From eecb40dbddbf8db9b21ce209f515e99179af92b6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Oct 2025 23:05:21 +0000
Subject: [PATCH 1/4] Initial plan


From 82728d86efcdb09eb4174c57749489cf4e3f2db7 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Oct 2025 23:45:00 +0000
Subject: [PATCH 2/4] Rename 'nodes' to 'n' in game generator functions

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>
---
 R/games.R                         | 44 +++++++++++++++----------------
 man/asymmetric.preference.game.Rd |  2 --
 man/callaway.traits.game.Rd       |  2 --
 man/establishment.game.Rd         |  2 --
 man/forest.fire.game.Rd           |  2 --
 man/grg.game.Rd                   |  2 --
 man/preference.game.Rd            |  2 --
 man/sample_forestfire.Rd          |  4 +--
 man/sample_grg.Rd                 |  4 +--
 man/sample_pref.Rd                |  6 ++---
 man/sample_traits_callaway.Rd     |  6 ++---
 11 files changed, 32 insertions(+), 44 deletions(-)

diff --git a/R/games.R b/R/games.R
index 57a106e4d9e..e0b505aed16 100644
--- a/R/games.R
+++ b/R/games.R
@@ -150,7 +150,7 @@ preference.game <- function(
   # nocov start
   lifecycle::deprecate_soft("2.0.0", "preference.game()", "sample_pref()")
   sample_pref(
-    nodes = nodes,
+    n = nodes,
     types = types,
     type.dist = type.dist,
     fixed.sizes = fixed.sizes,
@@ -252,7 +252,7 @@ interconnected.islands.game <- function(
 grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) {
   # nocov start
   lifecycle::deprecate_soft("2.0.0", "grg.game()", "sample_grg()")
-  sample_grg(nodes = nodes, radius = radius, torus = torus, coords = coords)
+  sample_grg(n = nodes, radius = radius, torus = torus, coords = coords)
 } # nocov end
 
