poly2nb: Construct neighbours list from polygon list

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/poly2nb.R

Description

The function builds a neighbours list based on regions with contiguous boundaries, that is sharing one or more boundary point. The current function is in part interpreted and may run slowly for many regions or detailed boundaries, but from 0.2-16 should not fail because of lack of memory when single polygons are built of very many border coordinates.

Usage

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poly2nb(pl, row.names = NULL, snap=sqrt(.Machine$double.eps),
 queen=TRUE, useC=TRUE, foundInBox=NULL)

Arguments

pl

list of polygons of class extending SpatialPolygons, or an sf or sfc object containing non-empty (multi-)polygon objects

row.names

character vector of region ids to be added to the neighbours list as attribute region.id, default seq(1, nrow(x)); if pl has row.names, they are used instead of the default sequence.

snap

boundary points less than snap distance apart are considered to indicate contiguity

queen

if TRUE, a single shared boundary point meets the contiguity condition, if FALSE, more than one shared point is required; note that more than one shared boundary point does not necessarily mean a shared boundary line

useC

default TRUE, doing the work loop in C, may be set to false to revert to R code calling two C functions in an n*k work loop, where k is the average number of candidate neighbours

foundInBox

default NULL using R code, possibly parallelised if a snow cluster is available, otherwise a list of length (n-1) with integer vectors of candidate neighbours (j > i), or NULL if all candidates were (j < i) (as created by the poly_findInBoxGEOS function in rgeos for clean polygons)

Value

A neighbours list with class nb. See card for details of “nb” objects.

Note

From 0.5-8, the function includes faster bounding box indexing and other improvements contributed by Micah Altman. If a cluster is provided using set.ClusterOption, it will be used for finding candidate bounding box overlaps for exact testing for contiguity.

Until 1.1-7, sf polygons included both start and end points, so could erroneously report rook neighbourhood where only queen was present, see https://github.com/r-spatial/spdep/issues/50.

From 1.1-9 with sf 1.0-0, s2 is used in bounding box indexing internally when pl is in geographical coordinates. Because the topology engine of s2 differs from the use of GEOS for planar coordinates by sf, some output differences may be expected. When s2 is used, (use_s2=TRUE and dfMaxLength > 0) segmenting is done to add points to bounding box edges, making them more likely to intersect on the sphere, but currently increasing timing and memory use substantially. If segmenting not is done, but use_s2=TRUE, candidate neighbours may be missed and others exchanged. Since treating spherical geometries as planar is also questionable, it is not clear whether spherical contiguous polygon neighbours should simply follow neighbours found by treating the geometries as planar https://github.com/r-spatial/s2/issues/125#issuecomment-864403372. However, current advice is not to use s2 for finding contiguity neighbours.

Author(s)

Roger Bivand Roger.Bivand@nhh.no with contributions from Micah Altman

See Also

summary.nb, card

Examples

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columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE)
col.gal.nb <- read.gal(system.file("weights/columbus.gal", package="spData")[1])
coords <- st_coordinates(st_centroid(st_geometry(columbus)))
xx <- poly2nb(as(columbus, "Spatial"))
dxx <- diffnb(xx, col.gal.nb)
plot(st_geometry(columbus), border="grey")
plot(col.gal.nb, coords, add=TRUE)
plot(dxx, coords, add=TRUE, col="red")
title(main=paste("Differences (red) in Columbus GAL weights (black)",
 "and polygon generated queen weights", sep="\n"), cex.main=0.6)
# poly2nb with sf sfc_MULTIPOLYGON objects
sf_xx <- poly2nb(columbus)
diffnb(sf_xx, xx)
sfc_xx <- poly2nb(st_geometry(columbus))
diffnb(sfc_xx, xx)
xxx <- poly2nb(as(columbus, "Spatial"), queen=FALSE)
dxxx <- diffnb(xxx, col.gal.nb)
plot(st_geometry(columbus), border = "grey")
plot(col.gal.nb, coords, add = TRUE)
plot(dxxx, coords, add = TRUE, col = "red")
title(main=paste("Differences (red) in Columbus GAL weights (black)",
 "and polygon generated rook weights", sep="\n"), cex.main=0.6)
cards <- card(xx)
maxconts <- which(cards == max(cards))
if(length(maxconts) > 1) maxconts <- maxconts[1]
fg <- rep("grey", length(cards))
fg[maxconts] <- "red"
fg[xx[[maxconts]]] <- "green"
plot(st_geometry(columbus), col=fg)
title(main="Region with largest number of contiguities", cex.main=0.6)
nc.sids <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE)
system.time(xxnb <- poly2nb(nc.sids))
system.time(xxnb <- poly2nb(as(nc.sids, "Spatial")))
plot(st_geometry(nc.sids))
plot(xxnb, coordinates(as(nc.sids, "Spatial")), add=TRUE, col="blue")
sq <- st_polygon(list(rbind(c(0,0), c(1,0), c(1,1), c(0,1), c(0,0))))
sq2 <- sq + c(0,1)
sq3 <- sq + c(1,0)
sq4 <- sq + c(1,1)
gm <- st_sfc(list(sq, sq2, sq3, sq4))
df <- st_as_sf(gm, id=1:4)
plot(st_geometry(df))
text(st_coordinates(st_centroid(gm)), as.character(df$id))
unclass(poly2nb(df, queen = FALSE))

Example output

Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1
Neighbour list object:
Number of regions: 49 
Number of nonzero links: 0 
Percentage nonzero weights: 0 
Average number of links: 0 
49 regions with no links:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
Neighbour list object:
Number of regions: 49 
Number of nonzero links: 0 
Percentage nonzero weights: 0 
Average number of links: 0 
49 regions with no links:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
   user  system elapsed 
  0.032   0.000   0.033 
   user  system elapsed 
  0.039   0.000   0.039 
[[1]]
[1] 2 3 4

[[2]]
[1] 1 4

[[3]]
[1] 1 4

[[4]]
[1] 1 2 3

attr(,"region.id")
[1] "1" "2" "3" "4"
attr(,"call")
poly2nb(pl = df, queen = FALSE)
attr(,"type")
[1] "rook"
attr(,"sym")
[1] TRUE

spdep documentation built on Sept. 7, 2021, 5:07 p.m.