docs: Automatic linking to C docs (#2518)

Co-authored-by: Kirill Müller <kirill@cynkra.com>

Author: maelle

CONTRIBUTING.md

@@ -154,11 +154,7 @@ pak::pak("igraph/igraph.r2cdocs")
 [roxygen2](https://roxygen2.r-lib.org/), and run `devtools::document()` or `make
 igraph` to update the `.Rd` files.
 
-- Links to C docs are added using the cdocs tag, for instance:
-
-```
-#' @cdocs igraph_assortativity
-```
+- Links to C docs are added automatically thanks to the igraph.r2cdocs's roclet.
 
 ### Maintaining igraph.r2cdocs
 

DESCRIPTION

@@ -80,7 +80,7 @@ Config/testthat/parallel: true
 Config/testthat/start-first: aaa-auto, vs-es, scan, vs-operators, weakref,
     watts.strogatz.game
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace", "devtag::dev_roclet"), packages =
-    "igraph.r2cdocs")
+Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace",
+    "igraph.r2cdocs::docs_rd", "devtag::dev_roclet"))
 RoxygenNote: 7.3.3.9000
 SystemRequirements: libxml2 (optional), glpk (>= 4.57, optional)

R/assortativity.R

@@ -160,7 +160,6 @@ assortativity.degree <- function(graph, directed = TRUE) {
 #'
 #' # BA model, tends to be dissortative
 #' assortativity_degree(sample_pa(10000, m = 4))
-#' @cdocs igraph_assortativity
 assortativity <- function(
   graph,
   values,
@@ -241,7 +240,6 @@ assortativity_legacy <- function(
 #'   [as.factor()].
 #' @rdname assortativity
 #' @export
-#' @cdocs igraph_assortativity_nominal
 assortativity_nominal <- function(
   graph,
   types,
@@ -263,7 +261,6 @@ assortativity_nominal <- function(
 
 #' @rdname assortativity
 #' @export
-#' @cdocs igraph_assortativity_degree
 assortativity_degree <- function(graph, directed = TRUE) {
   assortativity_degree_impl(
     graph = graph,

R/bipartite.R

@@ -226,7 +226,6 @@ bipartite_projection <- function(
 
 #' @rdname bipartite_projection
 #' @export
-#' @cdocs igraph_bipartite_projection_size
 bipartite_projection_size <- function(graph, types = NULL) {
   bipartite_projection_size_impl(
     graph = graph,
@@ -283,7 +282,6 @@ bipartite_projection_size <- function(graph, types = NULL) {
 #' bipartite_mapping(g3)
 #' @family bipartite
 #' @export
-#' @cdocs igraph_is_bipartite
 bipartite_mapping <- function(graph) {
   is_bipartite_impl(
     graph = graph

R/centrality.R

@@ -1291,7 +1291,6 @@ eigen_defaults <- function() {
 #' eigen_centrality(g)
 #' @family centrality
 #' @export
-#' @cdocs igraph_eigenvector_centrality
 eigen_centrality <- function(
   graph,
   directed = FALSE,
@@ -1371,7 +1370,6 @@ eigen_centrality <- function(
 #' strength(g)
 #' @family centrality
 #' @export
-#' @cdocs igraph_strength
 strength <- function(
   graph,
   vids = V(graph),
@@ -1429,7 +1427,6 @@ strength <- function(
 #' diversity(g3)
 #' @family centrality
 #' @export
-#' @cdocs igraph_diversity
 diversity <- function(graph, weights = NULL, vids = V(graph)) {
   diversity_impl(
     graph = graph,
@@ -1497,7 +1494,6 @@ diversity <- function(graph, weights = NULL, vids = V(graph)) {
 #' g2 <- make_ring(10)
 #' hits_scores(g2)
 #' @family centrality
-#' @cdocs igraph_hub_and_authority_scores
 hits_scores <- function(
   graph,
   ...,
@@ -1681,7 +1677,6 @@ hub_score <- function(
 #' page_rank(g3, personalized = reset)$vector
 #' @family centrality
 #' @export
-#' @cdocs igraph_personalized_pagerank
 page_rank <- function(
   graph,
   algo = c("prpack", "arpack"),
@@ -1749,7 +1744,6 @@ page_rank <- function(
 #' harmonic_centrality(g2, mode = "out")
 #' harmonic_centrality(g %du% make_full_graph(5), mode = "all")
 #'
-#' @cdocs igraph_harmonic_centrality_cutoff
 harmonic_centrality <- function(
   graph,
   vids = V(graph),

