docs: reorganize function reference

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
@@ -971,7 +971,7 @@ NULL
 #' @method $ igraph
 #' @name igraph-dollar
 #' @export
-#' @family graph attributes
+#' @family attributes
 #' @examples
 #' g <- make_ring(10)
 #' g$name

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),

_pkgdown.yml

@@ -4,40 +4,37 @@ template:
   bootstrap: 5
 
 reference:
-- title: Adjacency
+- title: Adjacency matrices
 - contents:
   - has_concept("adjacency")
-- title: Graph attributes
+- title: Vertex, edge and graph attributes
 - contents:
   - has_concept("graph attributes")
 - title: Structural queries
 - contents:
   - has_concept("structural queries")
-- title: Bipartite
+- title: Bipartite graphs
 - contents:
   - has_concept("bipartite")
-- title: Centrality
+  - has_concept("incidence")
+- title: Centrality measures
 - contents:
   - has_concept("centrality")
+  - has_concept("efficiency")
 - title: Centralization related
 - contents:
   - has_concept("centralization related")
 - title: Cliques
 - contents:
   - has_concept("cliques")
-- title: Cocitation
-- contents:
-  - has_concept("cocitation")
-- title: Cohesive blocks
-- contents:
-  - has_concept("cohesive.blocks")
-- title: Coloring
+  - has_concept("glet")
+- title: Graph coloring
 - contents:
   - has_concept("coloring")
-- title: Community
+- title: Community detection
 - contents:
   - has_concept("community")
-- title: Components
+- title: Connected components
 - contents:
   - has_concept("components")
 - title: Console
@@ -49,28 +46,23 @@ reference:
 - title: Deterministic constructors
 - contents:
   - has_concept("deterministic constructors")
-- title: Decomposition
-- contents:
-  - has_concept("decomposition")
 - title: Graphical degree sequences
 - contents:
   - has_concept("graphical degree sequences")
 - title: Demo
 - contents:
   - has_concept("demo")
-- title: Efficiency
-- contents:
-  - has_concept("efficiency")
 - title: Latent position vector samplers
 - contents:
   - has_concept("latent position vector samplers")
 - title: Env and data
 - contents:
   - has_concept("env-and-data")
-- title: Epi
+- title: Processes on graphs
 - contents:
   - has_concept("epi")
-- title: Eulerian
+  - has_concept("random_walk")
+- title: Graph cycles
 - contents:
   - has_concept("eulerian")
 - title: Fit
@@ -79,21 +71,15 @@ reference:
 - title: Flow
 - contents:
   - has_concept("flow")
-- title: Foreign
+- title: Foreign format readers
 - contents:
   - has_concept("foreign")
-- title: Games
+- title: Random graph models (games)
 - contents:
   - has_concept("games")
-- title: Glet
-- contents:
-  - has_concept("glet")
 - title: Hierarchical random graph functions
 - contents:
   - has_concept("hierarchical random graph functions")
-- title: Incidence
-- contents:
-  - has_concept("incidence")
 - title: Structural queries
 - contents:
   - has_concept("structural queries")
@@ -103,85 +89,53 @@ reference:
 - title: Functions for manipulating graph structure
 - contents:
   - has_concept("functions for manipulating graph structure")
-- title: Structural queries
-- contents:
-  - has_concept("structural queries")
 - title: Vertex and edge sequences
 - contents:
   - has_concept("vertex and edge sequences")
-- title: Vertex and edge sequence operations
-- contents:
   - has_concept("vertex and edge sequence operations")
-- title: Graph attributes
-- contents:
-  - has_concept("graph attributes")
-- title: Graph layouts
+- title: Visualization
 - contents:
   - has_concept("graph layouts")
-- title: Layout modifiers
-- contents:
   - has_concept("layout modifiers")
-- title: Layout drl
-- contents:
   - has_concept("layout_drl")
+  - has_concept("palettes")
+  - has_concept("plot")
+  - has_concept("plot.common")
+  - has_concept("plot.shapes")