 #' Growing random graph generation
@@ -299,7 +299,7 @@ forest.fire.game <- function(
     "sample_forestfire()"
   )
   sample_forestfire(
-    nodes = nodes,
+    n = nodes,
     fw.prob = fw.prob,
     bw.factor = bw.factor,
     ambs = ambs,
@@ -328,7 +328,7 @@ establishment.game <- function(
   # nocov start
   lifecycle::deprecate_soft("2.0.0", "establishment.game()", "sample_traits()")
   sample_traits(
-    nodes = nodes,
+    n = nodes,
     types = types,
     k = k,
     type.dist = type.dist,
@@ -470,7 +470,7 @@ callaway.traits.game <- function(
     "sample_traits_callaway()"
   )
   sample_traits_callaway(
-    nodes = nodes,
+    n = nodes,
     types = types,
     edge.per.step = edge.per.step,
     type.dist = type.dist,
@@ -615,7 +615,7 @@ asymmetric.preference.game <- function(
     "sample_asym_pref()"
   )
   sample_asym_pref(
-    nodes = nodes,
+    n = nodes,
     types = types,
     type.dist.matrix = type.dist.matrix,
     pref.matrix = pref.matrix,
@@ -1729,7 +1729,7 @@ pa_age <- function(...) constructor_spec(sample_pa_age, ...)
 #' depends on the types of the vertices involved and is taken from
 #' `pref.matrix`.
 #'
-#' @param nodes The number of vertices in the graph.
+#' @param n The number of vertices in the graph.
 #' @param types The number of different vertex types.
 #' @param edge.per.step The number of edges to add to the graph per time step.
 #' @param type.dist The distribution of the vertex types. This is assumed to be
@@ -1749,7 +1749,7 @@ pa_age <- function(...) constructor_spec(sample_pa_age, ...)
 #' g1 <- sample_traits_callaway(1000, 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2))
 #' g2 <- sample_traits(1000, 2, k = 2, pref.matrix = matrix(c(1, 0, 0, 1), ncol = 2))
 sample_traits_callaway <- function(
-  nodes,
+  n,
   types,
   edge.per.step = 1,
   type.dist = rep(1, types),
@@ -1759,7 +1759,7 @@ sample_traits_callaway <- function(
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
     R_igraph_callaway_traits_game,
-    as.double(nodes),
+    as.double(n),
     as.double(types),
     as.double(edge.per.step),
     as.double(type.dist),
@@ -1789,7 +1789,7 @@ traits_callaway <- function(...) constructor_spec(sample_traits_callaway, ...)
 #' @rdname sample_traits_callaway
 #' @export
 sample_traits <- function(
-  nodes,
+  n,
   types,
   k = 1,
   type.dist = rep(1, types),
@@ -1799,7 +1799,7 @@ sample_traits <- function(
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
     R_igraph_establishment_game,
-    as.double(nodes),
+    as.double(n),
     as.double(types),
     as.double(k),
     as.double(type.dist),
@@ -1833,7 +1833,7 @@ traits <- function(...) constructor_spec(sample_traits, ...)
 #' Euclidean norm than a given radius. If the `torus` argument is
 #' `TRUE` then a unit area torus is used instead of a square.
 #'
-#' @param nodes The number of vertices in the graph.
+#' @param n 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.
@@ -1851,11 +1851,11 @@ traits <- function(...) constructor_spec(sample_traits, ...)
 #' g <- sample_grg(1000, 0.05, torus = FALSE)
 #' g2 <- sample_grg(1000, 0.05, torus = TRUE)
 #'
-sample_grg <- function(nodes, radius, torus = FALSE, coords = FALSE) {
+sample_grg <- function(n, radius, torus = FALSE, coords = FALSE) {
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
     R_igraph_grg_game,
-    as.double(nodes),
+    as.double(n),
     as.double(radius),
     as.logical(torus),
     as.logical(coords)
@@ -1901,7 +1901,7 @@ grg <- function(...) constructor_spec(sample_grg, ...)
 #' `type` vertex attribute for `sample_pref()` and from the
 #' `intype` and `outtype` vertex attribute for `sample_asym_pref()`.
 #'
-#' @param nodes The number of vertices in the graphs.
+#' @param n The number of vertices in the graphs.
 #' @param types The number of different vertex types.
 #' @param type.dist The distribution of the vertex types, a numeric vector of
 #'   length \sQuote{types} containing non-negative numbers. The vector will be
@@ -1938,7 +1938,7 @@ grg <- function(...) constructor_spec(sample_grg, ...)
 #' tkplot(g, layout = layout_in_circle)
 #'
 sample_pref <- function(
-  nodes,
+  n,
   types,
   type.dist = rep(1, types),
   fixed.sizes = FALSE,
@@ -1956,7 +1956,7 @@ sample_pref <- function(
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
     R_igraph_preference_game,
-    as.numeric(nodes),
+    as.numeric(n),
     as.numeric(types),
     as.double(type.dist),
     as.logical(fixed.sizes),
@@ -1985,7 +1985,7 @@ pref <- function(...) constructor_spec(sample_pref, ...)
 #' @rdname sample_pref
 #' @export
 sample_asym_pref <- function(
-  nodes,
+  n,
   types,
   type.dist.matrix = matrix(1, types, types),
   pref.matrix = matrix(1, types, types),
@@ -2007,7 +2007,7 @@ sample_asym_pref <- function(
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
     R_igraph_asymmetric_preference_game,
-    as.numeric(nodes),
+    as.numeric(n),
     as.numeric(types),
     as.numeric(types),
     matrix(as.double(type.dist.matrix), types, types),
@@ -3120,7 +3120,7 @@ sample_fitness_pl <- function(
 #' available then we cite all of them.  \item The same procedure is applied to
 #' all the newly cited vertices.  }
 #'
-#' @param nodes The number of vertices in the graph.
+#' @param n The number of vertices in the graph.
 #' @param fw.prob The forward burning probability, see details below.
 #' @param bw.factor The backward burning ratio. The backward burning
 #'   probability is calculated as `bw.factor*fw.prob`.
@@ -3157,14 +3157,14 @@ sample_fitness_pl <- function(
 #' points(seq(along.with = dd2) - 1, dd2, col = 2, pch = 2)
 #' @cdocs igraph_forest_fire_game
 sample_forestfire <- function(
-  nodes,
+  n,
   fw.prob,
   bw.factor = 1,
   ambs = 1,
   directed = TRUE
 ) {
   forest_fire_game_impl(
-    nodes = nodes,
+    nodes = n,
     fw.prob = fw.prob,
     bw.factor = bw.factor,
     ambs = ambs,
diff --git a/man/asymmetric.preference.game.Rd b/man/asymmetric.preference.game.Rd
index 00b6b8a1494..6e362bc21b3 100644
--- a/man/asymmetric.preference.game.Rd
+++ b/man/asymmetric.preference.game.Rd
@@ -13,8 +13,6 @@ asymmetric.preference.game(
 )
 }
 \arguments{
-\item{nodes}{The number of vertices in the graphs.}
-
 \item{types}{The number of different vertex types.}
 
