Errors in the spdep::skater documentation

[SpatLyu]

There are numerous errors in the demo of the spdep::skater documentation.

There were no issues when I tested it locally：

library(spdep)
#> Loading required package: spData
#> Loading required package: sf
#> Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
(GDAL37 <- as.numeric_version(unname(sf_extSoftVersion()["GDAL"])) >= "3.7.0")
#> [1] TRUE
file <- "etc/shapes/bhicv.gpkg.zip"
zipfile <- system.file(file, package="spdep")
if (GDAL37) {
  bh <- st_read(zipfile)
} else {
  td <- tempdir()
  bn <- sub(".zip", "", basename(file), fixed=TRUE)
  target <- unzip(zipfile, files=bn, exdir=td)
  bh <- st_read(target)
}
#> Reading layer `bhicv' from data source 
#>   `C:\Users\dell\R\pkgR\spdep\etc\shapes\bhicv.gpkg.zip' using driver `GPKG'
#> Simple feature collection with 98 features and 8 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -45.02175 ymin: -20.93007 xmax: -42.50321 ymax: -18.08342
#> Geodetic CRS:  Corrego Alegre 1970-72

dpad <- data.frame(scale(as.data.frame(bh)[,5:8]))

bh.nb <- poly2nb(bh)

lcosts <- nbcosts(bh.nb, dpad)

nb.w <- nb2listw(bh.nb, lcosts, style="B")

mst.bh <- mstree(nb.w,5)

par(mar=c(0,0,0,0))
plot(st_geometry(bh), border=gray(.5))
pts <- st_coordinates(st_centroid(bh))
#> Warning: st_centroid assumes attributes are constant over geometries
plot(mst.bh, pts, col=2, 
     cex.lab=.6, cex.circles=0.035, fg="blue", add=TRUE)

res1 <- skater(mst.bh[,1:2], dpad, 2)
table(res1$groups)
#> 
#>  1  2  3 
#> 18 23 57
opar <- par(mar=c(0,0,0,0))
plot(res1, pts, cex.circles=0.035, cex.lab=.7)

plot(res1, pts, cex.circles=0.035, cex.lab=.7,
     groups.colors=heat.colors(length(res1$ed)))

plot(st_geometry(bh), col=heat.colors(length(res1$edg))[res1$groups])

My local configuration is as follows:

sessionInfo()
#> R version 4.4.1 (2024-06-14 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 22631)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.utf8 
#> [2] LC_CTYPE=Chinese (Simplified)_China.utf8   
#> [3] LC_MONETARY=Chinese (Simplified)_China.utf8
#> [4] LC_NUMERIC=C                               
#> [5] LC_TIME=Chinese (Simplified)_China.utf8    
#> 
#> time zone: Asia/Shanghai
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.37     fastmap_1.2.0     xfun_0.47         glue_1.7.0       
#>  [5] knitr_1.48        htmltools_0.5.8.1 rmarkdown_2.28    lifecycle_1.0.4  
#>  [9] cli_3.6.3         reprex_2.1.1      withr_3.0.1       compiler_4.4.1   
#> [13] rstudioapi_0.16.0 tools_4.4.1       evaluate_1.0.0    yaml_2.3.10      
#> [17] rlang_1.1.4       fs_1.6.4

^{Created on 2024-09-28 with reprex v2.1.1}

[rsbivand]

Struggling to get pkgdown to generate clean output, still working on this.

[rsbivand]

Seems OK now, thanks for reporting!