 - title: Constructor modifiers
 - contents:
   - has_concept("constructor modifiers")
-- title: Deterministic constructors
-- contents:
-  - has_concept("deterministic constructors")
-- title: Minimum spanning tree
-- contents:
-  - has_concept("minimum.spanning.tree")
 - title: Graph motifs
 - contents:
   - has_concept("graph motifs")
-- title: Nexus
-- contents:
-  - has_concept("nexus")
 - title: Functions for manipulating graph structure
 - contents:
   - has_concept("functions for manipulating graph structure")
 - title: Other
 - contents:
   - has_concept("other")
-- title: Palettes
-- contents:
-  - has_concept("palettes")
-- title: Igraph options
+- title: igraph options
 - contents:
   - has_concept("igraph options")
 - title: Paths
 - contents:
   - has_concept("paths")
-- title: Plot
-- contents:
-  - has_concept("plot")
-- title: Plot common
-- contents:
-  - has_concept("plot.common")
-- title: Plot shapes
-- contents:
-  - has_concept("plot.shapes")
 - title: Print
 - contents:
   - has_concept("print")
 - title: Printer callbacks
 - contents:
   - has_concept("printer callbacks")
-- title: Random walk
-- contents:
-  - has_concept("random_walk")
 - title: Rewiring functions
 - contents:
   - has_concept("rewiring functions")
 - title: Scan statistics
 - contents:
   - has_concept("scan statistics")
-- title: Scg
+- title: Spectral Coarse Graining
 - contents:
   - has_concept("scg")
-- title: Sgm
+- title: Graph matching
 - contents:
   - has_concept("sgm")
 - title: Similarity
@@ -190,33 +144,36 @@ reference:
 - title: Simple
 - contents:
   - has_concept("simple")
-- title: Socnet
+- title: Interactive functions
 - contents:
   - has_concept("socnet")
+  - has_concept("tkplot")
 - title: Structural properties
 - contents:
   - has_concept("structural.properties")
+  - has_concept("cocitation")
+  - has_concept("cohesive.blocks")
+  - has_concept("decomposition")
+  - has_concept("triangles")
 - title: Structural queries
 - contents:
   - has_concept("structural queries")
 - title: Test
 - contents:
   - has_concept("test")
-- title: Tkplot
-- contents:
-  - has_concept("tkplot")
 - title: Graph isomorphism
 - contents:
   - has_concept("graph isomorphism")
 - title: Trees
 - contents:
   - has_concept("trees")
-- title: Triangles
-- contents:
-  - has_concept("triangles")
+  - has_concept("minimum.spanning.tree")
 - title: Versions
 - contents:
   - has_concept("versions")
 - title: Others
 - contents:
   - lacks_concepts(c("adjacency", "graph attributes", "structural queries", "bipartite", "centrality", "centralization related", "cliques", "cocitation", "cohesive.blocks", "coloring", "community", "components", "console", "conversion", "deterministic constructors", "decomposition", "graphical degree sequences", "demo", "efficiency", "latent position vector samplers", "env-and-data", "epi", "eulerian", "fit", "flow", "foreign", "games", "glet", "hierarchical random graph functions", "incidence", "structural queries", "functions for manipulating graph structure", "functions for manipulating graph structure", "structural queries", "vertex and edge sequences", "vertex and edge sequence operations", "graph attributes", "graph layouts", "layout modifiers", "layout_drl", "constructor modifiers", "deterministic constructors", "minimum.spanning.tree", "graph motifs", "nexus", "functions for manipulating graph structure", "other", "palettes", "igraph options", "paths", "plot", "plot.common", "plot.shapes", "print", "printer callbacks", "random_walk", "rewiring functions", "scan statistics", "scg", "sgm", "similarity", "simple", "socnet", "structural.properties", "structural queries", "test", "tkplot", "graph isomorphism", "trees", "triangles", "versions"))
+- title: Internal
+- contents:
+  - has_concept("nexus")