 \item{type.dist.matrix}{The joint distribution of the in- and out-vertex
diff --git a/man/callaway.traits.game.Rd b/man/callaway.traits.game.Rd
index 532d56b26a1..e2bf60f03b6 100644
--- a/man/callaway.traits.game.Rd
+++ b/man/callaway.traits.game.Rd
@@ -14,8 +14,6 @@ callaway.traits.game(
 )
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
-
 \item{types}{The number of different vertex types.}
 
 \item{edge.per.step}{The number of edges to add to the graph per time step.}
diff --git a/man/establishment.game.Rd b/man/establishment.game.Rd
index 5147127c9ba..80c68934ea9 100644
--- a/man/establishment.game.Rd
+++ b/man/establishment.game.Rd
@@ -14,8 +14,6 @@ establishment.game(
 )
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
-
 \item{types}{The number of different vertex types.}
 
 \item{k}{The number of trials per time step, see details below.}
diff --git a/man/forest.fire.game.Rd b/man/forest.fire.game.Rd
index 574211f1df1..180d6a879d0 100644
--- a/man/forest.fire.game.Rd
+++ b/man/forest.fire.game.Rd
@@ -7,8 +7,6 @@
 forest.fire.game(nodes, fw.prob, bw.factor = 1, ambs = 1, directed = TRUE)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
-
 \item{fw.prob}{The forward burning probability, see details below.}
 
 \item{bw.factor}{The backward burning ratio. The backward burning
diff --git a/man/grg.game.Rd b/man/grg.game.Rd
index 4c430f572d5..20a0895322b 100644
--- a/man/grg.game.Rd
+++ b/man/grg.game.Rd
@@ -7,8 +7,6 @@
 grg.game(nodes, radius, torus = FALSE, coords = FALSE)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
-
 \item{radius}{The radius within which the vertices will be connected by an
 edge.}
 
diff --git a/man/preference.game.Rd b/man/preference.game.Rd
index 2cd83f95a8c..5453e80a4c4 100644
--- a/man/preference.game.Rd
+++ b/man/preference.game.Rd
@@ -15,8 +15,6 @@ preference.game(
 )
 }
 \arguments{
-\item{nodes}{The number of vertices in the graphs.}
-
 \item{types}{The number of different vertex types.}
 
 \item{type.dist}{The distribution of the vertex types, a numeric vector of
diff --git a/man/sample_forestfire.Rd b/man/sample_forestfire.Rd
index 76eff55ac99..378df20da1c 100644
--- a/man/sample_forestfire.Rd
+++ b/man/sample_forestfire.Rd
@@ -4,10 +4,10 @@
 \alias{sample_forestfire}
 \title{Forest Fire Network Model}
 \usage{
-sample_forestfire(nodes, fw.prob, bw.factor = 1, ambs = 1, directed = TRUE)
+sample_forestfire(n, fw.prob, bw.factor = 1, ambs = 1, directed = TRUE)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
+\item{n}{The number of vertices in the graph.}
 
 \item{fw.prob}{The forward burning probability, see details below.}
 
diff --git a/man/sample_grg.Rd b/man/sample_grg.Rd
index 009fcf6f650..89ae93047ca 100644
--- a/man/sample_grg.Rd
+++ b/man/sample_grg.Rd
@@ -5,12 +5,12 @@
 \alias{grg}
 \title{Geometric random graphs}
 \usage{
-sample_grg(nodes, radius, torus = FALSE, coords = FALSE)
+sample_grg(n, radius, torus = FALSE, coords = FALSE)
 
 grg(...)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
+\item{n}{The number of vertices in the graph.}
 
 \item{radius}{The radius within which the vertices will be connected by an
 edge.}
diff --git a/man/sample_pref.Rd b/man/sample_pref.Rd
index 43aadaa2faa..2aee8e1a4b5 100644
--- a/man/sample_pref.Rd
+++ b/man/sample_pref.Rd
@@ -8,7 +8,7 @@
 \title{Trait-based random generation}
 \usage{
 sample_pref(
-  nodes,
+  n,
   types,
   type.dist = rep(1, types),
   fixed.sizes = FALSE,
@@ -20,7 +20,7 @@ sample_pref(
 pref(...)
 
 sample_asym_pref(
-  nodes,
+  n,
   types,
   type.dist.matrix = matrix(1, types, types),
   pref.matrix = matrix(1, types, types),
@@ -30,7 +30,7 @@ sample_asym_pref(
 asym_pref(...)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graphs.}
+\item{n}{The number of vertices in the graphs.}
 
