_matrix.Rd b/man/graph_from_biadjacency_matrix.Rd index eb6cf2cb94c..e8bc2de2fd3 100644 --- a/man/graph_from_biadjacency_matrix.Rd +++ b/man/graph_from_biadjacency_matrix.Rd @@ -17,7 +17,7 @@ graph_from_biadjacency_matrix( \item{incidence}{The input bipartite adjacency matrix. It can also be a sparse matrix from the \code{Matrix} package.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} \item{mode}{A character constant, defines the direction of the edges in directed graphs, ignored for undirected graphs. If \sQuote{\code{out}}, then @@ -26,7 +26,7 @@ bipartite adjacency matrix) to vertices of the second kind (columns in the incid matrix). If \sQuote{\verb{in}}, then the opposite direction is used. If \sQuote{\code{all}} or \sQuote{\code{total}}, then mutual edges are created.} -\item{multiple}{Logical scalar, specifies how to interpret the matrix +\item{multiple}{Logical, specifies how to interpret the matrix elements. See details below.} \item{weighted}{This argument specifies whether to create a weighted graph diff --git a/man/graph_from_data_frame.Rd b/man/graph_from_data_frame.Rd index ea6ab3ebaf1..051542d9420 100644 --- a/man/graph_from_data_frame.Rd +++ b/man/graph_from_data_frame.Rd @@ -23,7 +23,7 @@ columns. Additional columns are considered as edge attributes. Since version 0.7 this argument is coerced to a data frame with \code{as.data.frame}.} -\item{directed}{Logical scalar, whether or not to create a directed graph.} +\item{directed}{Logical, whether or not to create a directed graph.} \item{vertices}{A data frame with vertex metadata, or \code{NULL}. See details below. Since version 0.7 this argument is coerced to a data frame diff --git a/man/graph_from_graphdb.Rd b/man/graph_from_graphdb.Rd index 6867b84d618..c49ca575acd 100644 --- a/man/graph_from_graphdb.Rd +++ b/man/graph_from_graphdb.Rd @@ -41,11 +41,11 @@ which one to read.} \item{base}{The base address of the database. See details below.} -\item{compressed}{Logical constant, if TRUE than the file is expected to be +\item{compressed}{Logical, if TRUE than the file is expected to be compressed by gzip. If \code{url} is \code{NULL} then a \sQuote{\code{.gz}} suffix is added to the filename.} -\item{directed}{Logical constant, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} } \value{ A new graph object. diff --git a/man/graph_from_graphnel.Rd b/man/graph_from_graphnel.Rd index 2305649758f..7741d81d942 100644 --- a/man/graph_from_graphnel.Rd +++ b/man/graph_from_graphnel.Rd @@ -9,14 +9,14 @@ graph_from_graphnel(graphNEL, name = TRUE, weight = TRUE, unlist.attrs = TRUE) \arguments{ \item{graphNEL}{The graphNEL graph.} -\item{name}{Logical scalar, whether to add graphNEL vertex names as an +\item{name}{Logical, whether to add graphNEL vertex names as an igraph vertex attribute called \sQuote{\code{name}}.} -\item{weight}{Logical scalar, whether to add graphNEL edge weights as an +\item{weight}{Logical, whether to add graphNEL edge weights as an igraph edge attribute called \sQuote{\code{weight}}. (graphNEL graphs are always weighted.)} -\item{unlist.attrs}{Logical scalar. graphNEL attribute query functions +\item{unlist.attrs}{Logical. graphNEL attribute query functions return the values of the attributes in R lists, if this argument is \code{TRUE} (the default) these will be converted to atomic vectors, whenever possible, before adding them to the igraph graph.} diff --git a/man/graph_from_literal.Rd b/man/graph_from_literal.Rd index 65f97689823..2c94ff61fb1 100644 --- a/man/graph_from_literal.Rd +++ b/man/graph_from_literal.Rd @@ -14,7 +14,7 @@ from_literal(...) structure of the graph, see details below. For \code{from_literal()} all arguments are passed to \code{graph_from_literal()}.} -\item{simplify}{Logical scalar, whether to call \code{\link[=simplify]{simplify()}} +\item{simplify}{Logical, whether to call \code{\link[=simplify]{simplify()}} on the created graph. By default the graph is simplified, loop and multiple edges are removed. \code{\link[=simplify]{simplify()}} is only called when the created graph is not already simple, so the edge order from the diff --git a/man/grg.game.Rd b/man/grg.game.Rd index bb1f0e76d49..22343e30481 100644 --- a/man/grg.game.Rd +++ b/man/grg.game.Rd @@ -12,9 +12,9 @@ grg.game(nodes, radius, torus = FALSE, coords = FALSE) \item{radius}{The radius within which the vertices will be connected by an edge.} -\item{torus}{Logical constant, whether to use a torus instead of a square.} +\item{torus}{Logical, whether to use a torus instead of a square.} -\item{coords}{Logical scalar, whether to add the positions of the vertices +\item{coords}{Logical, whether to add the positions of the vertices as vertex attributes called \sQuote{\code{x}} and \sQuote{\code{y}}.} } \description{ diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd index 6a52994bfcf..1589c600d38 100644 --- a/man/harmonic_centrality.Rd +++ b/man/harmonic_centrality.Rd @@ -29,7 +29,7 @@ harmonic centrality. If the graph has a \code{weight} edge attribute, then this is used by default. Weights are used for calculating weighted shortest paths, so they are interpreted as distances.} -\item{normalized}{Logical scalar, whether to calculate the normalized +\item{normalized}{Logical, whether to calculate the normalized harmonic centrality. If true, the result is the mean inverse path length to other vertices, i.e. it is normalized by the number of vertices minus one. If false, the result is the sum of inverse path lengths to other vertices.} diff --git a/man/hits_scores.Rd b/man/hits_scores.Rd index d42c342581e..83db1d61160 100644 --- a/man/hits_scores.Rd +++ b/man/hits_scores.Rd @@ -17,7 +17,7 @@ hits_scores( \item{...}{These dots are for future extensions and must be empty.} -\item{scale}{Logical scalar, whether to scale the result to have a maximum +\item{scale}{Logical, whether to scale the result to have a maximum score of one. If no scaling is used then the result vector has unit length in the Euclidean norm.