docs: reorganize function reference

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, config-draft]
+    branches: [main, master]
   pull_request:
     branches: [main, master]
   release:

R/aaa-auto.R

@@ -1518,6 +1518,8 @@ count_triangles <- function(graph, vids=V(graph)) {
   res
 }
 
+#' @family triangles
+#' @rdname count_triangles
 #' @export
 triangles <- function(graph) {
   # Argument checks
@@ -2143,6 +2145,7 @@ embed_adjacency_matrix <- function(graph, no, weights=NULL, which=c("lm", "la",
   res
 }
 
+#' @family embedding
 #' @export
 embed_laplacian_matrix <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), type=c("default", "D-A", "DAD", "I-DAD", "OAP"), scaled=TRUE, options=igraph.arpack.default) {
   # Argument checks

R/attributes.R

@@ -43,7 +43,7 @@
 #' @return A list of graph attributes, or a single graph attribute.
 #'
 #' @aliases get.graph.attribute graph.attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -72,7 +72,7 @@ graph_attr <- function(graph, name) {
 #' @return The graph, with the attribute(s) added.
 #'
 #' @aliases graph.attributes<-
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -102,7 +102,7 @@ graph_attr <- function(graph, name) {
 #' @param value New value of the attribute.
 #' @return The graph with the new graph attribute added or set.
 #'
-#' @family graph attributes
+#' @family attributes
 #' @aliases set.graph.attribute
 #'
 #' @export
@@ -152,7 +152,7 @@ graph.attributes <- function(graph) {
 #'   all vertex attributes, if `name` is missing.
 #'
 #' @aliases get.vertex.attribute vertex.attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -197,7 +197,7 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #' @return The graph, with the vertex attribute(s) added or set.
 #'
 #' @aliases vertex.attributes<-
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -229,7 +229,7 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #' @return The graph, with the vertex attribute added or set.
 #'
 #' @aliases set.vertex.attribute
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -363,7 +363,7 @@ vertex.attributes <- function(graph, index = V(graph)) {
 #'   edge attributes if `name` is missing.
 #'
 #' @aliases get.edge.attribute edge.attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -407,7 +407,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #' @return The graph, with the edge attribute(s) added or set.
 #'
 #' @aliases edge.attributes<-
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -439,7 +439,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #' @return The graph, with the edge attribute added or set.
 #'
 #' @aliases set.edge.attribute
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -567,7 +567,7 @@ edge.attributes <- function(graph, index = E(graph)) {
 #' @return Character vector, the names of the graph attributes.
 #'
 #' @aliases list.graph.attributes attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -590,7 +590,7 @@ graph_attr_names <- function(graph) {
 #' @return Character vector, the names of the vertex attributes.
 #'
 #' @aliases list.vertex.attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -617,7 +617,7 @@ vertex_attr_names <- function(graph) {
 #' @return Character vector, the names of the edge attributes.
 #'
 #' @aliases list.edge.attributes
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -643,7 +643,7 @@ edge_attr_names <- function(graph) {
 #' @return The graph, with the specified attribute removed.
 #'
 #' @aliases remove.graph.attribute
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -673,7 +673,7 @@ delete_graph_attr <- function(graph, name) {
 #' @return The graph, with the specified vertex attribute removed.
 #'
 #' @aliases remove.vertex.attribute
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -704,7 +704,7 @@ delete_vertex_attr <- function(graph, name) {
 #' @return The graph, with the specified edge attribute removed.
 #'
 #' @aliases remove.edge.attribute
-#' @family graph attributes
+#' @family attributes
 #'
 #' @export
 #' @examples
@@ -809,6 +809,7 @@ is_weighted <- function(graph) {
 }
 
 #' @rdname make_bipartite_graph
+#' @family bipartite
 #' @export
 is_bipartite <- function(graph) {
   if (!is_igraph(graph)) {
@@ -895,6 +896,7 @@ igraph.i.attribute.combination <- function(comb) {
 #' new edge should be sum of the weights of the corresponding edges in the old
 #' graph; and that the rest of the attributes should be ignored (=dropped).
 #'
+#' @family attributes
 #' @name igraph-attribute-combination
 #' @aliases attribute.combination
 #' @section Predefined combination functions: The following combination
@@ -971,7 +973,7 @@ NULL
 #' @method $ igraph
 #' @name igraph-dollar
 #' @export
-#' @family graph attributes
+#' @family attributes
 #' @examples
 #' g <- make_ring(10)
 #' g$name