 \item{types}{The number of different vertex types.}
 
diff --git a/man/sample_traits_callaway.Rd b/man/sample_traits_callaway.Rd
index 7d7886783e0..31ebfa1bba4 100644
--- a/man/sample_traits_callaway.Rd
+++ b/man/sample_traits_callaway.Rd
@@ -8,7 +8,7 @@
 \title{Graph generation based on different vertex types}
 \usage{
 sample_traits_callaway(
-  nodes,
+  n,
   types,
   edge.per.step = 1,
   type.dist = rep(1, types),
@@ -19,7 +19,7 @@ sample_traits_callaway(
 traits_callaway(...)
 
 sample_traits(
-  nodes,
+  n,
   types,
   k = 1,
   type.dist = rep(1, types),
@@ -30,7 +30,7 @@ sample_traits(
 traits(...)
 }
 \arguments{
-\item{nodes}{The number of vertices in the graph.}
+\item{n}{The number of vertices in the graph.}
 
 \item{types}{The number of different vertex types.}
 

From 457cd86c0d617fc512e200d02818e2c5873aebff Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Oct 2025 23:53:36 +0000
Subject: [PATCH 3/4] Rename 'nodes' to 'vertices' in centrality and structural
 functions

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>
---
 R/centrality.R            | 24 ++++++++++++------------
 R/structural-properties.R | 24 ++++++++++++------------
 man/alpha.centrality.Rd   |  4 ----
 man/alpha_centrality.Rd   |  4 ++--
 man/bonpow.Rd             |  3 ---
 man/constraint.Rd         |  4 ++--
 man/ego.Rd                | 14 +++++++-------
 man/graph.neighborhood.Rd |  2 --
 man/neighborhood.size.Rd  |  2 --
 man/page.rank.Rd          |  2 --
 man/page_rank.Rd          |  4 ++--
 man/power_centrality.Rd   |  4 ++--
 12 files changed, 39 insertions(+), 52 deletions(-)

diff --git a/R/centrality.R b/R/centrality.R
index fec7751b215..7d6c107ddfe 100644
--- a/R/centrality.R
+++ b/R/centrality.R
@@ -43,7 +43,7 @@ page.rank <- function(
   page_rank(
     graph = graph,
     algo = algo,
-    vids = vids,
+    vertices = vids,
     directed = directed,
     damping = damping,
     personalized = personalized,
@@ -255,7 +255,7 @@ bonpow <- function(
   lifecycle::deprecate_soft("2.0.0", "bonpow()", "power_centrality()")
   power_centrality(
     graph = graph,
-    nodes = nodes,
+    vertices = nodes,
     loops = loops,
     exponent = exponent,
     rescale = rescale,
@@ -288,7 +288,7 @@ alpha.centrality <- function(
   lifecycle::deprecate_soft("2.0.0", "alpha.centrality()", "alpha_centrality()")
   alpha_centrality(
     graph = graph,
-    nodes = nodes,
+    vertices = nodes,
     alpha = alpha,
     loops = loops,
     exo = exo,
@@ -1653,7 +1653,7 @@ hub_score <- function(
 #'   for all but small graphs.  `"arpack"` uses the ARPACK library, the
 #'   default implementation from igraph version 0.5 until version 0.7. It computes
 #'   PageRank scores by solving an eingevalue problem.
-#' @param vids The vertices of interest.
+#' @param vertices The vertices of interest.
 #' @param directed Logical, if true directed paths will be considered for
 #'   directed graphs. It is ignored for undirected graphs.
 #' @param damping The damping factor (\sQuote{d} in the original paper).
@@ -1714,7 +1714,7 @@ hub_score <- function(
 page_rank <- function(
   graph,
   algo = c("prpack", "arpack"),
-  vids = V(graph),
+  vertices = V(graph),
   directed = TRUE,
   damping = 0.85,
   personalized = NULL,
@@ -1724,7 +1724,7 @@ page_rank <- function(
   personalized_pagerank_impl(
     graph = graph,
     algo = algo,
-    vids = vids,
+    vids = vertices,
     directed = directed,
     damping = damping,
     personalized = personalized,
@@ -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 vertices 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
@@ -1975,14 +1975,14 @@ bonpow.sparse <- function(
 #'
 power_centrality <- function(
   graph,
-  nodes = V(graph),
+  vertices = V(graph),
   loops = FALSE,
   exponent = 1,
   rescale = FALSE,
   tol = 1e-7,
   sparse = TRUE
 ) {
-  nodes <- as_igraph_vs(graph, nodes)
+  nodes <- as_igraph_vs(graph, vertices)
   if (sparse) {
     res <- bonpow.sparse(graph, nodes, loops, exponent, rescale, tol)
   } else {
@@ -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 vertices 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),
+  vertices = V(graph),
   alpha = 1,
   loops = FALSE,
   exo = 1,
@@ -2168,7 +2168,7 @@ alpha_centrality <- function(
   tol = 1e-7,
   sparse = TRUE
 ) {
-  nodes <- as_igraph_vs(graph, nodes)
+  nodes <- as_igraph_vs(graph, vertices)
   if (sparse) {
     res <- alpha.centrality.sparse(
       graph,
diff --git a/R/structural-properties.R b/R/structural-properties.R
index cd56b513890..b1e34e19c4c 100644
--- a/R/structural-properties.R
+++ b/R/structural-properties.R
@@ -184,7 +184,7 @@ neighborhood.size <- function(
   ego_size(
     graph = graph,
     order = order,
-    nodes = nodes,
+    vertices = nodes,
     mode = mode,
     mindist = mindist
   )
@@ -378,7 +378,7 @@ graph.neighborhood <- function(
   make_ego_graph(
     graph = graph,
     order = order,
-    nodes = nodes,
+    vertices = nodes,
     mode = mode,
     mindist = mindist
   )
@@ -1899,7 +1899,7 @@ 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 vertices 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
@@ -1918,9 +1918,9 @@ transitivity <- function(
 #' g <- sample_gnp(20, 5 / 20)
 #' constraint(g)
 #'
-constraint <- function(graph, nodes = V(graph), weights = NULL) {
+constraint <- function(graph, vertices = V(graph), weights = NULL) {
   ensure_igraph(graph)
-  nodes <- as_igraph_vs(graph, nodes)
+  nodes <- as_igraph_vs(graph, vertices)
 
