add dodgr_centrality fn; closes #90

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dodgr
 Title: Distances on Directed Graphs
-Version: 0.2.5.005
+Version: 0.2.5.006
 Authors@R: c(
     person("Mark", "Padgham", email="[email protected]", role=c("aut", "cre")),
     person("Andreas", "Petutschnig", role="aut"),

NAMESPACE

@@ -7,6 +7,7 @@ export(clear_dodgr_cache)
 export(compare_heaps)
 export(dodgr_cache_off)
 export(dodgr_cache_on)
+export(dodgr_centrality)
 export(dodgr_components)
 export(dodgr_contract_graph)
 export(dodgr_distances)

R/RcppExports.R

@@ -4,8 +4,8 @@
 #' rcpp_centrality
 #'
 #' @noRd
-rcpp_centrality <- function(graph, vert_map_in, heap_type, vertices) {
-    .Call(`_dodgr_rcpp_centrality`, graph, vert_map_in, heap_type, vertices)
+rcpp_centrality <- function(graph, vert_map_in, heap_type, edges) {
+    .Call(`_dodgr_rcpp_centrality`, graph, vert_map_in, heap_type, edges)
 }
 
 #' Make unordered_set of all new edge names

R/centrality.R

@@ -0,0 +1,68 @@
+#' dodgr_centrality
+#'
+#' Calculate betweenness centrality for a `dodgr` network, in either vertex- or
+#' edge-based form.
+#'
+#' @param graph `data.frame` or equivalent object representing the network
+#' graph (see Details)
+#' @param contract If `TRUE`, centrality is calculated on contracted graph
+#' before mapping back on to the original full graph. Note that for street
+#' networks, in particular those obtained from the \pkg{osmdata} package, vertex
+#' placement is effectively arbitrary except at junctions; centrality for such
+#' graphs should only be calculated between the latter points, and thus
+#' `contract` should always be `TRUE`.
+#' @param edges If `TRUE`, centrality is calculated for graph edges, returning
+#' the input `graph` with an additional `centrality` column; otherwise
+#' centrality is calculated for vertices, returning the equivalent of
+#' `dodgr_vertices(graph)`, with an additional vertex-based `centrality` column.
+#' @param heap Type of heap to use in priority queue. Options include
+#' Fibonacci Heap (default; `FHeap`), Binary Heap (`BHeap`),
+#' `Radix`, Trinomial Heap (`TriHeap`), Extended Trinomial Heap
+#' (`TriHeapExt`, and 2-3 Heap (`Heap23`).
+#' @return Modified version of graph with additonal `centrality` column added.
+#'
+#' @export
+dodgr_centrality <- function (graph, contract = TRUE, edges = TRUE, heap = "BHeap")
+{
+    if ("centrality" %in% names (graph))
+        warning ("graph already has a 'centrality' column; ",
+                  "this will be overwritten")
+
+    hps <- get_heap (heap, graph)
+    heap <- hps$heap
+    graph <- hps$graph
+
+    gr_cols <- dodgr_graph_cols (graph)
+
+    if (contract & !methods::is (graph, "dodgr_contracted"))
+    {
+        graph_full <- graph
+        graph <- dodgr_contract_graph (graph)
+        hashc <- get_hash (graph, hash = FALSE)
+        fname_c <- file.path (tempdir (),
+                              paste0 ("dodgr_edge_map_", hashc, ".Rds"))
+        if (!file.exists (fname_c))
+            stop ("something went wrong extracting the edge_map ... ") # nocov
+        edge_map <- readRDS (fname_c)
+    }
+
+    vert_map <- make_vert_map (graph, gr_cols)
+
+    graph2 <- convert_graph (graph, gr_cols)
+
+    centrality <- rcpp_centrality (graph2, vert_map, "BHeap", edges)
+
+    if (edges)
+    {
+        graph$centrality <- centrality
+        if (contract)
+            graph <- uncontract_graph (graph, edge_map, graph_full)
+        res <- graph
+    } else
+    {
+        res <- dodgr_vertices (graph)
+        res$centrality <- centrality
+    }
+
+    return (res)
+}

