diff --git a/R/centrality.R b/R/centrality.R index a79e3410bed..ed73c9f6c60 100644 --- a/R/centrality.R +++ b/R/centrality.R @@ -390,7 +390,7 @@ betweenness.estimate <- estimate_betweenness #' @aliases betweenness.estimate #' @aliases edge.betweenness.estimate #' @param graph The graph to analyze. -#' @param v The vertices for which the vertex betweenness will be calculated. +#' @param vids The vertices for which the vertex betweenness will be calculated. #' @param directed Logical, whether directed paths should be considered while #' determining the shortest paths. #' @param weights Optional positive weight vector for calculating weighted @@ -411,7 +411,7 @@ betweenness.estimate <- estimate_betweenness #' @param cutoff The maximum shortest path length to consider when calculating #' betweenness. If negative, then there is no such limit. #' @return A numeric vector with the betweenness score for each vertex in -#' `v` for `betweenness()`. +#' `vids` for `betweenness()`. #' #' A numeric vector with the edge betweenness score for each edge in `e` #' for `edge_betweenness()`. @@ -438,7 +438,7 @@ betweenness.estimate <- estimate_betweenness #' betweenness <- function( graph, - v = V(graph), + vids = V(graph), directed = TRUE, weights = NULL, normalized = FALSE, @@ -446,7 +446,7 @@ betweenness <- function( ) { res <- betweenness_cutoff_impl( graph = graph, - vids = v, + vids = vids, directed = directed, weights = weights, cutoff = cutoff @@ -1800,7 +1800,7 @@ harmonic_centrality <- function( bonpow.dense <- function( graph, - nodes = V(graph), + vids = V(graph), loops = FALSE, exponent = 1, rescale = FALSE, @@ -1823,12 +1823,12 @@ bonpow.dense <- function( } else { ev <- ev * sqrt(n / sum((ev)^2)) } - ev[as.numeric(nodes)] + ev[as.numeric(vids)] } bonpow.sparse <- function( graph, - nodes = V(graph), + vids = V(graph), loops = FALSE, exponent = 1, rescale = FALSE, @@ -1856,7 +1856,7 @@ bonpow.sparse <- function( ev <- ev * sqrt(vcount(graph) / sum((ev)^2)) } - ev[as.numeric(nodes)] + ev[as.numeric(vids)] } @@ -1914,7 +1914,7 @@ bonpow.sparse <- function( #' is important to think about the edge direction and what it represents. #' #' @param graph the input graph. -#' @param nodes vertex sequence indicating which vertices are to be included in +#' @param vids 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 #' treated as valid data. Set this true if and only if the data can contain @@ -1975,22 +1975,22 @@ bonpow.sparse <- function( #' power_centrality <- function( graph, - nodes = V(graph), + vids = V(graph), loops = FALSE, exponent = 1, rescale = FALSE, tol = 1e-7, sparse = TRUE ) { - nodes <- as_igraph_vs(graph, nodes) + vids <- as_igraph_vs(graph, vids) if (sparse) { - res <- bonpow.sparse(graph, nodes, loops, exponent, rescale, tol) + res <- bonpow.sparse(graph, vids, loops, exponent, rescale, tol) } else { - res <- bonpow.dense(graph, nodes, loops, exponent, rescale, tol) + res <- bonpow.dense(graph, vids, loops, exponent, rescale, tol) } if (igraph_opt("add.vertex.names") && is_named(graph)) { - names(res) <- vertex_attr(graph, "name", nodes) + names(res) <- vertex_attr(graph, "name", vids) } res @@ -1998,7 +1998,7 @@ power_centrality <- function( alpha.centrality.dense <- function( graph, - nodes = V(graph), + vids = V(graph), alpha = 1, loops = FALSE, exo = 1, @@ -2037,12 +2037,12 @@ alpha.centrality.dense <- function( diag(id) <- 1 ev <- solve(id - alpha * d, tol = tol) %*% exo - ev[as.numeric(nodes)] + ev[as.numeric(vids)] } alpha.centrality.sparse <- function( graph, - nodes = V(graph), + vids = V(graph), alpha = 1, loops = FALSE, exo = 1, @@ -2092,7 +2092,7 @@ alpha.centrality.sparse <- function( M3 <- M2 - alpha * M r <- Matrix::solve(M3, tol = tol, exo) - r[as.numeric(nodes)] + r[as.numeric(vids)] } @@ -2114,7 +2114,7 @@ alpha.centrality.sparse <- function( #' #' @param graph The input graph, can be directed or undirected. In undirected #' graphs, edges are treated as if they were reciprocal directed ones. -#' @param nodes Vertex sequence, the vertices for which the alpha centrality +#' @param