   if (is.null(weights)) {
     if ("weight" %in% edge_attr_names(graph)) {
@@ -2034,7 +2034,7 @@ edge_density <- function(graph, loops = FALSE) {
 ego_size <- function(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 ) {
@@ -2047,7 +2047,7 @@ ego_size <- function(
   .Call(
     R_igraph_neighborhood_size,
     graph,
-    as_igraph_vs(graph, nodes) - 1,
+    as_igraph_vs(graph, vertices) - 1,
     as.numeric(order),
     as.numeric(mode),
     mindist
@@ -2090,7 +2090,7 @@ 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 vertices 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
@@ -2148,7 +2148,7 @@ neighborhood_size <- ego_size
 ego <- function(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 ) {
@@ -2161,7 +2161,7 @@ ego <- function(
   res <- .Call(
     R_igraph_neighborhood,
     graph,
-    as_igraph_vs(graph, nodes) - 1,
+    as_igraph_vs(graph, vertices) - 1,
     as.numeric(order),
     as.numeric(mode),
     mindist
@@ -2183,7 +2183,7 @@ neighborhood <- ego
 make_ego_graph <- function(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 ) {
@@ -2196,7 +2196,7 @@ make_ego_graph <- function(
   res <- .Call(
     R_igraph_neighborhood_graphs,
     graph,
-    as_igraph_vs(graph, nodes) - 1,
+    as_igraph_vs(graph, vertices) - 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..3d732ec28f2 100644
--- a/man/alpha_centrality.Rd
+++ b/man/alpha_centrality.Rd
@@ -6,7 +6,7 @@
 \usage{
 alpha_centrality(
   graph,
-  nodes = V(graph),
+  vertices = 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{vertices}{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/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/constraint.Rd b/man/constraint.Rd
index ae337644aa5..542d4fdee56 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, vertices = 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{vertices}{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/ego.Rd b/man/ego.Rd
index 69c018240fe..15437e92066 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),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 )
@@ -24,7 +24,7 @@ ego_size(
 neighborhood_size(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 )
@@ -32,7 +32,7 @@ neighborhood_size(
 ego(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 )
@@ -40,7 +40,7 @@ ego(
 neighborhood(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in"),
   mindist = 0
 )
@@ -48,7 +48,7 @@ neighborhood(
 make_ego_graph(
   graph,
   order = 1,
-  nodes = V(graph),
+  vertices = 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),
+  vertices = 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{vertices}{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/page.rank.Rd b/man/page.rank.Rd
index 69075bee792..cf0452c3e7b 100644
--- a/man/page.rank.Rd
+++ b/man/page.rank.Rd
@@ -27,8 +27,6 @@ for all but small graphs.  \code{"arpack"} uses the ARPACK library, the
 default implementation from igraph version 0.5 until version 0.7. It computes
 PageRank scores by solving an eingevalue problem.}
 