R/centralization.R

@@ -314,7 +314,6 @@ NULL
 #' g1 <- make_star(10, mode = "undirected")
 #' centr_eigen(g0)$centralization
 #' centr_eigen(g1)$centralization
-#' @cdocs igraph_centralization
 centralize <- function(scores, theoretical.max = 0, normalized = TRUE) {
   centralization_impl(
     scores = scores,
@@ -362,7 +361,6 @@ centralize <- function(scores, theoretical.max = 0, normalized = TRUE) {
 #' centr_clo(g, mode = "all")$centralization
 #' centr_betw(g, directed = FALSE)$centralization
 #' centr_eigen(g, directed = FALSE)$centralization
-#' @cdocs igraph_centralization_degree
 centr_degree <- function(
   graph,
   mode = c("all", "out", "in", "total"),
@@ -511,7 +509,6 @@ centr_betw <- function(graph, directed = TRUE, normalized = TRUE) {
 #' centr_betw(g, normalized = FALSE)$centralization %>%
 #'   `/`(centr_betw_tmax(g))
 #' centr_betw(g, normalized = TRUE)$centralization
-#' @cdocs igraph_centralization_betweenness_tmax
 centr_betw_tmax <- function(graph = NULL, nodes = 0, directed = TRUE) {
   centralization_betweenness_tmax_impl(
     graph = graph,
@@ -556,7 +553,6 @@ centr_betw_tmax <- function(graph = NULL, nodes = 0, directed = TRUE) {
 #' centr_clo(g, mode = "all")$centralization
 #' centr_betw(g, directed = FALSE)$centralization
 #' centr_eigen(g, directed = FALSE)$centralization
-#' @cdocs igraph_centralization_closeness
 centr_clo <- function(
   graph,
   mode = c("out", "in", "all", "total"),
@@ -593,7 +589,6 @@ centr_clo <- function(
 #' centr_clo(g, normalized = FALSE)$centralization %>%
 #'   `/`(centr_clo_tmax(g))
 #' centr_clo(g, normalized = TRUE)$centralization
-#' @cdocs igraph_centralization_closeness_tmax
 centr_clo_tmax <- function(
   graph = NULL,
   nodes = 0,
@@ -655,7 +650,6 @@ centr_clo_tmax <- function(
 #' g1 <- make_star(10, mode = "undirected")
 #' centr_eigen(g0)$centralization
 #' centr_eigen(g1)$centralization
-#' @cdocs igraph_centralization_eigenvector_centrality
 centr_eigen <- function(
   graph,
   directed = FALSE,
@@ -707,7 +701,6 @@ centr_eigen <- function(
 #' centr_eigen(g, normalized = FALSE)$centralization %>%
 #'   `/`(centr_eigen_tmax(g))
 #' centr_eigen(g, normalized = TRUE)$centralization
-#' @cdocs igraph_centralization_eigenvector_centrality_tmax
 centr_eigen_tmax <- function(
   graph = NULL,
   nodes = 0,

R/cliques.R

@@ -254,7 +254,6 @@ clique.number <- function(graph) {
 #'
 #' # Check that all returned vertex sets are indeed cliques
 #' all(sapply(max_cliques(g), function (c) is_clique(g, c)))
-#' @cdocs igraph_cliques igraph_cliques_callback
 cliques <- function(graph, min = NULL, max = NULL, ..., callback = NULL) {
   ensure_igraph(graph)
   check_dots_empty()
@@ -280,7 +279,6 @@ cliques <- function(graph, min = NULL, max = NULL, ..., callback = NULL) {
 
 #' @rdname cliques
 #' @export
-#' @cdocs igraph_largest_cliques
 largest_cliques <- function(graph) {
   largest_cliques_impl(
     graph = graph
@@ -410,7 +408,6 @@ count_max_cliques <- function(graph, min = NULL, max = NULL, subset = NULL) {
 
