Revert "update igraph use; interrupt depht-first search in n.comp.nb,…

… add igraph argument to n.comp.nb"

This reverts commit e64720c.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spdep
-Version: 1.3-6
-Date: 2024-06-11
+Version: 1.3-5
+Date: 2024-06-10
 Title: Spatial Dependence: Weighting Schemes, Statistics
 Encoding: UTF-8
 Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), 

NEWS.md

@@ -1,8 +1,4 @@
-# Version 1.3-6 (development)
-
-* add user interrupt to `n.comp.nb` #160
-
-# Version 1.3-5 (2024-06-10)
+# Version 1.3-5 (development)
 
 * #157 migrate ESRI Shapefile to GPKG files; convert bhicv.shp to GPKG 
 

R/components.R

@@ -1,33 +1,13 @@
-# Copyright 2001 by Nicholas Lewin-Koh, igraph added RSB 2024
+# Copyright 2001 by Nicholas Lewin-Koh 
 #
 
 
-n.comp.nb <- function(nb.obj, igraph=FALSE){
+n.comp.nb <- function(nb.obj){
   if(!inherits(nb.obj,"nb"))stop("not a neighbours list")
-  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)
-  }
+  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)
   answ
 }
 

man/compon.Rd

@@ -1,4 +1,4 @@
-% Copyright 2001-24 by Roger S. Bivand and Nicholas Lewin-Koh
+% Copyright 2001 by Roger S. Bivand and Nicholas Lewin-Koh
 \name{Graph Components}
 \alias{n.comp.nb}
 %\alias{reach.ij}
@@ -8,13 +8,11 @@
   \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, igraph=FALSE)
+n.comp.nb(nb.obj)
 }
 \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}
@@ -34,11 +32,11 @@ 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_from_adjacency_matrix(B, mode="undirected")
-c1 <- components(g1)
+g1 <- graph.adjacency(B, mode="undirected")
+c1 <- clusters(g1)
 print(c1$no == res$nc)
 }
 if (run) {
@@ -48,17 +46,21 @@ if (run) {
 print(all.equal(c1$csize, c(table(res$comp.id)), check.attributes=FALSE))
 }
 if (run) {
-resi <- n.comp.nb(col2, igraph=TRUE)
-print(resi$nc == res$nc)
+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))
 }
 if (run) {
-print(all.equal(resi$comp.id, res$comp.id))
+ow <- options("warn")$warn
+options("warn"=2L)
+# Matrix 1.4-2 vulnerability work-around
+B1 <- try(get.adjacency(g1), silent=TRUE)
+if (!inherits(B1, "try-error")) {
+#B1 <- get.adjacency(g1)
+print(all.equal(B, B1))
 }
-if (run) {
-W <- as(nb2listw(col2, style="W", zero.policy=TRUE), "CsparseMatrix")
-g1W <- graph_from_adjacency_matrix(W, mode="directed", weighted="W")
-c1W <- components(g1W)
-print(all.equal(c1W$membership, res$comp.id, check.attributes=FALSE))
+options("warn"=ow)
 }
 }
 

man/lm.RStests.Rd

@@ -88,7 +88,7 @@ lw <- nb2listw(COL.nb)
 res <- lm.RStests(oldcrime.lm, listw=lw, test="all")
 summary(res)
 if (require("spatialreg", quietly=TRUE)) {
-  oldcrime.slx <- lmSLX(CRIME ~ HOVAL + INC, data = COL.OLD, listw=lw)
+  oldcrime.slx <- lm(CRIME ~ HOVAL + INC, data = COL.OLD, listw=lw)
   summary(lm.RStests(oldcrime.slx, listw=lw, test=c("adjRSerr", "adjRSlag")))
 }
 }

man/lm.morantest.exact.Rd

@@ -54,6 +54,7 @@ must be one of greater (default), less or two.sided.}
 \examples{
 eire <- st_read(system.file("shapes/eire.gpkg", package="spData")[1])
 row.names(eire) <- as.character(eire$names)
+st_crs(eire) <- "+proj=utm +zone=30 +ellps=airy +units=km"
 eire.nb <- poly2nb(eire)
 e.lm <- lm(OWNCONS ~ ROADACC, data=eire)
 lm.morantest(e.lm, nb2listw(eire.nb))

man/lm.morantest.sad.Rd

@@ -70,6 +70,7 @@ Geographical Analysis, 34, pp. 187--206; Bivand RS, Wong DWS 2018 Comparing impl
 \examples{
 eire <- st_read(system.file("shapes/eire.gpkg", package="spData")[1])
 row.names(eire) <- as.character(eire$names)
+st_crs(eire) <- "+proj=utm +zone=30 +ellps=airy +units=km"
 eire.nb <- poly2nb(eire)
 e.lm <- lm(OWNCONS ~ ROADACC, data=eire)
 lm.morantest(e.lm, nb2listw(eire.nb))

man/mstree.Rd

@@ -47,6 +47,7 @@ mstree(nbw, ini = NULL)
 ### loading data
 bh <- st_read(system.file("etc/shapes/bhicv.gpkg",
       package="spdep")[1], quiet=TRUE)
+st_crs(bh) <- "OGC:CRS84"
 ### data padronized
 dpad <- data.frame(scale(as.data.frame(bh)[,5:8]))
 

man/nblag.Rd

@@ -40,14 +40,14 @@ run <- FALSE
 if (require(igraph, quietly=TRUE) && require(spatialreg, quietly=TRUE)) run <- TRUE
 if (run) {
 W <- as(nb2listw(col.gal.nb), "CsparseMatrix")
-G <- graph_from_adjacency_matrix(W, mode="directed", weight="W")
+G <- graph.adjacency(W, mode="directed", weight="W")
 D <- diameter(G)
 nbs <- nblag(col.gal.nb, maxlag=D)
 n <- length(col.gal.nb)
 lmat <- lapply(nbs, nb2mat, style="B", zero.policy=TRUE)
 mat <- matrix(0, n, n)
 for (i in seq(along=lmat)) mat = mat + i*lmat[[i]]
-G2 <- distances(G)
+G2 <- shortest.paths(G)
 print(all.equal(G2, mat, check.attributes=FALSE))
 }
 }

man/skater.Rd

@@ -74,6 +74,7 @@ skater(edges, data, ncuts, crit, vec.crit, method = c("euclidean",
 ### loading data
 bh <- st_read(system.file("etc/shapes/bhicv.gpkg",
       package="spdep")[1], quiet=TRUE)
+st_crs(bh) <- "OGC:CRS84"
 ### data standardized 
 dpad <- data.frame(scale(as.data.frame(bh)[,5:8]))
 

src/dfs_ncomp.c

@@ -1,5 +1,4 @@
-/* Copyright 2001 by Nicholas Lewin-Koh.
- * interrupt added RSB 2024 */
+/* Copyright 2001 by Nicholas Lewin-Koh. */
 
 #include "spdep.h"
 
@@ -34,7 +33,6 @@ 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){