From 88032b5bd76a855a569300cd3fb27683c6cf0f9e Mon Sep 17 00:00:00 2001 From: Roger Bivand Date: Sat, 8 Jun 2024 16:33:51 +0200 Subject: [PATCH 1/2] address #157 --- DESCRIPTION | 4 ++-- NEWS.md | 4 +++- inst/etc/shapes/bhicv.dbf | Bin 13421 -> 0 bytes inst/etc/shapes/bhicv.gpkg | Bin 0 -> 143360 bytes inst/etc/shapes/bhicv.shp | Bin 27604 -> 0 bytes inst/etc/shapes/bhicv.shx | Bin 884 -> 0 bytes inst/etc/shapes/columbus.dbf | Bin 10082 -> 0 bytes inst/etc/shapes/columbus.shp | Bin 21980 -> 0 bytes inst/etc/shapes/columbus.shx | Bin 492 -> 0 bytes inst/etc/shapes/eire.dbf | Bin 5059 -> 0 bytes inst/etc/shapes/eire.shp | Bin 14040 -> 0 bytes inst/etc/shapes/eire.shx | Bin 308 -> 0 bytes man/EBImoran.mc.Rd | 2 +- man/EBest.Rd | 2 +- man/EBlocal.Rd | 2 +- man/SD.RStests.Rd | 2 +- man/autocov_dist.Rd | 2 +- man/bhicv.Rd | 2 +- man/choynowski.Rd | 2 +- man/columbus.Rd | 2 +- man/compon.Rd | 2 +- man/diffnb.Rd | 2 +- man/dnearneigh.Rd | 2 +- man/edit.nb.Rd | 2 +- man/globalG.test.Rd | 2 +- man/graphneigh.Rd | 2 +- man/include.self.Rd | 2 +- man/joincount.multi.Rd | 2 +- man/joincount.test.Rd | 2 +- man/knearneigh.Rd | 2 +- man/knn2nb.Rd | 2 +- man/listw2sn.Rd | 2 +- man/lm.morantest.exact.Rd | 2 +- man/lm.morantest.sad.Rd | 2 +- man/localGS.Rd | 2 +- man/localmoran.exact.Rd | 2 +- man/localmoran.sad.Rd | 2 +- man/localmoran_bv.Rd | 2 +- man/mat2listw.Rd | 2 +- man/moran.test.Rd | 2 +- man/mstree.Rd | 2 +- man/nb2lines.Rd | 2 +- man/nb2listw.Rd | 2 +- man/nb2mat.Rd | 2 +- man/nbdists.Rd | 2 +- man/nblag.Rd | 2 +- man/nboperations.Rd | 2 +- man/plot.nb.Rd | 2 +- man/poly2nb.Rd | 4 ++-- man/probmap.Rd | 2 +- man/skater.Rd | 2 +- man/sp.correlogram.Rd | 2 +- man/subset.listw.Rd | 2 +- man/subset.nb.Rd | 2 +- man/summary.nb.Rd | 2 +- man/testnb.Rd | 2 +- man/tri2nb.Rd | 2 +- vignettes/CO69.Rmd | 6 +++--- vignettes/nb.Rmd | 2 +- vignettes/nb_sf.Rmd | 2 +- vignettes/sids.Rmd | 14 +++++++------- 61 files changed, 63 insertions(+), 61 deletions(-) delete mode 100644 inst/etc/shapes/bhicv.dbf create mode 100644 inst/etc/shapes/bhicv.gpkg delete mode 100644 inst/etc/shapes/bhicv.shp delete mode 100644 inst/etc/shapes/bhicv.shx delete mode 100644 inst/etc/shapes/columbus.dbf delete mode 100644 inst/etc/shapes/columbus.shp delete mode 100644 inst/etc/shapes/columbus.shx delete mode 100644 inst/etc/shapes/eire.dbf delete mode 100644 inst/etc/shapes/eire.shp delete mode 100644 inst/etc/shapes/eire.shx diff --git a/DESCRIPTION b/DESCRIPTION index e11ae10f..01d33f2a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: spdep Version: 1.3-5 -Date: 2024-06-02 +Date: 2024-06-08 Title: Spatial Dependence: Weighting Schemes, Statistics Encoding: UTF-8 Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), @@ -38,7 +38,7 @@ Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), person("René", "Westerholt", role="ctb"), person("Levi", "Wolf", role = "ctb"), person("Danlin", "Yu", role = "ctb")) -Depends: R (>= 3.3.0), methods, spData (>= 0.2.6.0), sf +Depends: R (>= 3.3.0), methods, spData (>= 2.3.2), sf Imports: stats, deldir, boot (>= 1.3-1), graphics, utils, grDevices, units, s2, e1071, sp (>= 1.0) Suggests: spatialreg (>= 1.2-1), Matrix, parallel, dbscan, RColorBrewer, lattice, xtable, foreign, igraph, RSpectra, knitr, classInt, tmap, spam, ggplot2, rmarkdown, tinytest, rgeoda URL: https://github.com/r-spatial/spdep/, https://r-spatial.github.io/spdep/ diff --git a/NEWS.md b/NEWS.md index b079dc28..8521f627 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,6 @@ -# Version 1.3-4 (development) +# Version 1.3-5 (development) + +* #157 migrate ESRI Shapefile to GPKG files; convert bhicv.shp to GPKG * #155 Throw error if `hotspot` despatched on object without a `"quadr"` attribute diff --git a/inst/etc/shapes/bhicv.dbf b/inst/etc/shapes/bhicv.dbf deleted file mode 100644 index a1de00764f9defb8ebf48343241999b307e12dc7..