R/centrality.R

@@ -303,7 +303,7 @@ estimate_closeness <- function(graph, vids = V(graph), mode = c("out", "in", "al
 }
 
 #' @rdname arpack
-#' @family centrality
+#' @family arpack
 #' @export
 arpack_defaults <- list(
   bmat = "I", n = 0, which = "XX", nev = 1, tol = 0.0,
@@ -497,7 +497,7 @@ arpack_defaults <- list(
 #'     which = "LM", maxiter = 2000
 #'   ))
 #' }
-#' @family centrality
+#' @family arpack
 #' @export
 arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults,
                    env = parent.frame(), complex = !sym) {
@@ -909,6 +909,7 @@ diversity <- diversity
 #' g2 <- make_ring(10)
 #' hub_score(g2)$vector
 #' authority_score(g2)$vector
+#' @family centrality
 hub_score <- hub_score
 
 

R/community.R

@@ -2548,6 +2548,6 @@ communities <- groups.communities
 #' ## combined using the 'toString' function.
 #' print(g2, g = TRUE, v = TRUE, e = TRUE)
 #'
-#' @family community
 #' @export
+#' @family functions for manipulating graph structure
 contract <- contract

R/decomposition.R

@@ -63,7 +63,7 @@
 #' linear-time algorithms to test chordality of graphs, test acyclicity of
 #' hypergraphs, and selectively reduce acyclic hypergraphs.  *SIAM Journal
 #' of Computation* 13, 566--579.
-#' @family decomposition
+#' @family chordal
 #' @export
 #' @keywords graphs
 #' @examples

R/embedding.R

@@ -88,6 +88,7 @@
 #' })
 #' RDP <- sample_dot_product(lpvs)
 #' embed <- embed_adjacency_matrix(RDP, 5)
+#' @family embedding
 #' @export
 embed_adjacency_matrix <- embed_adjacency_matrix
 
@@ -148,6 +149,7 @@ embed_adjacency_matrix <- embed_adjacency_matrix
 #' RDP.graph.3 <- sample_dot_product(lpvs.sph)
 #' dim_select(embed_adjacency_matrix(RDP.graph.3, 10)$D)
 #'
+#' @family embedding
 #' @export
 dim_select <- dim_select
 

R/epi.R

@@ -19,15 +19,15 @@
 #
 ###################################################################
 
-#' @family epi
+#' @family processes
 #' @export
 time_bins <- function(x, middle = TRUE) {
   UseMethod("time_bins")
 }
 
 #' @method time_bins sir
 #' @rdname sir
-#' @family epi
+#' @family processes
 #' @export
 #' @importFrom stats IQR
 time_bins.sir <- function(x, middle = TRUE) {
@@ -52,7 +52,7 @@ time_bins.sir <- function(x, middle = TRUE) {
 #' @importFrom stats median
 #' @method median sir
 #' @rdname sir
-#' @family epi
+#' @family processes
 #' @export
 median.sir <- function(x, na.rm = FALSE, ...) {
   sir <- x
@@ -73,7 +73,7 @@ median.sir <- function(x, na.rm = FALSE, ...) {
 #' @importFrom stats quantile
 #' @method quantile sir
 #' @rdname sir
-#' @family epi
+#' @family processes
 #' @export
 quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) {
   sir <- x
@@ -144,7 +144,7 @@ quantile.sir <- function(x, comp = c("NI", "NS", "NR"), prob, ...) {
 #' @references Bailey, Norman T. J. (1975). The mathematical theory of
 #' infectious diseases and its applications (2nd ed.). London: Griffin.
 #' @method plot sir
-#' @family epi
+#' @family processes
 #' @export
 #' @importFrom graphics plot lines
 #' @keywords graphs

