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Read and write spatial neighbour files

read.gwt2nb.Rd

The "gwt" functions read and write GeoDa GWT files (the example file baltk4.GWT was downloaded from the site given in the reference), and the "dat" functions read and write Matlab sparse matrix files as used by James LeSage's Spatial Econometrics Toolbox (the example file wmat.dat was downloaded from the site given in the reference). The body of the files after any headers should have three columns separated by white space, and the third column must be numeric in the locale of the reading platform (correct decimal separator).

Usage

read.gwt2nb(file, region.id=NULL)
write.sn2gwt(sn, file, shpfile=NULL, ind=NULL, useInd=FALSE, legacy=FALSE)
read.dat2listw(file)
write.sn2dat(sn, file)
read.swmdbf2listw(fn, region.id=NULL, style=NULL, zero.policy=NULL)
read_swm_dbf(fn)
write.swmdbf(listw, file, ind, region.id = attr(listw, "region.id"))
write_swm_dbf(listw, file, ind, region.id = attr(listw, "region.id"))
write.sn2DBF(sn, file)

Arguments

file, fn

name of file with weights data

region.id

a character vector of region IDs - for ArcGIS SWM DBFs, the values must be character integers (only numbers not starting with zero)

listw

a listw object

sn

a spatial.neighbour object

shpfile

character string: if not given Shapefile name taken from GWT file for this dataset

ind

character string: region id indicator field name

useInd

default FALSE, if TRUE, write region.id attribute ID key tags to output file (use in OpenGeoDa will depend on the shapefile having the field named in the ind argument matching the exported tags)

legacy

default FALSE; if TRUE, header has single field with number of observations only

style

default NULL, missing, set to "M" and warning given; if not "M", passed to nb2listw to re-build the object

zero.policy

default NULL, use global option value; if FALSE stop with error for any empty neighbour sets, if TRUE permit the weights list to be formed with zero-length weights vectors

Details

Attempts to honour the region.id argument given when reading GWT and SWM/DBF files. If the region IDs given in region.id= do not match the origins or destinations in the GWT file, an error or warning will be thrown, which should be considered carefully. read_swm_dbf is a simplified interface to read.swmdbf2listw When no-neighbour observations are present, it is advised that region.id= be given in read.swmdbf2listw; while the function should read correctly if the minimum and maximum IDs are present as observations with neighbours without region.id= set, reading using read.swmdbf2listw will fail when the minimum or maximum ID observations have no neighbours and region.id= is not given.

Value

read.gwt2nb returns a neighbour "nb" object with the generalised weights stored as a list element called "dlist" of the "GeoDa" attribute; read.swmdbf2listw returns a "listw" object read from a DBF file exported from an ArcGIS SWM object.

References

Luc Anselin (2003) GeoDa 0.9 User's Guide, pp. 80–81, Spatial Analysis Laboratory, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, http://geodacenter.github.io/docs/geoda093.pdf; also material formerly at spatial-econometrics.com/data/contents.html