} diff --git a/man/hub.score.Rd b/man/hub.score.Rd index 64216c3c114..c36dff232ed 100644 --- a/man/hub.score.Rd +++ b/man/hub.score.Rd @@ -9,7 +9,7 @@ hub.score(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) \arguments{ \item{graph}{The input graph.} -\item{scale}{Logical scalar, whether to scale the result to have a maximum +\item{scale}{Logical, whether to scale the result to have a maximum score of one. If no scaling is used then the result vector has unit length in the Euclidean norm.} diff --git a/man/hub_score.Rd b/man/hub_score.Rd index 4c3a341d60e..8bfd4b8636d 100644 --- a/man/hub_score.Rd +++ b/man/hub_score.Rd @@ -17,7 +17,7 @@ hub_score(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) \arguments{ \item{graph}{The input graph.} -\item{scale}{Logical scalar, whether to scale the result to have a maximum +\item{scale}{Logical, whether to scale the result to have a maximum score of one. If no scaling is used then the result vector has unit length in the Euclidean norm.} diff --git a/man/igraph.from.graphNEL.Rd b/man/igraph.from.graphNEL.Rd index d60e9cc6e32..e539b1235f4 100644 --- a/man/igraph.from.graphNEL.Rd +++ b/man/igraph.from.graphNEL.Rd @@ -9,14 +9,14 @@ igraph.from.graphNEL(graphNEL, name = TRUE, weight = TRUE, unlist.attrs = TRUE) \arguments{ \item{graphNEL}{The graphNEL graph.} -\item{name}{Logical scalar, whether to add graphNEL vertex names as an +\item{name}{Logical, whether to add graphNEL vertex names as an igraph vertex attribute called \sQuote{\code{name}}.} -\item{weight}{Logical scalar, whether to add graphNEL edge weights as an +\item{weight}{Logical, whether to add graphNEL edge weights as an igraph edge attribute called \sQuote{\code{weight}}. (graphNEL graphs are always weighted.)} -\item{unlist.attrs}{Logical scalar. graphNEL attribute query functions +\item{unlist.attrs}{Logical. graphNEL attribute query functions return the values of the attributes in R lists, if this argument is \code{TRUE} (the default) these will be converted to atomic vectors, whenever possible, before adding them to the igraph graph.} diff --git a/man/infomap.community.Rd b/man/infomap.community.Rd index ab495bde6d1..d94f900ada3 100644 --- a/man/infomap.community.Rd +++ b/man/infomap.community.Rd @@ -31,7 +31,7 @@ jumps to that vertex.} \item{nb.trials}{The number of attempts to partition the network (can be any integer value equal or larger than 1).} -\item{modularity}{Logical scalar, whether to calculate the modularity score +\item{modularity}{Logical, whether to calculate the modularity score of the detected community structure.} } \description{ diff --git a/man/intersection.igraph.Rd b/man/intersection.igraph.Rd index e7345de60f7..b90e4cdb300 100644 --- a/man/intersection.igraph.Rd +++ b/man/intersection.igraph.Rd @@ -10,13 +10,13 @@ \arguments{ \item{\dots}{Graph objects or lists of graph objects.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if all graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and some (but not all) graphs are named.} -\item{keep.all.vertices}{Logical scalar, whether to keep vertices that only +\item{keep.all.vertices}{Logical, whether to keep vertices that only appear in a subset of the input graphs.} } \value{ diff --git a/man/is.chordal.Rd b/man/is.chordal.Rd index 9a6926bde62..5217977bbb9 100644 --- a/man/is.chordal.Rd +++ b/man/is.chordal.Rd @@ -25,9 +25,9 @@ that is given..} \code{NULL}, then it is automatically calculated by calling \code{\link[=max_cardinality]{max_cardinality()}}, or from \code{alpha}.} -\item{fillin}{Logical scalar, whether to calculate the fill-in edges.} +\item{fillin}{Logical, whether to calculate the fill-in edges.} -\item{newgraph}{Logical scalar, whether to calculate the triangulated graph.} +\item{newgraph}{Logical, whether to calculate the triangulated graph.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/is_chordal.Rd b/man/is_chordal.Rd index a195435641d..e47d548bcab 100644 --- a/man/is_chordal.Rd +++ b/man/is_chordal.Rd @@ -25,15 +25,15 @@ that is given..} \code{NULL}, then it is automatically calculated by calling \code{\link[=max_cardinality]{max_cardinality()}}, or from \code{alpha}.} -\item{fillin}{Logical scalar, whether to calculate the fill-in edges.} +\item{fillin}{Logical, whether to calculate the fill-in edges.} -\item{newgraph}{Logical scalar, whether to calculate the triangulated graph.} +\item{newgraph}{Logical, whether to calculate the triangulated graph.} } \value{ A list with three members: \describe{ \item{chordal}{ -Logical scalar, it is \code{TRUE} iff the input graph is chordal. +Logical, it is \code{TRUE} iff the input graph is chordal. } \item{fillin}{ If requested, then a numeric vector giving the fill-in edges. \code{NULL} otherwise. diff --git a/man/is_directed.Rd b/man/is_directed.Rd index ff6113c90e7..4294879ff67 100644 --- a/man/is_directed.Rd +++ b/man/is_directed.Rd @@ -10,7 +10,7 @@ is_directed(graph) \item{graph}{The input graph} } \value{ -Logical scalar, whether the graph is directed. +Logical, whether the graph is directed. } \description{ Check whether a graph is directed diff --git a/man/is_min_separator.Rd b/man/is_min_separator.Rd index 6c062bed948..7dc7fb1e483 100644 --- a/man/is_min_separator.Rd +++ b/man/is_min_separator.Rd @@ -14,7 +14,7 @@ ignored.} separator.} } \value{ -A logical scalar, whether the supplied vertex set is a (minimal) +A Logical, whether the supplied vertex set is a (minimal) vertex separator or not. } \description{ diff --git a/man/is_separator.Rd b/man/is_separator.Rd index f08f2a3304c..f9df1711a41 100644 --- a/man/is_separator.Rd +++ b/man/is_separator.Rd @@ -14,7 +14,7 @@ ignored.} separator.} } \value{ -A logical scalar, whether the supplied vertex set is a (minimal) +A Logical, whether the supplied vertex set is a (minimal) vertex separator or not. lists all vertex separator of minimum size. } diff --git a/man/k.regular.game.Rd b/man/k.regular.game.Rd index d814216743c..c69be583a5e 100644 --- a/man/k.regular.game.Rd +++ b/man/k.regular.game.Rd @@ -13,9 +13,9 @@ graph.} \item{k}{Integer scalar, the degree of each vertex in the graph, or the out-degree and in-degree in a directed graph.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{multiple}{Logical scalar, whether multiple edges are allowed.