vids Vertex sequence, the vertices for which the alpha centrality #' values are returned. (For technical reasons they will be calculated for all #' vertices, anyway.) #' @param alpha Parameter specifying the relative importance of endogenous @@ -2160,7 +2160,7 @@ alpha.centrality.sparse <- function( #' alpha_centrality <- function( graph, - nodes = V(graph), + vids = V(graph), alpha = 1, loops = FALSE, exo = 1, @@ -2168,11 +2168,11 @@ alpha_centrality <- function( tol = 1e-7, sparse = TRUE ) { - nodes <- as_igraph_vs(graph, nodes) + vids <- as_igraph_vs(graph, vids) if (sparse) { res <- alpha.centrality.sparse( graph, - nodes, + vids, alpha, loops, exo, @@ -2182,7 +2182,7 @@ alpha_centrality <- function( } else { res <- alpha.centrality.dense( graph, - nodes, + vids, alpha, loops, exo, @@ -2191,7 +2191,7 @@ alpha_centrality <- function( ) } if (igraph_opt("add.vertex.names") && is_named(graph)) { - names(res) <- vertex_attr(graph, "name", nodes) + names(res) <- vertex_attr(graph, "name", vids) } res } diff --git a/R/cocitation.R b/R/cocitation.R index 01d9fdbfdbe..a190ddb8fd2 100644 --- a/R/cocitation.R +++ b/R/cocitation.R @@ -27,22 +27,22 @@ #' both cite, `bibcoupling()` calculates this. #' #' `cocitation()` calculates the cocitation counts for the vertices in the -#' `v` argument and all vertices in the graph. +#' `vids` argument and all vertices in the graph. #' #' `bibcoupling()` calculates the bibliographic coupling for vertices in -#' `v` and all vertices in the graph. +#' `vids` and all vertices in the graph. #' #' Calculating the cocitation or bibliographic coupling for only one vertex #' costs the same amount of computation as for all vertices. This might change #' in the future. #' #' @param graph The graph object to analyze -#' @param v Vertex sequence or numeric vector, the vertex ids for which the +#' @param vids Vertex sequence or numeric vector, the vertex ids for which the #' cocitation or bibliographic coupling values we want to calculate. The #' default is all vertices. -#' @return A numeric matrix with `length(v)` lines and +#' @return A numeric matrix with `length(vids)` lines and #' `vcount(graph)` columns. Element `(i,j)` contains the cocitation -#' or bibliographic coupling for vertices `v[i]` and `j`. +#' or bibliographic coupling for vertices `vids[i]` and `j`. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com} #' @family cocitation #' @export @@ -53,14 +53,14 @@ #' cocitation(g) #' bibcoupling(g) #' -cocitation <- function(graph, v = V(graph)) { +cocitation <- function(graph, vids = V(graph)) { ensure_igraph(graph) - v <- as_igraph_vs(graph, v) + vids <- as_igraph_vs(graph, vids) on.exit(.Call(R_igraph_finalizer)) - res <- .Call(Rx_igraph_cocitation, graph, v - 1) + res <- .Call(Rx_igraph_cocitation, graph, vids - 1) if (igraph_opt("add.vertex.names") && is_named(graph)) { - rownames(res) <- vertex_attr(graph, "name", v) + rownames(res) <- vertex_attr(graph, "name", vids) colnames(res) <- vertex_attr(graph, "name") } res @@ -68,14 +68,14 @@ cocitation <- function(graph, v = V(graph)) { #' @rdname cocitation #' @export -bibcoupling <- function(graph, v = V(graph)) { +bibcoupling <- function(graph, vids = V(graph)) { ensure_igraph(graph) - v <- as_igraph_vs(graph, v) + vids <- as_igraph_vs(graph, vids) on.exit(.Call(R_igraph_finalizer)) - res <- .Call(Rx_igraph_bibcoupling, graph, v - 1) + res <- .Call(Rx_igraph_bibcoupling, graph, vids - 1) if (igraph_opt("add.vertex.names") && is_named(graph)) { - rownames(res) <- vertex_attr(graph, "name", v) + rownames(res) <- vertex_attr(graph, "name", vids) colnames(res) <- vertex_attr(graph, "name") } res diff --git a/R/structural-properties.R b/R/structural-properties.R index 71f8bc54bbe..083d11bf4a0 100644 --- a/R/structural-properties.R +++ b/R/structural-properties.R @@ -875,7 +875,7 @@ mean_distance <- function( #' #' #' @param graph The graph to analyze. -#' @param v The ids of vertices of which the degree will be calculated. +#' @param vids The ids of vertices of which the degree will be calculated. #' @param mode Character