 #' @rdname cliques
 #' @export
-#' @cdocs igraph_clique_number
 clique_num <- function(graph) {
   clique_number_impl(
     graph = graph
@@ -467,7 +464,6 @@ clique_num <- function(graph) {
 #' weighted_cliques(g, maximal = TRUE)
 #' largest_weighted_cliques(g)
 #' weighted_clique_num(g)
-#' @cdocs igraph_weighted_cliques
 weighted_cliques <- function(
   graph,
   vertex.weights = NULL,
@@ -485,7 +481,6 @@ weighted_cliques <- function(
 }
 #' @export
 #' @rdname cliques
-#' @cdocs igraph_largest_weighted_cliques
 largest_weighted_cliques <- function(graph, vertex.weights = NULL) {
   largest_weighted_cliques_impl(
     graph = graph,
@@ -494,7 +489,6 @@ largest_weighted_cliques <- function(graph, vertex.weights = NULL) {
 }
 #' @export
 #' @rdname cliques
-#' @cdocs igraph_weighted_clique_number
 weighted_clique_num <- function(graph, vertex.weights = NULL) {
   weighted_clique_number_impl(
     graph = graph,
@@ -639,8 +633,6 @@ independence_number <- ivs_size
 
 #' @rdname cliques
 #' @export
-#' @cdocs igraph_maximal_cliques_hist
-#' @cdocs igraph_clique_size_hist
 clique_size_counts <- function(graph, min = 0, max = 0, maximal = FALSE) {
   if (maximal) {
     maximal_cliques_hist_impl(
@@ -669,7 +661,6 @@ clique_size_counts <- function(graph, min = 0, max = 0, maximal = FALSE) {
 #' @keywords graphs
 #' @seealso [make_full_graph()]
 #' @export
-#' @cdocs igraph_is_complete
 #' @examples
 #'
 #' g <- make_full_graph(6, directed = TRUE)
@@ -697,7 +688,6 @@ is_complete <- function(graph) {
 #'   a clique.
 #' @keywords graphs
 #' @export
-#' @cdocs igraph_is_clique
 is_clique <- function(graph, candidate, directed = FALSE) {
   is_clique_impl(
     graph = graph,
@@ -714,7 +704,6 @@ is_clique <- function(graph, candidate, directed = FALSE) {
 #'   independent set.
 #' @keywords graphs
 #' @export
-#' @cdocs igraph_is_independent_vertex_set
 is_ivs <- function(graph, candidate) {
   is_independent_vertex_set_impl(
     graph = graph,

R/coloring.R

@@ -30,7 +30,6 @@
 #' col <- greedy_vertex_coloring(g)
 #' plot(g, vertex.color = col)
 #'
-#' @cdocs igraph_vertex_coloring_greedy
 greedy_vertex_coloring <- function(
   graph,
   heuristic = c("colored_neighbors", "dsatur")

R/community.R

@@ -3197,7 +3197,6 @@ communities <- groups.communities
 #'
 #' @export
 #' @family functions for manipulating graph structure
-#' @cdocs igraph_contract_vertices
 contract <- function(
   graph,
   mapping,
@@ -3253,7 +3252,6 @@ contract <- function(
 #'
 #' @export
 #' @family community
-#' @cdocs igraph_voronoi
 voronoi_cells <- function(
   graph,
   generators,

R/components.R

@@ -253,7 +253,6 @@ decompose <- function(
 #'
 #' @family components
 #' @export
-#' @cdocs igraph_articulation_points
 articulation_points <- function(graph) {
   articulation_points_impl(
     graph = graph
@@ -262,7 +261,6 @@ articulation_points <- function(graph) {
 
 #' @rdname articulation_points
 #' @export
-#' @cdocs igraph_bridges
 bridges <- function(graph) {
   bridges_impl(
     graph = graph
@@ -317,7 +315,6 @@ bridges <- function(graph) {
 #' bc <- biconnected_components(g)
 #' @family components
 #' @export
-#' @cdocs igraph_biconnected_components
 biconnected_components <- function(graph) {
   # Function call
   res <- biconnected_components_impl(
@@ -389,7 +386,6 @@ biconnected_components <- function(graph) {
 #' is_biconnected(make_full_graph(2))
 #' @family components
 #' @export
-#' @cdocs igraph_is_biconnected
 is_biconnected <- function(graph) {
   is_biconnected_impl(
     graph = graph