} +\item{multiple}{Logical, whether multiple edges are allowed.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/laplacian_matrix.Rd b/man/laplacian_matrix.Rd index 3b78256487e..93aae57f231 100644 --- a/man/laplacian_matrix.Rd +++ b/man/laplacian_matrix.Rd @@ -21,7 +21,7 @@ matrix. If this is \code{NULL} and the graph has an edge attribute called you want the unweighted Laplacian on a graph that has a \code{weight} edge attribute.} -\item{sparse}{Logical scalar, whether to return the result as a sparse +\item{sparse}{Logical, whether to return the result as a sparse matrix. The \code{Matrix} package is required for sparse matrices.} \item{normalization}{The normalization method to use when calculating the diff --git a/man/lastcit.game.Rd b/man/lastcit.game.Rd index af171384131..ec2be851281 100644 --- a/man/lastcit.game.Rd +++ b/man/lastcit.game.Rd @@ -23,7 +23,7 @@ lastcit.game( matrix (\code{sample_cit_cit_types()}) giving the (unnormalized) citation probabilities for the different vertex types.} -\item{directed}{Logical scalar, whether to generate directed networks.} +\item{directed}{Logical, whether to generate directed networks.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/layout.drl.Rd b/man/layout.drl.Rd index 5a235fd94e0..f8c21417d89 100644 --- a/man/layout.drl.Rd +++ b/man/layout.drl.Rd @@ -16,7 +16,7 @@ layout.drl( \arguments{ \item{graph}{The input graph, in can be directed or undirected.} -\item{use.seed}{Logical scalar, whether to use the coordinates given in the +\item{use.seed}{Logical, whether to use the coordinates given in the \code{seed} argument as a starting point.} \item{seed}{A matrix with two columns, the starting coordinates for the diff --git a/man/layout_as_tree.Rd b/man/layout_as_tree.Rd index 60ede455c74..313ba6b8684 100644 --- a/man/layout_as_tree.Rd +++ b/man/layout_as_tree.Rd @@ -27,7 +27,7 @@ topological sorting, performed with the opposite mode than the \code{mode} argument. After the vertices have been sorted, one is selected from each component.} -\item{circular}{Logical scalar, whether to plot the tree in a circular +\item{circular}{Logical, whether to plot the tree in a circular fashion. Defaults to \code{FALSE}, so the tree branches are going bottom-up (or top-down, see the \code{flip.y} argument.} @@ -43,7 +43,7 @@ edges are used (this was the behavior in igraph 0.5 and before). This parameter also influences how the root vertices are calculated, if they are not given. See the \code{roots} parameter.} -\item{flip.y}{Logical scalar, whether to flip the \sQuote{y} coordinates. +\item{flip.y}{Logical, whether to flip the \sQuote{y} coordinates. The default is flipping because that puts the root vertex on the top.} \item{...}{Passed to \code{layout_as_tree()}.} diff --git a/man/layout_with_drl.Rd b/man/layout_with_drl.Rd index 16781d7ede3..4e4db7155ea 100644 --- a/man/layout_with_drl.Rd +++ b/man/layout_with_drl.Rd @@ -25,7 +25,7 @@ with_drl(...) \arguments{ \item{graph}{The input graph, in can be directed or undirected.} -\item{use.seed}{Logical scalar, whether to use the coordinates given in the +\item{use.seed}{Logical, whether to use the coordinates given in the \code{seed} argument as a starting point.} \item{seed}{A matrix with two columns, the starting coordinates for the diff --git a/man/local_scan.Rd b/man/local_scan.Rd index 8359f3636d1..bd8618f85e4 100644 --- a/man/local_scan.Rd +++ b/man/local_scan.Rd @@ -34,7 +34,7 @@ default value), \code{ecount()} is used for unweighted graphs (if weights is used for weighted graphs (if \code{weighted=TRUE}). This argument is ignored if \code{k} is zero.} -\item{weighted}{Logical scalar, TRUE if the edge weights should be used +\item{weighted}{Logical, TRUE if the edge weights should be used for computation of the scan statistic. If TRUE, the graph should be weighted. Note that this argument is ignored if \code{FUN} is not \code{NULL}, \code{"ecount"} and \code{"sumweights"}.} diff --git a/man/make_bipartite_graph.Rd b/man/make_bipartite_graph.Rd index 83bb20b0db9..4123cf5c557 100644 --- a/man/make_bipartite_graph.Rd +++ b/man/make_bipartite_graph.Rd @@ -20,7 +20,7 @@ regular \code{\link[=make_graph]{make_graph()}} function. It is checked that the connect vertices of different kind, according to the supplied \code{types} vector. The vector may be a string vector if \code{types} is a named vector.} -\item{directed}{Whether to create a directed graph, boolean constant. Note +\item{directed}{Logical, whether to create a directed graph. Note that by default undirected graphs are created, as this is more common for bipartite graphs.} } @@ -28,7 +28,7 @@ bipartite graphs.} \code{make_bipartite_graph()} returns a bipartite igraph graph. In other words, an igraph graph that has a vertex attribute named \code{type}. -\code{is_bipartite()} returns a logical scalar. +\code{is_bipartite()} returns a Logical. } \description{ A bipartite graph has two kinds of vertices and connections are only allowed diff --git a/man/make_chordal_ring.Rd b/man/make_chordal_ring.Rd index 8dc3ac435cc..18d6aada0cd 100644 --- a/man/make_chordal_ring.Rd +++ b/man/make_chordal_ring.Rd @@ -15,7 +15,7 @@ chordal_ring(n, w, directed = FALSE) \item{w}{A matrix which specifies the extended chordal ring. See details below.} -\item{directed}{Logical scalar, whether or not to create a directed graph.} +\item{directed}{Logical, whether or not to create a directed graph.} } \value{ An igraph graph. diff --git a/man/make_circulant.Rd b/man/make_circulant.Rd index 46645edfadf..bd2cde282d2 100644 --- a/man/make_circulant.Rd +++ b/man/make_circulant.Rd @@ -14,7 +14,7 @@ circulant(n, shifts, directed = FALSE) \item{shifts}{Integer vector, a list of the offsets within the circulant graph.} -\item{directed}{Boolean, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} } \value{ An igraph graph. diff --git a/man/make_full_bipartite_graph.Rd b/man/make_full_bipartite_graph.Rd index 2accad21ed9..8a3cab331c7 100644 --- a/man/make_full_bipartite_graph.Rd +++ b/man/make_full_bipartite_graph.Rd @@ -19,7 +19,7 @@ full_bipartite_graph(n1, n2, directed = FALSE, mode = c("all", "out", "in")) \item{n2}{The number of vertices of the second kind.