string, \dQuote{out} for out-degree, \dQuote{in} for #' 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}. @@ -885,7 +885,7 @@ mean_distance <- function( #' number of vertices in the graph. #' @inheritParams rlang::args_dots_empty #' @return For `degree()` a numeric vector of the same length as argument -#' `v`. +#' `vids`. #' #' For `degree_distribution()` a numeric vector of the same length as the #' maximum degree plus one. The first element is the relative frequency zero @@ -913,18 +913,18 @@ mean_distance <- function( #' degree <- function( graph, - v = V(graph), + vids = V(graph), mode = c("all", "out", "in", "total"), loops = TRUE, normalized = FALSE ) { ensure_igraph(graph) - v <- as_igraph_vs(graph, v) + vids <- as_igraph_vs(graph, vids) mode <- igraph.match.arg(mode) res <- degree_impl( graph = graph, - vids = v, + vids = vids, mode = mode, loops = loops ) @@ -933,7 +933,7 @@ degree <- function( res <- res / (vcount(graph) - 1) } if (igraph_opt("add.vertex.names") && is_named(graph)) { - names(res) <- V(graph)$name[v] + names(res) <- V(graph)$name[vids] } res } @@ -1045,7 +1045,7 @@ degree_distribution <- function(graph, cumulative = FALSE, ...) { #' histogram. #' #' @param graph The graph to work on. -#' @param v Numeric vector, the vertices from which the shortest paths will be +#' @param vids Numeric vector, the vertices from which the shortest paths will be #' calculated. #' @param to Numeric vector, the vertices to which the shortest paths will be #' calculated. By default it includes all vertices. Note that for @@ -1082,7 +1082,7 @@ degree_distribution <- function(graph, cumulative = FALSE, ...) { #' FALSE, the length of the missing paths are considered as having infinite #' length, making the mean distance infinite as well. #' @return For `distances()` a numeric matrix with `length(to)` -#' columns and `length(v)` rows. The shortest path length from a vertex to +#' columns and `length(vids)` rows. The shortest path length from a vertex to #' itself is always zero. For unreachable vertices `Inf` is included. #' #' For `shortest_paths()` a named list with four entries is returned: @@ -1190,7 +1190,7 @@ degree_distribution <- function(graph, cumulative = FALSE, ...) { #' distances <- function( graph, - v = V(graph), + vids = V(graph), to = V(graph), mode = c("all", "out", "in"), weights = NULL, @@ -1212,7 +1212,7 @@ distances <- function( mode <- "out" } - v <- as_igraph_vs(graph, v) + vids <- as_igraph_vs(graph, vids) to <- as_igraph_vs(graph, to) mode <- igraph.match.arg(mode) mode <- switch(mode, "out" = 1, "in" = 2, "all" = 3) @@ -1248,7 +1248,7 @@ distances <- function( res <- .Call( R_igraph_shortest_paths, graph, - v - 1, + vids - 1, to - 1, as.numeric(mode), weights, @@ -1256,7 +1256,7 @@ distances <- function( ) if (igraph_opt("add.vertex.names") && is_named(graph)) { - rownames(res) <- V(graph)$name[v] + rownames(res) <- V(graph)$name[vids] colnames(res) <- V(graph)$name[to] } res @@ -1914,7 +1914,7 @@ transitivity <- function( #' graph adjacency matrix. For isolated vertices, constraint is undefined. #' #' @param graph A graph object, the input graph. -#' @param nodes The vertices for which the constraint will be calculated. +#' @param vids The vertices for which the constraint will be calculated. #' Defaults to all vertices. #' @param weights The weights of the edges. If this is `NULL` and there is #' a `weight` edge attribute this is used. If there is no such edge @@ -1933,9 +1933,9 @@ transitivity <- function( #' g <- sample_gnp(20, 5 / 20) #' constraint(g) #' -constraint <- function(graph, nodes = V(graph), weights = NULL) { +constraint <- function(graph, vids = V(graph), weights = NULL) { ensure_igraph(graph) - nodes <- as_igraph_vs(graph, nodes) + vids <- as_igraph_vs(graph, vids) if (is.null(weights)) { if ("weight" %in% edge_attr_names(graph)) { @@ -1944,9 +1944,9 @@ constraint <- function(graph, nodes = V(graph), weights = NULL) { } on.exit(.Call(R_igraph_finalizer)) - res <- .Call(Rx_igraph_constraint, graph, nodes - 1, as.numeric(weights)) + res <- .Call(Rx_igraph_constraint, graph, vids - 1, as.numeric(weights)) if (igraph_opt("add.vertex.names") && is_named(graph)) { - names(res) <- V(graph)$name[nodes] + names(res) <- V(graph)$name[vids] } res } @@ -2049,7 +2049,7 @@ edge_density <- function(graph, loops = FALSE) { ego_size <- function( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) { @@ -2062,7 +2062,7 @@ ego_size <- function( .Call( R_igraph_neighborhood_size, graph, - as_igraph_vs(graph, nodes) - 1, + as_igraph_vs(graph, vids) - 1, as.numeric(order), as.numeric(mode), mindist @@ -2105,7 +2105,7 @@ neighborhood_size <- ego_size #' @param graph The input graph. #' @param order Integer giving the order of the neighborhood. Negative values #' indicate an infinite order. -#' @param nodes The vertices for which the calculation is performed. +#' @param vids The vertices for which the calculation is performed. #' @param mode Character constant, it specifies how to use the direction of #' the edges if a directed graph is analyzed. For \sQuote{out} only the #' outgoing edges are followed, so all vertices reachable from the source @@ -2163,7 +2163,7 @@ neighborhood_size <- ego_size ego <- function( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) { @@ -2176,7 +2176,7 @@ ego <- function( res <- .Call( R_igraph_neighborhood, graph, - as_igraph_vs(graph, nodes) - 1, + as_igraph_vs(graph, vids) - 1, as.numeric(order), as.numeric(mode), mindist @@ -2198,7 +2198,7 @@ neighborhood <- ego make_ego_graph <- function( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) { @@ -2211,7 +2211,7 @@ make_ego_graph <- function( res <- .Call( R_igraph_neighborhood_graphs, graph, - as_igraph_vs(graph, nodes) - 1, + as_igraph_vs(graph, vids) - 1, as.numeric(order), as.integer(mode), mindist diff --git a/man/alpha.centrality.Rd b/man/alpha.centrality.Rd index 530eedc75c4..a4fd36b81a1 100644 --- a/man/alpha.centrality.Rd +++ b/man/alpha.centrality.Rd @@ -19,10 +19,6 @@ alpha.centrality( \item{graph}{The input graph, can be directed or undirected. In undirected graphs, edges are treated as if they were reciprocal directed ones.} -\item{nodes}{Vertex sequence, the vertices for which the alpha centrality -values are returned. (For technical reasons they will be calculated for all -vertices, anyway.)} - \item{alpha}{Parameter specifying the relative importance of endogenous versus exogenous factors in the determination of centrality. See details below.} diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd index b41a3223e03..ff70035bb14 100644 --- a/man/alpha_centrality.Rd +++ b/man/alpha_centrality.Rd @@ -6,7 +6,7 @@ \usage{ alpha_centrality( graph, - nodes = V(graph), + vids = V(graph), alpha = 1, loops = FALSE, exo = 1, @@ -19,7 +19,7 @@ alpha_centrality( \item{graph}{The input graph, can be directed or undirected. In undirected graphs, edges are treated as if they were reciprocal directed ones.} -\item{nodes}{Vertex sequence, the vertices for which the alpha centrality +\item{vids}{Vertex sequence, the vertices for which the alpha centrality values are returned. (For technical reasons they will be calculated for all vertices, anyway.)} diff --git a/man/betweenness.Rd b/man/betweenness.Rd index 085d04c5232..cb484536806 100644 --- a/man/betweenness.Rd +++ b/man/betweenness.Rd @@ -9,7 +9,7 @@ \usage{ betweenness( graph, - v = V(graph), + vids = V(graph), directed = TRUE, weights = NULL, normalized = FALSE, @@ -27,7 +27,7 @@ edge_betweenness( \arguments{ \item{graph}{The graph to analyze.} -\item{v}{The vertices for which the vertex betweenness will be calculated.} +\item{vids}{The vertices for which the vertex betweenness will be calculated.} \item{directed}{Logical, whether directed paths should be considered while determining the shortest paths.} @@ -56,7 +56,7 @@ betweenness. If negative, then there is no such limit.} } \value{ A numeric vector with the betweenness score for each vertex in -\code{v} for \code{betweenness()}. +\code{vids} for \code{betweenness()}. A numeric vector with the edge betweenness score for each edge in \code{e} for \code{edge_betweenness()}. diff --git a/man/bonpow.Rd b/man/bonpow.Rd index 4377272047a..1830d90750b 100644 --- a/man/bonpow.Rd +++ b/man/bonpow.Rd @@ -17,9 +17,6 @@ bonpow( \arguments{ \item{graph}{the input graph.