-\item{vids}{The vertices of interest.}
-
 \item{directed}{Logical, if true directed paths will be considered for
 directed graphs. It is ignored for undirected graphs.}
 
diff --git a/man/page_rank.Rd b/man/page_rank.Rd
index 182032cf711..df7f1522378 100644
--- a/man/page_rank.Rd
+++ b/man/page_rank.Rd
@@ -7,7 +7,7 @@
 page_rank(
   graph,
   algo = c("prpack", "arpack"),
-  vids = V(graph),
+  vertices = V(graph),
   directed = TRUE,
   damping = 0.85,
   personalized = NULL,
@@ -27,7 +27,7 @@ for all but small graphs.  \code{"arpack"} uses the ARPACK library, the
 default implementation from igraph version 0.5 until version 0.7. It computes
 PageRank scores by solving an eingevalue problem.}
 
-\item{vids}{The vertices of interest.}
+\item{vertices}{The vertices of interest.}
 
 \item{directed}{Logical, if true directed paths will be considered for
 directed graphs. It is ignored for undirected graphs.}
diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd
index aeb2c85dd24..df37ede746c 100644
--- a/man/power_centrality.Rd
+++ b/man/power_centrality.Rd
@@ -6,7 +6,7 @@
 \usage{
 power_centrality(
   graph,
-  nodes = V(graph),
+  vertices = 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{vertices}{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

From 1cb98aad895532b05ed510ffc80826e7cc0a7146 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Oct 2025 23:58:03 +0000
Subject: [PATCH 4/4] Rename 'vids' to 'vertices' in additional centrality and
 path functions

Co-authored-by: krlmlr <1741643+krlmlr@users.noreply.github.com>
---
 R/centrality.R             | 26 +++++++++++++-------------
 R/paths.R                  |  6 +++---
 man/closeness.Rd           |  4 ++--
 man/diversity.Rd           |  4 ++--
 man/eccentricity.Rd        |  4 ++--
 man/estimate_closeness.Rd  |  2 --
 man/graph.diversity.Rd     |  2 --
 man/graph.strength.Rd      |  2 --
 man/harmonic_centrality.Rd |  4 ++--
 man/strength.Rd            |  4 ++--
 10 files changed, 26 insertions(+), 32 deletions(-)

diff --git a/R/centrality.R b/R/centrality.R
index 7d6c107ddfe..0ae4c7867d4 100644
--- a/R/centrality.R
+++ b/R/centrality.R
@@ -120,7 +120,7 @@ graph.strength <- function(
   lifecycle::deprecate_soft("2.0.0", "graph.strength()", "strength()")
   strength(
     graph = graph,
-    vids = vids,
+    vertices = vids,
     mode = mode,
     loops = loops,
     weights = weights
@@ -543,7 +543,7 @@ edge.betweenness.estimate <- estimate_edge_betweenness
 #'
 #' @aliases closeness.estimate
 #' @param graph The graph to analyze.
-#' @param vids The vertices for which closeness will be calculated.
+#' @param vertices The vertices for which closeness will be calculated.
 #' @param mode Character string, defined the types of the paths used for
 #'   measuring the distance in directed graphs. \dQuote{in} measures the paths
 #'   *to* a vertex, \dQuote{out} measures paths *from* a vertex,
@@ -578,7 +578,7 @@ edge.betweenness.estimate <- estimate_edge_betweenness
 #'
 closeness <- function(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("out", "in", "all", "total"),
   weights = NULL,
   normalized = FALSE,
@@ -587,7 +587,7 @@ closeness <- function(
   # Argument checks
   ensure_igraph(graph)
 