Author

Roger Bivand Roger.Bivand@nhh.no

See also

read.gal

Examples

data(baltimore, package="spData")
STATION <- baltimore$STATION
gwt1 <- read.gwt2nb(system.file("weights/baltk4.GWT", package="spData")[1],
 STATION)
#> Warning: 102, 115, 208 are not destinations
cat(paste("Neighbours list symmetry;", is.symmetric.nb(gwt1, FALSE, TRUE),
 "\n"))
#> Neighbours list symmetry; FALSE 
listw1 <- nb2listw(gwt1, style="B", glist=attr(gwt1, "GeoDa")$dist)
tmpGWT <- tempfile()
write.sn2gwt(listw2sn(listw1), tmpGWT)
gwt2 <- read.gwt2nb(tmpGWT, STATION)
#> Warning: 102, 115, 208 are not destinations
cat(paste("Neighbours list symmetry;", is.symmetric.nb(gwt2, FALSE, TRUE),
 "\n"))
#> Neighbours list symmetry; FALSE 
diffnb(gwt1, gwt2)
#> Warning: neighbour object has 211 sub-graphs
#> Neighbour list object:
#> Number of regions: 211 
#> Number of nonzero links: 0 
#> Percentage nonzero weights: 0 
#> Average number of links: 0 
#> 211 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, 50, 51, 52, 53, 54, 55, 56,
#> 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
#> 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
#> 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107,
#> 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,
#> 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
#> 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149,
#> 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163,
#> 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177,
#> 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
#> 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205,
#> 206, 207, 208, 209, 210, 211
#> 211 disjoint connected subgraphs
data(oldcol)
tmpMAT <- tempfile()
COL.W <- nb2listw(COL.nb)
write.sn2dat(listw2sn(COL.W), tmpMAT)
listwmat1 <- read.dat2listw(tmpMAT)
#> Warning: style is M (missing); style should be set to a valid value
diffnb(listwmat1$neighbours, COL.nb, verbose=TRUE)
#> Warning: region.id differ; using ids of first list
#> Warning: neighbour object has 49 sub-graphs
#> Neighbour list object:
#> Number of regions: 49 
#> Number of nonzero links: 0 
#> Percentage nonzero weights: 0 
#> Average number of links: 0 
#> 49 regions with no links:
#> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
#> 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
#> 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49
#> 49 disjoint connected subgraphs
listwmat2 <- read.dat2listw(system.file("etc/weights/wmat.dat", 
 package="spdep")[1])
#> Warning: style is M (missing); style should be set to a valid value
diffnb(listwmat1$neighbours, listwmat2$neighbours, verbose=TRUE)
#> Warning: neighbour object has 49 sub-graphs
#> Neighbour list object:
#> Number of regions: 49 
#> Number of nonzero links: 0 
#> Percentage nonzero weights: 0 
#> Average number of links: 0 
#> 49 regions with no links:
#> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
#> 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
#> 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49
#> 49 disjoint connected subgraphs
if (require("foreign", quietly=TRUE)) {
nc_sf <- sf::st_read(system.file("gpkg/nc.gpkg", package="sf")[1])
nc_sf$UniqueID <- 1:nrow(nc_sf)
fn <- system.file("etc/misc/nc_contiguity_unique_id.dbf", package="spdep")[1]
nc1 <- read.swmdbf2listw(fn, style="B")
nc1
nc1a <- read.swmdbf2listw(fn, region.id=as.character(nc_sf$UniqueID),
 style="B")
all.equal(nc1, nc1a)
fn <- system.file("etc/misc/nc_contiguity_unique_id_islands.dbf",
 package="spdep")[1]
try(nc1i <- read.swmdbf2listw(fn, style="B"))
nc1i <- read.swmdbf2listw(fn, style="B", zero.policy=TRUE)
nc1ia <- read.swmdbf2listw(fn, region.id=as.character(nc_sf$UniqueID),
 style="B", zero.policy=TRUE)
nc1ia
all.equal(nc1i, nc1ia)
(GDAL37 <- as.numeric_version(unname(sf_extSoftVersion()["GDAL"])) >= "3.7.0")
file <- "etc/shapes/california.gpkg.zip"
zipfile <- system.file(file, package="spdep")
if (GDAL37) {
    cal <- st_read(zipfile)
} else {
    td <- tempdir()
    bn <- sub(".zip", "", basename(file), fixed=TRUE)
    target <- unzip(zipfile, files=bn, exdir=td)
    cal <- st_read(target)
}
fn <- system.file("etc/misc/contiguity_myid.dbf", package="spdep")[1]
cal1 <- read.swmdbf2listw(fn, style="B")
cal1a <- read.swmdbf2listw(fn, region.id=as.character(cal$MYID), style="B")
all.equal(cal1, cal1a)
fn <- system.file("etc/misc/contiguity_unique_id.dbf", package="spdep")[1]
cal2 <- read.swmdbf2listw(fn, style="B")
cal2a <- read.swmdbf2listw(fn, region.id=as.character(cal$UniqueID), style="B")
all.equal(cal2, cal2a)
fn <- system.file("etc/misc/contiguity_unique_id_islands.dbf", package="spdep")[1]
try(cal3i <- read.swmdbf2listw(fn, style="B"))
cal3i <- read.swmdbf2listw(fn, style="B", zero.policy=TRUE)
cal3ia <- read.swmdbf2listw(fn, region.id=as.character(cal$UniqueID), style="B", zero.policy=TRUE)
all.equal(cal3i, cal3ia)
cal1a_1n_nb <- cal1a$neighbours
cal1a_1n_nb <- droplinks(cal1a_1n_nb, drop=c("158", "180", "215"), sym=TRUE)
cal1a_1n <- nb2listw(cal1a_1n_nb, style="B", zero.policy=TRUE)
cal1a_1n_sn <- listw2sn(cal1a_1n)
file <- tempfile(fileext=".dbf")
write.sn2DBF(cal1a_1n_sn, file)
cal1a_1n_rt <- read.swmdbf2listw(file, region.id=as.character(cal$MYID),
 style="B", zero.policy=TRUE)
all.equal(cal1a_1n$neighbours, cal1a_1n_rt$neighbours)
all.equal(cal1a_1n$weights, cal1a_1n_rt$weights, check.attributes=FALSE)
cal1_1n_rt <- read.swmdbf2listw(file, style="B", zero.policy=TRUE)
all(isTRUE(all.equal(cal1a_1n$neighbours, cal1_1n_rt$neighbours)))
all(isTRUE(all.equal(cal1a_1n$weights, cal1_1n_rt$weights)))

}
#> Reading layer `nc.gpkg' from data source `/home/rsb/lib/r_libs/sf/gpkg/nc.gpkg' using driver `GPKG'
#> Simple feature collection with 100 features and 14 fields
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
#> Geodetic CRS:  NAD27
#> Warning: region.id not given, c(MYID, NID) range is 1:100
#> Warning: region.id not given, c(MYID, NID) range is 1:100
#> Warning: 81 is not an origin
#> Error in read.swmdbf2listw(fn, style = "B") : 
#>   Error in sn2listw(df1, style = style, zero.policy = zero.policy) : 
#>   no-neighbour observations found, set zero.policy to TRUE
#> 
#> Warning: region.id not given, c(MYID, NID) range is 1:100
#> Reading layer `california' from data source 
#>   `/tmp/RtmpXVTJuL/temp_libpath3b356d487bad39/spdep/etc/shapes/california.gpkg.zip' 
#>   using driver `GPKG'
#> Simple feature collection with 58 features and 2 fields
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -13847330 ymin: 3810869 xmax: -12704360 ymax: 5132708
#> Projected CRS: World_Mercator
#> Warning: region.id not given, c(MYID, NID) range is 158:215
#> Warning: region.id not given, c(MYID, NID) range is 1:58
#> Warning: region.id not given, c(MYID, NID) range is 1:58
#> Warning: 21, 38 are not origins
#> Error in read.swmdbf2listw(fn, style = "B") : 
#>   Error in sn2listw(df1, style = style, zero.policy = zero.policy) : 
#>   no-neighbour observations found, set zero.policy to TRUE
#> 
#> Warning: region.id not given, c(MYID, NID) range is 1:58
#> Warning: some observations have no neighbours
#> Warning: neighbour object has 4 sub-graphs
#> Warning: neighbour object has 4 sub-graphs
#> Warning: region.id not given, c(MYID, NID) range is 159:214
#> Warning: neighbour object has 2 sub-graphs
#> [1] FALSE