} -\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 treated as valid data. Set this true if and only if the data can contain loops. \code{loops} is \code{FALSE} by default.} diff --git a/man/cocitation.Rd b/man/cocitation.Rd index 8a6e5f8826d..06f22fdc474 100644 --- a/man/cocitation.Rd +++ b/man/cocitation.Rd @@ -5,21 +5,21 @@ \alias{bibcoupling} \title{Cocitation coupling} \usage{ -cocitation(graph, v = V(graph)) +cocitation(graph, vids = V(graph)) -bibcoupling(graph, v = V(graph)) +bibcoupling(graph, vids = V(graph)) } \arguments{ \item{graph}{The graph object to analyze} -\item{v}{Vertex sequence or numeric vector, the vertex ids for which the +\item{vids}{Vertex sequence or numeric vector, the vertex ids for which the cocitation or bibliographic coupling values we want to calculate. The default is all vertices.} } \value{ -A numeric matrix with \code{length(v)} lines and +A numeric matrix with \code{length(vids)} lines and \code{vcount(graph)} columns. Element \verb{(i,j)} contains the cocitation -or bibliographic coupling for vertices \code{v[i]} and \code{j}. +or bibliographic coupling for vertices \code{vids[i]} and \code{j}. } \description{ Two vertices are cocited if there is another vertex citing both of them. @@ -29,10 +29,10 @@ both cite, \code{bibcoupling()} calculates this. } \details{ \code{cocitation()} calculates the cocitation counts for the vertices in the -\code{v} argument and all vertices in the graph. +\code{vids} argument and all vertices in the graph. \code{bibcoupling()} calculates the bibliographic coupling for vertices in -\code{v} and all vertices in the graph. +\code{vids} and all vertices in the graph. Calculating the cocitation or bibliographic coupling for only one vertex costs the same amount of computation as for all vertices. This might change diff --git a/man/constraint.Rd b/man/constraint.Rd index ae337644aa5..90ee1aeed23 100644 --- a/man/constraint.Rd +++ b/man/constraint.Rd @@ -4,12 +4,12 @@ \alias{constraint} \title{Burt's constraint} \usage{ -constraint(graph, nodes = V(graph), weights = NULL) +constraint(graph, vids = V(graph), weights = NULL) } \arguments{ \item{graph}{A graph object, the input graph.} -\item{nodes}{The vertices for which the constraint will be calculated. +\item{vids}{The vertices for which the constraint will be calculated. Defaults to all vertices.} \item{weights}{The weights of the edges. If this is \code{NULL} and there is diff --git a/man/degree.Rd b/man/degree.Rd index 2bd19522f86..b22354eb021 100644 --- a/man/degree.Rd +++ b/man/degree.Rd @@ -9,7 +9,7 @@ \usage{ degree( graph, - v = V(graph), + vids = V(graph), mode = c("all", "out", "in", "total"), loops = TRUE, normalized = FALSE @@ -30,7 +30,7 @@ degree_distribution(graph, cumulative = FALSE, ...) \arguments{ \item{graph}{The graph to analyze.} -\item{v}{The ids of vertices of which the degree will be calculated.} +\item{vids}{The ids of vertices of which the degree will be calculated.} \item{mode}{Character string, \dQuote{out} for out-degree, \dQuote{in} for in-degree or \dQuote{total} for the sum of the two. For undirected graphs @@ -49,7 +49,7 @@ be calculated.} } \value{ For \code{degree()} a numeric vector of the same length as argument -\code{v}. +\code{vids}. For \code{degree_distribution()} a numeric vector of the same length as the maximum degree plus one. The first element is the relative frequency zero diff --git a/man/distances.Rd b/man/distances.Rd index 96ffa1c2860..c4382a77965 100644 --- a/man/distances.Rd +++ b/man/distances.Rd @@ -20,7 +20,7 @@ mean_distance( distances( graph, - v = V(graph), + vids = V(graph), to = V(graph), mode = c("all", "out", "in"), weights = NULL, @@ -71,7 +71,7 @@ Functions accepting this argument (like \code{mean_distance()}) return additional information like the number of disconnected vertex pairs in the result when this parameter is set to \code{TRUE}.