} -\item{directed}{Logical scalar, whether the graphs is directed.} +\item{directed}{Logical, whether the graphs is directed.} \item{mode}{Scalar giving the kind of edges to create for directed graphs. If this is \sQuote{\code{out}} then all vertices of the first kind are diff --git a/man/make_full_multipartite.Rd b/man/make_full_multipartite.Rd index 667e7634632..549acb049bd 100644 --- a/man/make_full_multipartite.Rd +++ b/man/make_full_multipartite.Rd @@ -12,7 +12,7 @@ full_multipartite(n, directed = FALSE, mode = c("all", "out", "in")) \arguments{ \item{n}{A numeric vector giving the number of vertices in each partition.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} \item{mode}{Character scalar, the type of connections for directed graphs. If \code{"out"}, then edges point from vertices of partitions with lower diff --git a/man/make_lattice.Rd b/man/make_lattice.Rd index f90fdc407b3..042ec5a6757 100644 --- a/man/make_lattice.Rd +++ b/man/make_lattice.Rd @@ -44,9 +44,9 @@ lattice will be connected. This parameter is not used right now.} \item{mutual}{Logical, if \code{TRUE} directed lattices will be mutually connected.} -\item{periodic}{Logical vector, Boolean vector, defines whether the generated lattice is -periodic along each dimension. This parameter may also be scalar boolen value which will -be extended to boolean vector with dimvector length.} +\item{periodic}{Logical vector, defines whether the generated lattice is +periodic along each dimension. This parameter may also be a single logical which will +be extended to a logical vector of `dimvector`` length.} \item{circular}{Deprecated, use \code{periodic} instead.} } diff --git a/man/min_cut.Rd b/man/min_cut.Rd index 45153d604d0..887c5354284 100644 --- a/man/min_cut.Rd +++ b/man/min_cut.Rd @@ -22,7 +22,7 @@ min_cut( \item{capacity}{Vector giving the capacity of the edges. If this is \code{NULL} (the default) then the \code{capacity} edge attribute is used.} -\item{value.only}{Logical scalar, if \code{TRUE} only the minimum cut value +\item{value.only}{Logical, if \code{TRUE} only the minimum cut value is returned, if \code{FALSE} the edges in the cut and a the two (or more) partitions are also returned.} } diff --git a/man/plot.igraph.Rd b/man/plot.igraph.Rd index a1c56863940..71fc17e8e40 100644 --- a/man/plot.igraph.Rd +++ b/man/plot.igraph.Rd @@ -26,7 +26,7 @@ \item{axes}{Logical, whether to plot axes, defaults to FALSE.} -\item{add}{Logical scalar, whether to add the plot to the current device, or +\item{add}{Logical, whether to add the plot to the current device, or delete the device's current contents first.} \item{xlim}{The limits for the horizontal axis, it is unlikely that you want diff --git a/man/plot.sir.Rd b/man/plot.sir.Rd index 27558fde988..7e3982742d2 100644 --- a/man/plot.sir.Rd +++ b/man/plot.sir.Rd @@ -29,7 +29,7 @@ function.} \item{comp}{Character scalar, which component to plot. Either \sQuote{NI} (infected, default), \sQuote{NS} (susceptible) or \sQuote{NR} (recovered).} -\item{median}{Logical scalar, whether to plot the (binned) median.} +\item{median}{Logical, whether to plot the (binned) median.} \item{quantiles}{A vector of (binned) quantiles to plot.} diff --git a/man/plot_dendrogram.communities.Rd b/man/plot_dendrogram.communities.Rd index 35d1bd6b60b..33a205c2861 100644 --- a/man/plot_dendrogram.communities.Rd +++ b/man/plot_dendrogram.communities.Rd @@ -24,7 +24,7 @@ plot_dendrogram(x, mode = igraph_opt("dend.plot.type"), ...) \item{\dots}{Additional arguments to supply to the dendrogram plotting function.} -\item{use.modularity}{Logical scalar, whether to use the modularity values +\item{use.modularity}{Logical, whether to use the modularity values to define the height of the branches.} \item{palette}{The color palette to use for colored plots.} diff --git a/man/power.law.fit.Rd b/man/power.law.fit.Rd index 39dec611e19..07170f5079c 100644 --- a/man/power.law.fit.Rd +++ b/man/power.law.fit.Rd @@ -29,7 +29,7 @@ argument makes it possible to fit only the tail of the distribution.} minimizing function, for the \sQuote{\code{R.mle}} implementation. Usually it is safe to leave this untouched.} -\item{force.continuous}{Logical scalar. Whether to force a continuous +\item{force.continuous}{Logical. Whether to force a continuous distribution for the \sQuote{\code{plfit}} implementation, even if the sample vector contains integer values only (by chance). If this argument is false, igraph will assume a continuous distribution if at least one sample diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index ad394ca50aa..18fe4481f65 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -21,7 +21,7 @@ power_centrality( \item{nodes}{vertex sequence indicating which vertices are to be included in the calculation. By default, all vertices are included.} -\item{loops}{boolean indicating whether or not the diagonal should be +\item{loops}{Logical indicating whether or not the diagonal should be treated as valid data. Set this true if and only if the data can contain loops. \code{loops} is \code{FALSE} by default.} @@ -34,7 +34,7 @@ score; can be negative} \item{tol}{tolerance for near-singularities during matrix inversion (see \code{\link[=solve]{solve()}})} -\item{sparse}{Logical scalar, whether to use sparse matrices for the +\item{sparse}{Logical, whether to use sparse matrices for the calculation. The \sQuote{Matrix} package is required for sparse matrix support} diff --git a/man/preference.game.Rd b/man/preference.game.Rd index 08a72291ebc..736009aab8a 100644 --- a/man/preference.game.Rd +++ b/man/preference.game.Rd @@ -31,9 +31,9 @@ vertices with the different labels) in this case.} types. The matrix has \sQuote{types} rows and columns. When generating an undirected graph, it must be symmetric.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{loops}{Logical scalar, whether self-loops are allowed in the graph.