update igraph use; interrupt depth-first search in n.comp.nb, add igr…

…aph argument to n.comp.nb

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spdep
-Version: 1.3-5
-Date: 2024-06-10
+Version: 1.3-6
+Date: 2024-06-12
 Title: Spatial Dependence: Weighting Schemes, Statistics
 Encoding: UTF-8
 Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), 

NEWS.md

@@ -1,4 +1,8 @@
-# Version 1.3-5 (development)
+# Version 1.3-6 (development)
+
+* #160 handle `n.comp.nb` delay in `print.nb` and elsewhere when the total number of neighbours is large
+
+# Version 1.3-5 (2025-06-10)
 
 * #157 migrate ESRI Shapefile to GPKG files; convert bhicv.shp to GPKG 
 

R/components.R

@@ -1,13 +1,33 @@
-# Copyright 2001 by Nicholas Lewin-Koh 
+# Copyright 2001 by Nicholas Lewin-Koh, igraph added RSB 2024
 #
 
 
-n.comp.nb <- function(nb.obj){
+n.comp.nb <- function(nb.obj, igraph=FALSE){
   if(!inherits(nb.obj,"nb"))stop("not a neighbours list")
-  nb.obj <- make.sym.nb(nb.obj)
-  comp <- rep(0,length(nb.obj))
-  comp <- .Call("g_components", nb.obj, as.integer(comp), PACKAGE="spdep")
-  answ <- list(nc=length(unique(comp)), comp.id=comp)
+  stopifnot(is.logical(igraph))
+  stopifnot(length(igraph) == 1L)
+  nb.sym <- is.symmetric.nb(nb.obj)
+  if (igraph) {
+    if (!requireNamespace("igraph", quietly=TRUE)) {
+      igraph <- !igraph
+      warning("igraph not available, set FALSE")
+    }
+  }
+  if (!igraph) {
+    if (!nb.sym) nb.obj <- make.sym.nb(nb.obj)
+    comp <- rep(0,length(nb.obj))
+    comp <- .Call("g_components", nb.obj, as.integer(comp), PACKAGE="spdep")
+    answ <- list(nc=length(unique(comp)), comp.id=comp)
+  } else {
+    stopifnot(requireNamespace("igraph", quietly=TRUE))
+    stopifnot(requireNamespace("spatialreg", quietly=TRUE))
+    B <- as(nb2listw(nb.obj, style="B", zero.policy=TRUE), "CsparseMatrix")
+
+    g1 <- igraph::graph_from_adjacency_matrix(B,
+      mode=ifelse(nb.sym, "undirected", "directed"))
+    c1 <- igraph::components(g1, mode="weak")
+    answ <- list(nc=c1$no, comp.id=c1$membership)
+  }
   answ
 }
 

man/compon.Rd

@@ -1,4 +1,4 @@
-% Copyright 2001 by Roger S. Bivand and Nicholas Lewin-Koh
+% Copyright 2001-24 by Roger S. Bivand and Nicholas Lewin-Koh
 \name{Graph Components}
 \alias{n.comp.nb}
 %\alias{reach.ij}
@@ -8,11 +8,13 @@
   \code{n.comp.nb()} finds the number of disjoint connected subgraphs in the graph depicted by \code{nb.obj} - a spatial neighbours list object.
 }
 \usage{
-n.comp.nb(nb.obj)
+n.comp.nb(nb.obj, igraph=FALSE)
 }
 \arguments{
  \item{nb.obj}{a neighbours list object of class \code{nb}}
+ \item{igraph}{default \code{FALSE}, if \code{TRUE} use \code{igraph::components} after converting the neighbour object to a sparse adjacency matrix then a graph}
 }
+\details{If \code{igraph=TRUE} and \code{attr(nb.obj, "sym")} is \code{FALSE}, the components of the directed graph will be found by a simple breadth-first search; if \code{igraph=FALSE} and \code{attr(nb.obj, "sym")} is \code{FALSE}, the object will be made symmetric (which may be time-consuming with large numbers of neighbours) and the components found by depth-first search. If \code{igraph=TRUE} or \code{FALSE} and \code{attr(nb.obj, "sym")} is \code{TRUE}, the components of the directed graph will be found by depth-first search.}
 \value{
 A list of:
 \item{nc}{number of disjoint connected subgraphs}
@@ -32,11 +34,11 @@ table(res$comp.id)
 plot(col2, coords, add=TRUE)
 points(coords, col=res$comp.id, pch=16)
 run <- FALSE
-if (require(igraph, quietly=TRUE) && require(spatialreg, quietly=TRUE)) run <- TRUE
+if (require("igraph", quietly=TRUE) && require("spatialreg", quietly=TRUE)) run <- TRUE
 if (run) {
 B <- as(nb2listw(col2, style="B", zero.policy=TRUE), "CsparseMatrix")
-g1 <- graph.adjacency(B, mode="undirected")
-c1 <- clusters(g1)
+g1 <- graph_from_adjacency_matrix(B, mode="undirected")
+c1 <- components(g1)
 print(c1$no == res$nc)
 }
 if (run) {
@@ -46,21 +48,17 @@ if (run) {
 print(all.equal(c1$csize, c(table(res$comp.id)), check.attributes=FALSE))
 }
 if (run) {
-W <- as(nb2listw(col2, style="W", zero.policy=TRUE), "CsparseMatrix")
-g1W <- graph.adjacency(W, mode="directed", weighted="W")
-c1W <- clusters(g1W)
-print(all.equal(c1W$membership, res$comp.id, check.attributes=FALSE))
+resi <- n.comp.nb(col2, igraph=TRUE)
+print(resi$nc == res$nc)
 }
 if (run) {
-ow <- options("warn")$warn
-options("warn"=2L)
-# Matrix 1.4-2 vulnerability work-around
-B1 <- try(get.adjacency(g1), silent=TRUE)
-if (!inherits(B1, "try-error")) {
-#B1 <- get.adjacency(g1)
-print(all.equal(B, B1))
+print(all.equal(resi$comp.id, res$comp.id))
 }
-options("warn"=ow)
+if (run) {
+W <- as(nb2listw(col2, style="W", zero.policy=TRUE), "CsparseMatrix")
+g1W <- graph_from_adjacency_matrix(W, mode="directed", weighted="W")
+c1W <- components(g1W)
+print(all.equal(c1W$membership, res$comp.id, check.attributes=FALSE))
 }
 }
 

src/dfs_ncomp.c

@@ -1,4 +1,5 @@
-/* Copyright 2001 by Nicholas Lewin-Koh. */
+/* Copyright 2001 by Nicholas Lewin-Koh.
+ * interrupt added RSB 2024 */
 
 #include "spdep.h"
 
@@ -33,6 +34,7 @@ SEXP g_components(SEXP nblst, SEXP cmpnm){
   }
 
   for(i=0; i < nvert; i++){
+    R_CheckUserInterrupt();
     if(INTEGER(visited)[i]==WHITE){ 
       INTEGER(visited)[i]=BLACK;
       if(INTEGER(VECTOR_ELT(nblst,i))[0]==0){