-  vids <- as_igraph_vs(graph, vids)
+  vids <- as_igraph_vs(graph, vertices)
   mode <- switch(
     igraph.match.arg(mode),
     "out" = 1,
@@ -1370,7 +1370,7 @@ eigen_centrality <- function(
 #'
 #'
 #' @param graph The input graph.
-#' @param vids The vertices for which the strength will be calculated.
+#' @param vertices The vertices for which the strength will be calculated.
 #' @param mode Character string, \dQuote{out} for out-degree, \dQuote{in} for
 #'   in-degree or \dQuote{all} for the sum of the two. For undirected graphs this
 #'   argument is ignored.
@@ -1403,14 +1403,14 @@ eigen_centrality <- function(
 #' @cdocs igraph_strength
 strength <- function(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in", "total"),
   loops = TRUE,
   weights = NULL
 ) {
   strength_impl(
     graph = graph,
-    vids = vids,
+    vids = vertices,
     mode = mode,
     loops = loops,
     weights = weights
@@ -1439,7 +1439,7 @@ strength <- function(
 #' @param weights `NULL`, or the vector of edge weights to use for the
 #'   computation. If `NULL`, then the \sQuote{weight} attibute is used. Note
 #'   that this measure is not defined for unweighted graphs.
-#' @param vids The vertex ids for which to calculate the measure.
+#' @param vertices The vertex ids for which to calculate the measure.
 #' @return A numeric vector, its length is the number of vertices.
 #' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
 #' @references Nathan Eagle, Michael Macy and Rob Claxton: Network Diversity
@@ -1459,11 +1459,11 @@ strength <- function(
 #' @family centrality
 #' @export
 #' @cdocs igraph_diversity
-diversity <- function(graph, weights = NULL, vids = V(graph)) {
+diversity <- function(graph, weights = NULL, vertices = V(graph)) {
   diversity_impl(
     graph = graph,
     weights = weights,
-    vids = vids
+    vids = vertices
   )
 }
 
@@ -1744,7 +1744,7 @@ page_rank <- function(
 #' default), then the function calculates the exact harmonic centrality scores.
 #'
 #' @param graph The graph to analyze.
-#' @param vids The vertices for which harmonic centrality will be calculated.
+#' @param vertices The vertices for which harmonic centrality will be calculated.
 #' @param mode Character string, defining the types of the paths used for
 #'   measuring the distance in directed graphs. \dQuote{out} follows paths along
 #'   the edge directions only, \dQuote{in} traverses the edges in reverse, while
@@ -1781,7 +1781,7 @@ page_rank <- function(
 #' @cdocs igraph_harmonic_centrality_cutoff
 harmonic_centrality <- function(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("out", "in", "all", "total"),
   weights = NULL,
   normalized = FALSE,
@@ -1789,7 +1789,7 @@ harmonic_centrality <- function(
 ) {
   harmonic_centrality_cutoff_impl(
     graph = graph,
-    vids = vids,
+    vids = vertices,
     mode = mode,
     weights = weights,
     normalized = normalized,
diff --git a/R/paths.R b/R/paths.R
index 972bcc136b7..b752413ebfa 100644
--- a/R/paths.R
+++ b/R/paths.R
@@ -268,7 +268,7 @@ max_cardinality <- function(graph) {
 #' Isolate vertices have eccentricity zero.
 #'
 #' @param graph The input graph, it can be directed or undirected.
-#' @param vids The vertices for which the eccentricity is calculated.
+#' @param vertices The vertices for which the eccentricity is calculated.
 #' @inheritParams distances
 #' @inheritParams rlang::args_dots_empty
 #' @return `eccentricity()` returns a numeric vector, containing the
@@ -285,7 +285,7 @@ max_cardinality <- function(graph) {
 #' @cdocs igraph_eccentricity_dijkstra
 eccentricity <- function(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   ...,
   weights = NULL,
   mode = c("all", "out", "in", "total")
@@ -308,7 +308,7 @@ eccentricity <- function(
 
   eccentricity_dijkstra_impl(
     graph = graph,
-    vids = vids,
+    vids = vertices,
     weights = weights,
     mode = mode
   )
diff --git a/man/closeness.Rd b/man/closeness.Rd
index dc860d003ed..03b7dd709f8 100644
--- a/man/closeness.Rd
+++ b/man/closeness.Rd
@@ -7,7 +7,7 @@
 \usage{
 closeness(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("out", "in", "all", "total"),
   weights = NULL,
   normalized = FALSE,
@@ -17,7 +17,7 @@ closeness(
 \arguments{
 \item{graph}{The graph to analyze.}
 
-\item{vids}{The vertices for which closeness will be calculated.}
+\item{vertices}{The vertices for which closeness will be calculated.}
 
 \item{mode}{Character string, defined the types of the paths used for
 measuring the distance in directed graphs. \dQuote{in} measures the paths
diff --git a/man/diversity.Rd b/man/diversity.Rd
index 570b68a7de6..3666b7b9d29 100644
--- a/man/diversity.Rd
+++ b/man/diversity.Rd
@@ -4,7 +4,7 @@
 \alias{diversity}
 \title{Graph diversity}
 \usage{
-diversity(graph, weights = NULL, vids = V(graph))
+diversity(graph, weights = NULL, vertices = V(graph))
 }
 \arguments{
 \item{graph}{The input graph. Edge directions are ignored.}
@@ -13,7 +13,7 @@ diversity(graph, weights = NULL, vids = V(graph))
 computation. If \code{NULL}, then the \sQuote{weight} attibute is used. Note
 that this measure is not defined for unweighted graphs.}
 