} +\item{loops}{Logical, whether self-loops are allowed 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]}} diff --git a/man/print.igraph.Rd b/man/print.igraph.Rd index c3326c9fff2..2b34d4b1303 100644 --- a/man/print.igraph.Rd +++ b/man/print.igraph.Rd @@ -24,17 +24,17 @@ \arguments{ \item{x}{The graph to print.} -\item{full}{Logical scalar, whether to print the graph structure itself as +\item{full}{Logical, whether to print the graph structure itself as well.} -\item{graph.attributes}{Logical constant, whether to print graph attributes.} +\item{graph.attributes}{Logical, whether to print graph attributes.} -\item{vertex.attributes}{Logical constant, whether to print vertex +\item{vertex.attributes}{Logical, whether to print vertex attributes.} -\item{edge.attributes}{Logical constant, whether to print edge attributes.} +\item{edge.attributes}{Logical, whether to print edge attributes.} -\item{names}{Logical constant, whether to print symbolic vertex names (i.e. +\item{names}{Logical, whether to print symbolic vertex names (i.e. the \code{name} vertex attribute) or vertex IDs.} \item{max.lines}{The maximum number of lines to use. The rest of the diff --git a/man/reciprocity.Rd b/man/reciprocity.Rd index 3137202b17f..bc7be7c50aa 100644 --- a/man/reciprocity.Rd +++ b/man/reciprocity.Rd @@ -9,7 +9,7 @@ reciprocity(graph, ignore.loops = TRUE, mode = c("default", "ratio")) \arguments{ \item{graph}{The graph object.} -\item{ignore.loops}{Logical constant, whether to ignore loop edges.} +\item{ignore.loops}{Logical, whether to ignore loop edges.} \item{mode}{See below.} } diff --git a/man/sample_bipartite.Rd b/man/sample_bipartite.Rd index a78699aebdd..efd94a3b519 100644 --- a/man/sample_bipartite.Rd +++ b/man/sample_bipartite.Rd @@ -31,7 +31,7 @@ be given for \eqn{G(n,m)} graphs.} \item{m}{Integer scalar, the number of edges for \eqn{G(n,m)} graphs. Should not be given for \eqn{G(n,p)} graphs.} -\item{directed}{Logical scalar, whether to create a directed graph. See also +\item{directed}{Logical, whether to create a directed graph. See also the \code{mode} argument.} \item{mode}{Character scalar, specifies how to direct the edges in directed diff --git a/man/sample_bipartite_gnm.Rd b/man/sample_bipartite_gnm.Rd index 957233f648d..486f62b5e61 100644 --- a/man/sample_bipartite_gnm.Rd +++ b/man/sample_bipartite_gnm.Rd @@ -38,7 +38,7 @@ sample_bipartite_gnp( \item{...}{These dots are for future extensions and must be empty.} -\item{directed}{Logical scalar, whether to create a directed graph. See also +\item{directed}{Logical, whether to create a directed graph. See also the \code{mode} argument.} \item{mode}{Character scalar, specifies how to direct the edges in directed diff --git a/man/sample_correlated_gnp_pair.Rd b/man/sample_correlated_gnp_pair.Rd index 12da0d185f6..6126b98548a 100644 --- a/man/sample_correlated_gnp_pair.Rd +++ b/man/sample_correlated_gnp_pair.Rd @@ -16,7 +16,7 @@ adjacency matrix being used as a vector).} \item{p}{A numeric scalar, the probability of an edge between two vertices, it must in the open (0,1) interval.} -\item{directed}{Logical scalar, whether to generate directed graphs.} +\item{directed}{Logical, whether to generate directed graphs.} \item{permutation}{A numeric vector, a permutation vector that is applied on the vertices of the first graph, to get the second graph. If \code{NULL}, diff --git a/man/sample_dot_product.Rd b/man/sample_dot_product.Rd index 06e64e79de6..adc71799e9c 100644 --- a/man/sample_dot_product.Rd +++ b/man/sample_dot_product.Rd @@ -13,7 +13,7 @@ dot_product(vecs, directed = FALSE) \item{vecs}{A numeric matrix in which each latent position vector is a column.} -\item{directed}{A logical scalar, TRUE if the generated graph should be +\item{directed}{A Logical, TRUE if the generated graph should be directed.} } \value{ diff --git a/man/sample_fitness.Rd b/man/sample_fitness.Rd index 51fff2836d2..c7a6a00d449 100644 --- a/man/sample_fitness.Rd +++ b/man/sample_fitness.Rd @@ -25,9 +25,9 @@ specifies the in-fitness of each vertex. If this argument is not \code{NULL}, then a directed graph is generated, otherwise an undirected one.} -\item{loops}{Logical scalar, whether to allow loop edges in the graph.} +\item{loops}{Logical, whether to allow loop edges in the graph.} -\item{multiple}{Logical scalar, whether to allow multiple edges in the +\item{multiple}{Logical, whether to allow multiple edges in the graph.} } \value{ diff --git a/man/sample_fitness_pl.Rd b/man/sample_fitness_pl.Rd index 55bd441053a..d516b6ae3ad 100644 --- a/man/sample_fitness_pl.Rd +++ b/man/sample_fitness_pl.Rd @@ -29,12 +29,12 @@ undirected. If greater than or equal to 2, this argument specifies the exponent of the in-degree distribution. If non-negative but less than 2, an error will be generated.} -\item{loops}{Logical scalar, whether to allow loop edges in the graph.} +\item{loops}{Logical, whether to allow loop edges in the graph.} -\item{multiple}{Logical scalar, whether to allow multiple edges in the +\item{multiple}{Logical, whether to allow multiple edges in the graph.} -\item{finite.size.correction}{Logical scalar, whether to use the proposed +\item{finite.size.correction}{Logical, whether to use the proposed finite size correction of Cho et al., see references below.} } \value{ diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd index 5dceb938dc0..fda1a971932 100644 --- a/man/sample_forestfire.Rd +++ b/man/sample_forestfire.Rd @@ -16,7 +16,7 @@ probability is calculated as \code{bw.factor*fw.prob}.} \item{ambs}{The number of ambassador vertices.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} } \value{ A simple graph, possibly directed if the \code{directed} argument is diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd index 196f98225ba..a0a0909d03d 100644 --- a/man/sample_grg.Rd +++ b/man/sample_grg.Rd @@ -15,9 +15,9 @@ grg(nodes, radius, torus = FALSE, coords = FALSE) \item{radius}{The radius within which the vertices will be connected by an edge.} -\item{torus}{Logical constant, whether to use a torus instead of a square.} +\item{torus}{Logical, whether to use a torus instead of a square.