R/eulerian.R

@@ -59,21 +59,21 @@
 #' has_eulerian_cycle(g)
 #' try(eulerian_cycle(g))
 #'
-#' @family eulerian
+#' @family cycles
 #' @export
 has_eulerian_path <- function(graph) is_eulerian(graph)$has_path
 
 #' @rdname has_eulerian_path
-#' @family eulerian
+#' @family cycles
 #' @export
 has_eulerian_cycle <- function(graph) is_eulerian(graph)$has_cycle
 
 #' @rdname has_eulerian_path
-#' @family eulerian
+#' @family cycles
 #' @export
 eulerian_path <- eulerian_path
 
 #' @rdname has_eulerian_path
-#' @family eulerian
+#' @family cycles
 #' @export
 eulerian_cycle <- eulerian_cycle

R/flow.R

@@ -614,6 +614,7 @@ dominator_tree <- function(graph, root, mode = c("out", "in", "all", "total")) {
 #'
 #' chvatal <- make_graph("chvatal")
 #' min_st_separators(chvatal)
+#' @family flow
 min_st_separators <- min_st_separators
 
 

R/games.R

@@ -355,6 +355,7 @@ gnm <- function(...) constructor_spec(sample_gnm, ...)
 #' @family games
 #' @export
 #' @keywords graphs
+#' @keywords internal
 #' @examples
 #'
 #' g <- erdos.renyi.game(1000, 1 / 1000)
@@ -1069,8 +1070,8 @@ asym_pref <- function(...) constructor_spec(sample_asym_pref, ...)
 
 
 #' @rdname ego
-#' @family games
 #' @export
+#' @family functions for manipulating graph structure
 connect <- function(graph, order, mode = c("all", "out", "in", "total")) {
   if (!is_igraph(graph)) {
     stop("Not a graph object")
@@ -1661,6 +1662,7 @@ sample_k_regular <- sample_k_regular
 #' distribution in scale-free networks. *Phys Rev Lett* 87(27):278701,
 #' 2001.
 #' @keywords graphs
+#' @family games
 #' @examples
 #'
 #' N <- 10000
@@ -1727,6 +1729,7 @@ sample_fitness <- sample_fitness
 #' Cho YS, Kim JS, Park J, Kahng B, Kim D: Percolation transitions in
 #' scale-free networks under the Achlioptas process. *Phys Rev Lett*
 #' 103:135702, 2009.
+#' @family games
 #' @keywords graphs
 #' @examples
 #'
@@ -1780,6 +1783,7 @@ sample_fitness_pl <- sample_fitness_pl
 #' time: densification laws, shrinking diameters and possible explanations.
 #' *KDD '05: Proceeding of the eleventh ACM SIGKDD international
 #' conference on Knowledge discovery in data mining*, 177--187, 2005.
+#' @family games
 #' @keywords graphs
 #' @examples
 #'
@@ -1821,6 +1825,7 @@ sample_forestfire <- sample_forestfire
 #' @references Lyzinski, V., Fishkind, D. E., Priebe, C. E. (2013).  Seeded
 #' graph matching for correlated Erdos-Renyi graphs.
 #' <https://arxiv.org/abs/1304.7844>
+#' @family games
 #' @examples
 #' g <- sample_gnp(1000, .1)
 #' g2 <- sample_correlated_gnp(g, corr = 0.5)
@@ -1857,6 +1862,7 @@ sample_correlated_gnp <- sample_correlated_gnp
 #' graph matching for correlated Erdos-Renyi graphs.
 #' <https://arxiv.org/abs/1304.7844>
 #' @keywords graphs
+#' @family games
 #' @examples
 #' gg <- sample_correlated_gnp_pair(
 #'   n = 10, corr = .8, p = .5,

R/iterators.R

@@ -1063,7 +1063,7 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
 #'
 #' @export
 #' @family vertex and edge sequences
-#' @family graph attributes
+#' @family attributes
 #' @examples
 #' g <- make_(
 #'   ring(10),
@@ -1789,6 +1789,7 @@ rev.igraph.es <- rev.igraph.vs
 #' V(g)$name <- letters[1:10]
 #' as_ids(V(g))
 #' as_ids(E(g))
+#' @family vertex and edge sequences
 as_ids <- function(seq) {
   UseMethod("as_ids")
 }