_pkgdown.yml

@@ -39,6 +39,7 @@ reference:
   - title: Miscellaneous Functions
     contents:
     - compare_heaps
+    - dodgr_centrality
     - dodgr_flowmap
     - dodgr_full_cycles
     - dodgr_fundamental_cycles

codemeta.json

@@ -10,7 +10,7 @@
   "codeRepository": "https://github.com/ATFutures/dodgr",
   "issueTracker": "https://github.com/ATFutures/dodgr/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.2.5.5",
+  "version": "0.2.5.6",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -392,5 +392,5 @@
     }
   ],
   "relatedLink": "https://CRAN.R-project.org/package=dodgr",
-  "fileSize": "639.821KB"
+  "fileSize": "640.631KB"
 }

src/RcppExports.cpp

@@ -6,16 +6,16 @@
 using namespace Rcpp;
 
 // rcpp_centrality
-Rcpp::NumericVector rcpp_centrality(const Rcpp::DataFrame graph, const Rcpp::DataFrame vert_map_in, const std::string& heap_type, bool vertices);
-RcppExport SEXP _dodgr_rcpp_centrality(SEXP graphSEXP, SEXP vert_map_inSEXP, SEXP heap_typeSEXP, SEXP verticesSEXP) {
+Rcpp::NumericVector rcpp_centrality(const Rcpp::DataFrame graph, const Rcpp::DataFrame vert_map_in, const std::string& heap_type, bool edges);
+RcppExport SEXP _dodgr_rcpp_centrality(SEXP graphSEXP, SEXP vert_map_inSEXP, SEXP heap_typeSEXP, SEXP edgesSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const Rcpp::DataFrame >::type graph(graphSEXP);
     Rcpp::traits::input_parameter< const Rcpp::DataFrame >::type vert_map_in(vert_map_inSEXP);
     Rcpp::traits::input_parameter< const std::string& >::type heap_type(heap_typeSEXP);
-    Rcpp::traits::input_parameter< bool >::type vertices(verticesSEXP);
-    rcpp_result_gen = Rcpp::wrap(rcpp_centrality(graph, vert_map_in, heap_type, vertices));
+    Rcpp::traits::input_parameter< bool >::type edges(edgesSEXP);
+    rcpp_result_gen = Rcpp::wrap(rcpp_centrality(graph, vert_map_in, heap_type, edges));
     return rcpp_result_gen;
 END_RCPP
 }

src/centrality.cpp

@@ -218,7 +218,7 @@ void PF::PathFinder::Centrality_edge (
 Rcpp::NumericVector rcpp_centrality (const Rcpp::DataFrame graph,
         const Rcpp::DataFrame vert_map_in,
         const std::string& heap_type,
-        bool vertices)
+        bool edges)
 {
     std::vector <std::string> from = graph ["from"];
     std::vector <std::string> to = graph ["to"];
@@ -247,10 +247,10 @@ Rcpp::NumericVector rcpp_centrality (const Rcpp::DataFrame graph,
             one_iso);
     */
     std::vector <double> w (nverts), cent;
-    if (vertices)
-        cent.resize (nverts);
-    else
+    if (edges)
         cent.resize (nedges);
+    else
+        cent.resize (nverts);
     std::fill (cent.begin (), cent.end (), 0.0);
 
     for (unsigned int i = 0; i < nverts; i++)
@@ -261,10 +261,10 @@ Rcpp::NumericVector rcpp_centrality (const Rcpp::DataFrame graph,
 
         pathfinder->init (g); // specify the graph
 
-        if (vertices)
-            pathfinder->Centrality_vertex (w, cent, i);
-        else
+        if (edges)
             pathfinder->Centrality_edge (w, cent, i, nedges);
+        else
+            pathfinder->Centrality_vertex (w, cent, i);
     }
 
     Rcpp::NumericVector dout = Rcpp::wrap (cent);

src/run_sp.h

@@ -64,5 +64,5 @@ Rcpp::List rcpp_get_paths (const Rcpp::DataFrame graph,
 Rcpp::NumericVector rcpp_centrality (const Rcpp::DataFrame graph,
         const Rcpp::DataFrame vert_map_in,
         const std::string& heap_type,
-        bool vertices); // FALSE for edge centrality
+        bool edges); // FALSE for vertex centrality