} -\item{coords}{Logical scalar, whether to add the positions of the vertices +\item{coords}{Logical, whether to add the positions of the vertices as vertex attributes called \sQuote{\code{x}} and \sQuote{\code{y}}.} } \value{ diff --git a/man/sample_k_regular.Rd b/man/sample_k_regular.Rd index e4caf2e068b..5d3a5d5fad5 100644 --- a/man/sample_k_regular.Rd +++ b/man/sample_k_regular.Rd @@ -13,9 +13,9 @@ graph.} \item{k}{Integer scalar, the degree of each vertex in the graph, or the out-degree and in-degree in a directed graph.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{multiple}{Logical scalar, whether multiple edges are allowed.} +\item{multiple}{Logical, whether multiple edges are allowed.} } \value{ An igraph graph. diff --git a/man/sample_last_cit.Rd b/man/sample_last_cit.Rd index 9e5213b32c9..7d27aadd0c7 100644 --- a/man/sample_last_cit.Rd +++ b/man/sample_last_cit.Rd @@ -72,12 +72,12 @@ cit_cit_types( matrix (\code{sample_cit_cit_types()}) giving the (unnormalized) citation probabilities for the different vertex types.} -\item{directed}{Logical scalar, whether to generate directed networks.} +\item{directed}{Logical, whether to generate directed networks.} \item{types}{Vector of length \sQuote{\code{n}}, the types of the vertices. Types are numbered from zero.} -\item{attr}{Logical scalar, whether to add the vertex types to the generated +\item{attr}{Logical, whether to add the vertex types to the generated graph as a vertex attribute called \sQuote{\code{type}}.} } \value{ diff --git a/man/sample_pa_age.Rd b/man/sample_pa_age.Rd index 3f5539e7414..d700b28006c 100644 --- a/man/sample_pa_age.Rd +++ b/man/sample_pa_age.Rd @@ -60,10 +60,10 @@ add in each time step if \code{out.seq} is NULL. See details below.} \item{out.seq}{The number of edges to add in each time step, a vector containing as many elements as the number of vertices. See details below.} -\item{out.pref}{Logical constant, whether to include edges not initiated by +\item{out.pref}{Logical, whether to include edges not initiated by the vertex as a basis of preferential attachment. See details below.} -\item{directed}{Logical constant, whether to generate a directed graph. See +\item{directed}{Logical, whether to generate a directed graph. See details below.} \item{zero.deg.appeal}{The degree-dependent part of the diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd index 07647dcb261..3dd9dba6571 100644 --- a/man/sample_pref.Rd +++ b/man/sample_pref.Rd @@ -60,9 +60,9 @@ vertices with the different labels) in this case.} types. The matrix has \sQuote{types} rows and columns. When generating an undirected graph, it must be symmetric.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{loops}{Logical scalar, whether self-loops are allowed in the graph.} +\item{loops}{Logical, whether self-loops are allowed in the graph.} \item{type.dist.matrix}{The joint distribution of the in- and out-vertex types.} diff --git a/man/sample_sbm.Rd b/man/sample_sbm.Rd index aa296563ad3..a212d4c7229 100644 --- a/man/sample_sbm.Rd +++ b/man/sample_sbm.Rd @@ -21,9 +21,9 @@ must be symmetric.} \item{block.sizes}{Numeric vector giving the number of vertices in each group. The sum of the vector must match the number of vertices.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{loops}{Logical scalar, whether self-loops are allowed in the graph.} +\item{loops}{Logical, whether self-loops are allowed in the graph.} } \value{ An igraph graph. diff --git a/man/sample_smallworld.Rd b/man/sample_smallworld.Rd index 85023581127..013ba60b89b 100644 --- a/man/sample_smallworld.Rd +++ b/man/sample_smallworld.Rd @@ -19,10 +19,10 @@ the lattice will be connected.} \item{p}{Real constant between zero and one, the rewiring probability.} -\item{loops}{Logical scalar, whether loops edges are allowed in the +\item{loops}{Logical, whether loops edges are allowed in the generated graph.} -\item{multiple}{Logical scalar, whether multiple edges are allowed int the +\item{multiple}{Logical, whether multiple edges are allowed int the generated graph.} } \value{ diff --git a/man/sample_sphere_surface.Rd b/man/sample_sphere_surface.Rd index de850b1a2eb..aeb14bcc0e0 100644 --- a/man/sample_sphere_surface.Rd +++ b/man/sample_sphere_surface.Rd @@ -13,7 +13,7 @@ sample_sphere_surface(dim, n = 1, radius = 1, positive = TRUE) \item{radius}{Numeric scalar, the radius of the sphere to sample.} -\item{positive}{Logical scalar, whether to sample from the positive orthant +\item{positive}{Logical, whether to sample from the positive orthant of the sphere.} } \value{ diff --git a/man/sample_sphere_volume.Rd b/man/sample_sphere_volume.Rd index 739453d9af3..1051108f533 100644 --- a/man/sample_sphere_volume.Rd +++ b/man/sample_sphere_volume.Rd @@ -13,7 +13,7 @@ sample_sphere_volume(dim, n = 1, radius = 1, positive = TRUE) \item{radius}{Numeric scalar, the radius of the sphere to sample.} -\item{positive}{Logical scalar, whether to sample from the positive orthant +\item{positive}{Logical, whether to sample from the positive orthant of the sphere.} } \value{ diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd index 8cee59a29e3..74b257d95d6 100644 --- a/man/sample_traits_callaway.Rd +++ b/man/sample_traits_callaway.Rd @@ -56,7 +56,7 @@ stationary in time.} \item{pref.matrix}{A matrix giving the preferences of the given vertex types. These should be probabilities, i.e. numbers between zero and one.} -\item{directed}{Logical constant, whether to generate directed graphs.} +\item{directed}{Logical, whether to generate directed graphs.} \item{k}{The number of trials per time step, see details below.} } diff --git a/man/sbm.game.Rd b/man/sbm.game.Rd index 425139bbc01..38025e0f302 100644 --- a/man/sbm.game.Rd +++ b/man/sbm.game.Rd @@ -18,9 +18,9 @@ must be symmetric.} \item{block.sizes}{Numeric vector giving the number of vertices in each group. The sum of the vector must match the number of vertices.} -\item{directed}{Logical scalar, whether to create a directed graph.} +\item{directed}{Logical, whether to create a directed graph.} -\item{loops}{Logical scalar, whether self-loops are allowed in the graph.