Warnings and error during the creation of the neighborhood matrix by recoding old code using deprecated rgdal in CRAN with sf and sp
200% echo everything said by Dr. Bivand below.
In addition, I would focus on the error message:
Empty neighbor sets found (zero.policy: FALSE)
This is the thing you need to solve. Why are there locations without
neighbors? A "cheap way out" which we offer in ArcGIS Pro is to provide a
union of the neighbor sets using KNN and contiguity. This ensures that each
location has at minimum k number of neighbors. You can accomplish this like
the example below. *However*, I would consider the implications of using
distance metrics for polygons. See if what you're doing actually makes
sense conceptually.
library(spdep)
geo <- system.file("shapes/columbus.gpkg", package="spData") |>
sf::st_read(quiet = TRUE) |>
sf::st_geometry()
nb_contig <- poly2nb(geo)
# helper from sfdep for st_centroid() -> knearneigh() -> knn2nb()
nb_k1 <- sfdep::st_knn(geo)
union.nb(nb_contig, nb_k1)
On Wed, Dec 17, 2025 at 1:06?AM Roger Bivand via R-sig-Geo <
r-sig-geo at r-project.org> wrote:
On Tue, 16 Dec 2025, Aymard Lo?c KWEKEU KWEKEU wrote: First, you do not show the versions of software being used, including the platform, versions of rgdal, sp, sf, spdep, mgcv, R2BayesX, possibly others. The versions of GDAL used in rgdal and sf may also matter, as GDAL also changes over time (the precision of coordinates in the same ESRI Shapefile may differ, artefacts in polygons bay be corrected differently). Comments inline.
*Initial code with rgdal's readOGR function: *
geo <- readOGR("./Data/Carto/COMMUNE_CARTO.shp")
Without an example file (all the files making up the ESRI shapefile, at least *.shp, *.shx, *.dbf, preferably with *.prj), there is no way to establish anything.
geo2 <- subset(geo, geo at data$INSEE_COM %in% selected_com)
Never refer to S4 slots using @ in workflows - geo$INSEE_COM has been sufficient now for 20 years.
DATA2BND <- sp2bnd(geo2, geo2 at data$INSEE_COM) plot(DATA2BND) list_names <- as.data.frame(names(DATA2BND)) %>% group_by(names(DATA2BND)) %>% summarise(n = n())
sp2bnd is a function in R2BayesX and is strictly superfluous to this question.
nb <- mgcv:::pol2nb(DATA2BND)$nb
mgcv:::pol2nb is a function in mgcv and is strictly superfluous to this question.
W.nb <- poly2nb( geo2, row.names = rownames(geo2 at data$INSEE_COM) ) w <- nb2mat(W.nb, style = "B")
This is the core of the question - why no warnings or errors?
*New code with sf and sp: *
geo_sf <- st_read("./Data/Carto/COMMUNE_CARTO.shp", quiet = TRUE)
Coercing to an sp-class is superfluous.
geo <- as(geo_sf, "Spatial") geo2 <- subset(geo, geo at data$INSEE_COM %in% selected_com) DATA2BND <- sp2bnd(geo2, geo2 at data$INSEE_COM) plot(DATA2BND) list_names <- as.data.frame(names(DATA2BND)) %>% group_by(names(DATA2BND)) %>% summarise(n = n()) nb <- mgcv:::pol2nb(DATA2BND)$nb
It is possible that the coordinate values of the polygons in geo2 differ here by a very small amount if the versions of GDAL used to install rgdal and sf differ, and also because sf's implementation for reading geometries is more modern and cleaner than that in rgdal (>20 years old).
W.nb <- poly2nb(geo2, row.names = rownames(geo2 at data$INSEE_COM),
queen=T)
Warning messages: 1: In poly2nb(geo2, row.names = rownames(geo2 at data$INSEE_COM), queen =
T):
some observations have no neighbors; if this seems unexpected, try increasing the snap argument.
Recent changes in spdep warn about observations with no neighbours, and about subgraphs. Please read the relevant vignette: https://cran.r-project.org/web/packages/spdep/vignettes/subgraphs.html No-neighbour observations may be detected when apparently contiguous polygons are separated by >10mm (default value) if the input polygons are an sf object, otherwise sqrt(.Machine$double.eps), (so the sp case is unchanged).
2: In poly2nb(geo2, row.names = rownames(geo2 at data$INSEE_COM), queen =
T):
neighbor object has 7 sub-graphs; if this sub-graph count seems unexpected, try increasing the snap
argument.
w_SMD_2025 <- nb2mat(W.nb, style = "B") Error in nb2listw(neighbors, glist = glist, style = style, zero.policy = zero.policy): Empty neighbor sets found (zero.policy: FALSE)
If you accept a neighbour object with subgraphs (probably no-neighbour observations), set zero.policy=TRUE in nb2mat. This may however cause problems later on. I suggest rather avoiding sp, subsetting geo_sf, and using that object in poly2nb. You also need to check whether the polygons are planar or spherical, as this affects the default value of snap. If you need to share data, do not attach to posts on this list, but rather raise an issue on https://github.com/r-spatial/spdep/issues/, where the data and code for a minimal reproducible example may be attached. Hope this clarifies, Roger -- Roger Bivand Emeritus Professor Department of Economics, Norwegian School of Economics, Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway. e-mail: Roger.Bivand at nhh.no
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