-\item{vids}{The vertex ids for which to calculate the measure.}
+\item{vertices}{The vertex ids for which to calculate the measure.}
 }
 \value{
 A numeric vector, its length is the number of vertices.
diff --git a/man/eccentricity.Rd b/man/eccentricity.Rd
index a4678a78d2d..e44d23c1ce5 100644
--- a/man/eccentricity.Rd
+++ b/man/eccentricity.Rd
@@ -6,7 +6,7 @@
 \usage{
 eccentricity(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   ...,
   weights = NULL,
   mode = c("all", "out", "in", "total")
@@ -15,7 +15,7 @@ eccentricity(
 \arguments{
 \item{graph}{The input graph, it can be directed or undirected.}
 
-\item{vids}{The vertices for which the eccentricity is calculated.}
+\item{vertices}{The vertices for which the eccentricity is calculated.}
 
 \item{...}{These dots are for future extensions and must be empty.}
 
diff --git a/man/estimate_closeness.Rd b/man/estimate_closeness.Rd
index 0441327d3b3..f136ea4d41c 100644
--- a/man/estimate_closeness.Rd
+++ b/man/estimate_closeness.Rd
@@ -16,8 +16,6 @@ estimate_closeness(
 \arguments{
 \item{graph}{The graph to analyze.}
 
-\item{vids}{The vertices for which closeness will be calculated.}
-
 \item{mode}{Character string, defined the types of the paths used for
 measuring the distance in directed graphs. \dQuote{in} measures the paths
 \emph{to} a vertex, \dQuote{out} measures paths \emph{from} a vertex,
diff --git a/man/graph.diversity.Rd b/man/graph.diversity.Rd
index 02d7a817d65..e190f9d33ef 100644
--- a/man/graph.diversity.Rd
+++ b/man/graph.diversity.Rd
@@ -12,8 +12,6 @@ graph.diversity(graph, weights = NULL, vids = V(graph))
 \item{weights}{\code{NULL}, or the vector of edge weights to use for the
 computation. If \code{NULL}, then the \sQuote{weight} attibute is used. Note
 that this measure is not defined for unweighted graphs.}
-
-\item{vids}{The vertex ids for which to calculate the measure.}
 }
 \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.strength.Rd b/man/graph.strength.Rd
index b0a556be306..073e9880837 100644
--- a/man/graph.strength.Rd
+++ b/man/graph.strength.Rd
@@ -15,8 +15,6 @@ graph.strength(
 \arguments{
 \item{graph}{The input graph.}
 
-\item{vids}{The vertices for which the strength will be calculated.}
-
 \item{mode}{Character string, \dQuote{out} for out-degree, \dQuote{in} for
 in-degree or \dQuote{all} for the sum of the two. For undirected graphs this
 argument is ignored.}
diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd
index c70629c847d..575e353db4d 100644
--- a/man/harmonic_centrality.Rd
+++ b/man/harmonic_centrality.Rd
@@ -6,7 +6,7 @@
 \usage{
 harmonic_centrality(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("out", "in", "all", "total"),
   weights = NULL,
   normalized = FALSE,
@@ -16,7 +16,7 @@ harmonic_centrality(
 \arguments{
 \item{graph}{The graph to analyze.}
 
-\item{vids}{The vertices for which harmonic centrality will be calculated.}
+\item{vertices}{The vertices for which harmonic centrality will be calculated.}
 
 \item{mode}{Character string, defining the types of the paths used for
 measuring the distance in directed graphs. \dQuote{out} follows paths along
diff --git a/man/strength.Rd b/man/strength.Rd
index 76a2e34f9b6..07ac64f98b8 100644
--- a/man/strength.Rd
+++ b/man/strength.Rd
@@ -6,7 +6,7 @@
 \usage{
 strength(
   graph,
-  vids = V(graph),
+  vertices = V(graph),
   mode = c("all", "out", "in", "total"),
   loops = TRUE,
   weights = NULL
@@ -15,7 +15,7 @@ strength(
 \arguments{
 \item{graph}{The input graph.}
 
-\item{vids}{The vertices for which the strength will be calculated.}
+\item{vertices}{The vertices for which the strength will be calculated.}
 
 \item{mode}{Character string, \dQuote{out} for out-degree, \dQuote{in} for
 in-degree or \dQuote{all} for the sum of the two. For undirected graphs this