} +\item{loops}{Logical, whether self-loops are allowed 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]}} diff --git a/man/sir.Rd b/man/sir.Rd index 7dd2fc5dd61..d7afbfc5394 100644 --- a/man/sir.Rd +++ b/man/sir.Rd @@ -21,10 +21,10 @@ sir(graph, beta, gamma, no.sim = 100) \arguments{ \item{x}{A \code{sir} object, returned by the \code{sir()} function.} -\item{middle}{Logical scalar, whether to return the middle of the time bins, +\item{middle}{Logical, whether to return the middle of the time bins, or the boundaries.} -\item{na.rm}{Logical scalar, whether to ignore \code{NA} values. \code{sir} +\item{na.rm}{Logical, whether to ignore \code{NA} values. \code{sir} objects do not contain any \code{NA} values currently, so this argument is effectively ignored.} diff --git a/man/spinglass.community.Rd b/man/spinglass.community.Rd index 24969137b61..e04e60c98e1 100644 --- a/man/spinglass.community.Rd +++ b/man/spinglass.community.Rd @@ -39,7 +39,7 @@ limit for the number of communities. It is not a problem to supply a (reasonably) big number here, in which case some spin states will be unpopulated.} -\item{parupdate}{Logical constant, whether to update the spins of the +\item{parupdate}{Logical, whether to update the spins of the vertices in parallel (synchronously) or not. This argument is ignored if the second form of the function is used (i.e. the \sQuote{\code{vertex}} argument is present). It is also not implemented in the \dQuote{neg} implementation.} diff --git a/man/static.fitness.game.Rd b/man/static.fitness.game.Rd index 69fefe3db2b..54ca3cf53ac 100644 --- a/man/static.fitness.game.Rd +++ b/man/static.fitness.game.Rd @@ -25,9 +25,9 @@ specifies the in-fitness of each vertex. If this argument is not \code{NULL}, then a directed graph is generated, otherwise an undirected one.} -\item{loops}{Logical scalar, whether to allow loop edges in the graph.} +\item{loops}{Logical, whether to allow loop edges in the graph.} -\item{multiple}{Logical scalar, whether to allow multiple edges in the +\item{multiple}{Logical, whether to allow multiple edges in the graph.} } \description{ diff --git a/man/static.power.law.game.Rd b/man/static.power.law.game.Rd index 0f7b5af522c..77f359c4acd 100644 --- a/man/static.power.law.game.Rd +++ b/man/static.power.law.game.Rd @@ -29,12 +29,12 @@ undirected. If greater than or equal to 2, this argument specifies the exponent of the in-degree distribution. If non-negative but less than 2, an error will be generated.} -\item{loops}{Logical scalar, whether to allow loop edges in the graph.} +\item{loops}{Logical, whether to allow loop edges in the graph.} -\item{multiple}{Logical scalar, whether to allow multiple edges in the +\item{multiple}{Logical, whether to allow multiple edges in the graph.} -\item{finite.size.correction}{Logical scalar, whether to use the proposed +\item{finite.size.correction}{Logical, whether to use the proposed finite size correction of Cho et al., see references below.} } \description{ diff --git a/man/stochastic_matrix.Rd b/man/stochastic_matrix.Rd index 74573536f5a..74f19821678 100644 --- a/man/stochastic_matrix.Rd +++ b/man/stochastic_matrix.Rd @@ -16,7 +16,7 @@ stochastic_matrix( \item{column.wise}{If \code{FALSE}, then the rows of the stochastic matrix sum up to one; otherwise it is the columns.} -\item{sparse}{Logical scalar, whether to return a sparse matrix. The +\item{sparse}{Logical, whether to return a sparse matrix. The \code{Matrix} package is needed for sparse matrices.} } \value{ diff --git a/man/sub-.igraph.Rd b/man/sub-.igraph.Rd index 75dec0f58e1..b893ea5aa88 100644 --- a/man/sub-.igraph.Rd +++ b/man/sub-.igraph.Rd @@ -42,9 +42,9 @@ be present together with any of the \code{i} and \code{j} arguments and if it is present, then the \code{from} argument must be present as well.} -\item{sparse}{Logical scalar, whether to return sparse matrices.} +\item{sparse}{Logical, whether to return sparse matrices.} -\item{edges}{Logical scalar, whether to return edge IDs.} +\item{edges}{Logical, whether to return edge IDs.} \item{drop}{Ignored.} diff --git a/man/sub-sub-.igraph.Rd b/man/sub-sub-.igraph.Rd index d40e320baa2..18a46757e5d 100644 --- a/man/sub-sub-.igraph.Rd +++ b/man/sub-sub-.igraph.Rd @@ -29,10 +29,10 @@ well.} \item{...}{Additional arguments are not used currently.} -\item{directed}{Logical scalar, whether to consider edge directions +\item{directed}{Logical, whether to consider edge directions in directed graphs. It is ignored for undirected graphs.} -\item{edges}{Logical scalar, whether to return edge IDs.} +\item{edges}{Logical, whether to return edge IDs.} \item{exact}{Ignored.} } diff --git a/man/subgraph.Rd b/man/subgraph.Rd index 530e94f5635..af1db33f770 100644 --- a/man/subgraph.Rd +++ b/man/subgraph.Rd @@ -33,7 +33,7 @@ result graph.} \item{eids}{The edge IDs of the edges that will be kept in the result graph.} -\item{delete.vertices}{Logical scalar, whether to remove vertices that do +\item{delete.vertices}{Logical, whether to remove vertices that do not have any adjacent edges in \code{eids}.} } \value{ diff --git a/man/subgraph.centrality.Rd b/man/subgraph.centrality.Rd index 42823666163..ae93e36ddcb 100644 --- a/man/subgraph.centrality.Rd +++ b/man/subgraph.centrality.Rd @@ -9,7 +9,7 @@ subgraph.centrality(graph, diag = FALSE) \arguments{ \item{graph}{The input graph. It will be treated as undirected.} -\item{diag}{Boolean scalar, whether to include the diagonal of the adjacency +\item{diag}{Logical, whether to include the diagonal of the adjacency matrix in the analysis. Giving \code{FALSE} here effectively eliminates the loops edges from the graph before the calculation.} } diff --git a/man/subgraph.edges.Rd b/man/subgraph.edges.Rd index b8abc54aa49..903f76914bf 100644 --- a/man/subgraph.edges.Rd +++ b/man/subgraph.edges.Rd @@ -11,7 +11,7 @@ subgraph.edges(graph, eids, delete.vertices = TRUE) \item{eids}{The edge IDs of the edges that will be kept in the result graph.} -\item{delete.vertices}{Logical scalar, whether to remove vertices that do +\item{delete.vertices}{Logical, whether to remove vertices that do not have any adjacent edges in \code{eids}.