} -\item{v}{Numeric vector, the vertices from which the shortest paths will be +\item{vids}{Numeric vector, the vertices from which the shortest paths will be calculated.} \item{to}{Numeric vector, the vertices to which the shortest paths will be @@ -124,7 +124,7 @@ are reached.} } \value{ For \code{distances()} a numeric matrix with \code{length(to)} -columns and \code{length(v)} rows. The shortest path length from a vertex to +columns and \code{length(vids)} rows. The shortest path length from a vertex to itself is always zero. For unreachable vertices \code{Inf} is included. For \code{shortest_paths()} a named list with four entries is returned: diff --git a/man/ego.Rd b/man/ego.Rd index 69c018240fe..9bd13311743 100644 --- a/man/ego.Rd +++ b/man/ego.Rd @@ -16,7 +16,7 @@ connect(graph, order, mode = c("all", "out", "in", "total")) ego_size( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -24,7 +24,7 @@ ego_size( neighborhood_size( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -32,7 +32,7 @@ neighborhood_size( ego( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -40,7 +40,7 @@ ego( neighborhood( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -48,7 +48,7 @@ neighborhood( make_ego_graph( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -56,7 +56,7 @@ make_ego_graph( make_neighborhood_graph( graph, order = 1, - nodes = V(graph), + vids = V(graph), mode = c("all", "out", "in"), mindist = 0 ) @@ -75,7 +75,7 @@ vertices from which the source vertex is reachable in at most \code{order} steps are counted. \sQuote{"all"} ignores the direction of the edges. This argument is ignored for undirected graphs.} -\item{nodes}{The vertices for which the calculation is performed.} +\item{vids}{The vertices for which the calculation is performed.} \item{mindist}{The minimum distance to include the vertex in the result.} } diff --git a/man/graph.neighborhood.Rd b/man/graph.neighborhood.Rd index 5e322a65d4b..f013c37a900 100644 --- a/man/graph.neighborhood.Rd +++ b/man/graph.neighborhood.Rd @@ -18,8 +18,6 @@ graph.neighborhood( \item{order}{Integer giving the order of the neighborhood. Negative values indicate an infinite order.} -\item{nodes}{The vertices for which the calculation is performed.} - \item{mode}{Character constant, it specifies how to use the direction of the edges if a directed graph is analyzed. For \sQuote{out} only the outgoing edges are followed, so all vertices reachable from the source diff --git a/man/neighborhood.size.Rd b/man/neighborhood.size.Rd index b52295c6916..7e9aae8cf08 100644 --- a/man/neighborhood.size.Rd +++ b/man/neighborhood.size.Rd @@ -18,8 +18,6 @@ neighborhood.size( \item{order}{Integer giving the order of the neighborhood. Negative values indicate an infinite order.} -\item{nodes}{The vertices for which the calculation is performed.} - \item{mode}{Character constant, it specifies how to use the direction of the edges if a directed graph is analyzed. For \sQuote{out} only the outgoing edges are followed, so all vertices reachable from the source diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd index aeb2c85dd24..927a6e714f4 100644 --- a/man/power_centrality.Rd +++ b/man/power_centrality.Rd @@ -6,7 +6,7 @@ \usage{ power_centrality( graph, - nodes = V(graph), + vids = V(graph), loops = FALSE, exponent = 1, rescale = FALSE, @@ -17,7 +17,7 @@ power_centrality( \arguments{ \item{graph}{the input graph.} -\item{nodes}{vertex sequence indicating which vertices are to be included in +\item{vids}{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 diff --git a/man/shortest.paths.Rd b/man/shortest.paths.Rd index f1d4343de3d..801c6089ccb 100644 --- a/man/shortest.paths.Rd +++ b/man/shortest.paths.Rd @@ -16,9 +16,6 @@ shortest.paths( \arguments{ \item{graph}{The graph to work on.} -\item{v}{Numeric vector, the vertices from which the shortest paths will be -calculated.} - \item{to}{Numeric vector, the vertices to which the shortest paths will be calculated. By default it includes all vertices. Note that for \code{distances()} every vertex must be included here at most once. (This