} } \description{ diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd index 08bc7de6429..b18e46f7914 100644 --- a/man/subgraph_centrality.Rd +++ b/man/subgraph_centrality.Rd @@ -9,7 +9,7 @@ subgraph_centrality(graph, diag = FALSE) \arguments{ \item{graph}{The input graph. It will be treated as undirected.} -\item{diag}{Boolean scalar, whether to include the diagonal of the adjacency +\item{diag}{Logical, whether to include the diagonal of the adjacency matrix in the analysis. Giving \code{FALSE} here effectively eliminates the loops edges from the graph before the calculation.} } diff --git a/man/union.igraph.Rd b/man/union.igraph.Rd index 86f77adc40d..4814df7a1d9 100644 --- a/man/union.igraph.Rd +++ b/man/union.igraph.Rd @@ -10,7 +10,7 @@ \arguments{ \item{\dots}{Graph objects or lists of graph objects.} -\item{byname}{A logical scalar, or the character scalar \code{auto}. Whether +\item{byname}{A Logical, or the character scalar \code{auto}. Whether to perform the operation based on symbolic vertex names. If it is \code{auto}, that means \code{TRUE} if all graphs are named and \code{FALSE} otherwise. A warning is generated if \code{auto} and some (but not all) diff --git a/man/vertex.connectivity.Rd b/man/vertex.connectivity.Rd index 1f19fb5ab5b..1f0d02c964b 100644 --- a/man/vertex.connectivity.Rd +++ b/man/vertex.connectivity.Rd @@ -13,7 +13,7 @@ can be \code{NULL}, see details below.} \item{target}{The ID of the target vertex, for \code{vertex_connectivity()} it can be \code{NULL}, see details below.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the vertex connectivity is also one. It is a good idea to diff --git a/man/vertex_connectivity.Rd b/man/vertex_connectivity.Rd index 689c5e151e2..35896753127 100644 --- a/man/vertex_connectivity.Rd +++ b/man/vertex_connectivity.Rd @@ -22,7 +22,7 @@ can be \code{NULL}, see details below.} \item{target}{The ID of the target vertex, for \code{vertex_connectivity()} it can be \code{NULL}, see details below.} -\item{checks}{Logical constant. Whether to check that the graph is connected +\item{checks}{Logical. Whether to check that the graph is connected and also the degree of the vertices. If the graph is not (strongly) connected then the connectivity is obviously zero. Otherwise if the minimum degree is one then the vertex connectivity is also one. It is a good idea to diff --git a/man/walktrap.community.Rd b/man/walktrap.community.Rd index f8155fbc2fd..6f96f8022b3 100644 --- a/man/walktrap.community.Rd +++ b/man/walktrap.community.Rd @@ -28,14 +28,14 @@ walker. In other words, larger edge weights correspond to stronger connections.} \item{steps}{The length of the random walks to perform.} -\item{merges}{Logical scalar, whether to include the merge matrix in the +\item{merges}{Logical, whether to include the merge matrix in the result.} -\item{modularity}{Logical scalar, whether to include the vector of the +\item{modularity}{Logical, whether to include the vector of the modularity scores in the result. If the \code{membership} argument is true, then it will always be calculated.} -\item{membership}{Logical scalar, whether to calculate the membership vector +\item{membership}{Logical, whether to calculate the membership vector for the split corresponding to the highest modularity value.} } \description{ diff --git a/man/watts.strogatz.game.Rd b/man/watts.strogatz.game.Rd index 9d21b78996b..a3946533b33 100644 --- a/man/watts.strogatz.game.Rd +++ b/man/watts.strogatz.game.Rd @@ -16,10 +16,10 @@ the lattice will be connected.} \item{p}{Real constant between zero and one, the rewiring probability.} -\item{loops}{Logical scalar, whether loops edges are allowed in the +\item{loops}{Logical, whether loops edges are allowed in the generated graph.} -\item{multiple}{Logical scalar, whether multiple edges are allowed int the +\item{multiple}{Logical, whether multiple edges are allowed int the generated graph.} } \description{ diff --git a/man/which_multiple.Rd b/man/which_multiple.Rd index ac17d8dfe4f..52f8c687398 100644 --- a/man/which_multiple.Rd +++ b/man/which_multiple.Rd @@ -28,7 +28,7 @@ count_loops(graph) all edges in the graph.} } \value{ -\code{any_loop()} and \code{any_multiple()} return a logical scalar. +\code{any_loop()} and \code{any_multiple()} return a Logical. \code{which_loop()} and \code{which_multiple()} return a logical vector. \code{count_loops()} returns a numeric scalar with the total number of loop edges. \code{count_multiple()} returns a numeric vector. diff --git a/src/cpp11.cpp b/src/cpp11.cpp index dfbdf12f4fc..bababf63294 100644 --- a/src/cpp11.cpp +++ b/src/cpp11.cpp @@ -596,12 +596,10 @@ extern SEXP Rx_igraph_vs_adj(SEXP, SEXP, SEXP, SEXP); extern SEXP Rx_igraph_vs_nei(SEXP, SEXP, SEXP, SEXP); extern SEXP Rx_igraph_walktrap_community(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP Rx_igraph_weak_ref_key(SEXP); -extern SEXP Rx_igraph_weak_ref_run_finalizer(SEXP); extern SEXP Rx_igraph_weak_ref_value(SEXP); extern SEXP Rx_igraph_write_graph_dimacs(SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP Rx_igraph_write_graph_lgl(SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP Rx_igraph_write_graph_ncol(SEXP, SEXP, SEXP, SEXP); -extern SEXP UUID_gen(SEXP); static const R_CallMethodDef CallEntries[] = { {"R_igraph_add_edge", (DL_FUNC) &R_igraph_add_edge, 3}, @@ -1178,12 +1176,10 @@ static const R_CallMethodDef CallEntries[] = { {"Rx_igraph_vs_nei", (DL_FUNC) &Rx_igraph_vs_nei, 4}, {"Rx_igraph_walktrap_community", (DL_FUNC) &Rx_igraph_walktrap_community, 6}, {"Rx_igraph_weak_ref_key", (DL_FUNC) &Rx_igraph_weak_ref_key, 1}, - {"Rx_igraph_weak_ref_run_finalizer", (DL_FUNC) &Rx_igraph_weak_ref_run_finalizer, 1}, {"Rx_igraph_weak_ref_value", (DL_FUNC) &Rx_igraph_weak_ref_value, 1}, {"Rx_igraph_write_graph_dimacs", (DL_FUNC) &Rx_igraph_write_graph_dimacs, 5}, {"Rx_igraph_write_graph_lgl", (DL_FUNC) &Rx_igraph_write_graph_lgl, 5}, {"Rx_igraph_write_graph_ncol", (DL_FUNC) &Rx_igraph_write_graph_ncol, 4}, - {"UUID_gen", (DL_FUNC) &UUID_gen, 1}, {"_igraph_getsphere", (DL_FUNC) &_igraph_getsphere, 7}, {"_igraph_igraph_hcass2", (DL_FUNC) &_igraph_igraph_hcass2, 3}, {NULL, NULL, 0}