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 13421 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5eab804d..2c58030f 100644 --- a/vignettes/nb.Rmd +++ b/vignettes/nb.Rmd @@ -45,7 +45,7 @@ read into R. ```{r} library(spdep) -NY8 <- as(sf::st_read(system.file("shapes/NY8_utm18.shp", package="spData")), "Spatial") +NY8 <- as(sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData")), "Spatial") NY_nb <- read.gal(system.file("weights/NY_nb.gal", package="spData"), region.id=as.character(as.integer(row.names(NY8))-1L)) ``` diff --git a/vignettes/nb_sf.Rmd b/vignettes/nb_sf.Rmd index de13feb8..dc207b0f 100644 --- a/vignettes/nb_sf.Rmd +++ b/vignettes/nb_sf.Rmd @@ -111,7 +111,7 @@ spdep::poly2nb uses two heuristics, first to find candidate neighbours from inte Next, we explore a further possible source of differences in neighbour object reproduction, using the original version of the tract boundaries used in ASDAR, but with some invalid geometries as mentioned earlier: ```{r, echo=dothis, eval=dothis} -NY8_sf_old <- st_read(system.file("shapes/NY8_utm18.shp", package="spData"), quiet=TRUE) +NY8_sf_old <- st_read(system.file("shapes/NY8_utm18.gpkg", package="spData"), quiet=TRUE) table(st_is_valid(NY8_sf_old)) ``` diff --git a/vignettes/sids.Rmd b/vignettes/sids.Rmd index 6c1eec13..a2777765 100644 --- a/vignettes/sids.Rmd +++ b/vignettes/sids.Rmd @@ -44,20 +44,20 @@ library(spdep) We will be using the **spdep** and **spreg** packages, here version: `r spdep()[1]`, the **sf** package and the **tmap** package. The data from the sources referred to above is documented in the help page for the `nc.sids` -data set in **spData**. The actual data, included in a shapefile of the county boundaries for North Carolina were made available in the **maptools** package [^1]. These data are known to be geographical coordinates (longitude-latitude in decimal degrees) and are assumed to use the NAD27 datum. +data set in **spData**. The actual data, included in a shapefile of the county boundaries for North Carolina were made available in the **maptools** package [^1]. These data are known to be geographical coordinates (longitude-latitude in decimal degrees) and are assumed to use the NAD27 datum. The ESRI Shapefile is deprecated, and was replaced here by a GeoPackage, written from reading the original files in **spData** 2.3.1: ```{r echo=TRUE,eval=TRUE} library(spdep) -nc <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE) -st_crs(nc) <- "EPSG:4267" +nc <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE) +#st_crs(nc) <- "EPSG:4267" row.names(nc) <- as.character(nc$FIPSNO) ``` -The shapefile format presupposes that you have three files with +The shapefile format presupposed that you had three files with extensions `.shp`, `.shx`, and `.dbf`, where the first contains the geometry data, the second the spatial index, and the third -the attribute data. They are required to have the same name apart from -the extension, and are read here using `sf::st_read()` into the +the attribute data. They were required to have the same name apart from +the extension, and were read here using `sf::st_read()` into the `sf` object `nc`; the class is defined in **sf**. The centroids of the largest polygon in each county are available using the `st_centroid` method from **sf** as an **sfc** POINT object, and can be used to place labels after the extraction of the coordinate matrix: @@ -463,4 +463,4 @@ tables of covariates rather than geographical grids. ## References [^1]: These data were taken with permission from a now-offline link: -[sal.agecon.uiuc.edu/datasets/sids.zip]; see also [GeoDa Center](https://geodacenter.github.io/data-and-lab/) for a contemporary source. \ No newline at end of file +[sal.agecon.uiuc.edu/datasets/sids.zip]; see also [GeoDa Center](https://geodacenter.github.io/data-and-lab/) for a contemporary source. From 37d5856832819ed12d4479f079601b9dbad5bf05 Mon Sep 17 00:00:00 2001 From: Roger Bivand Date: Mon, 10 Jun 2024 11:10:53 +0200 Subject: [PATCH 2/2] workaround NY8 file differences, #157 --- DESCRIPTION | 4 ++-- vignettes/nb.Rmd | 13 ++++++++++--- vignettes/nb_sf.Rmd | 8 +++++++- 3 files changed, 19 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 01d33f2a..537ce3a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: spdep Version: 1.3-5 -Date: 2024-06-08 +Date: 2024-06-10 Title: Spatial Dependence: Weighting Schemes, Statistics Encoding: UTF-8 Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), @@ -38,7 +38,7 @@ Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), person("René", "Westerholt", role="ctb"), person("Levi", "Wolf", role = "ctb"), person("Danlin", "Yu", role = "ctb")) -Depends: R (>= 3.3.0), methods, spData (>= 2.3.2), sf +Depends: R (>= 3.3.0), methods, spData (>= 2.3.1), sf Imports: stats, deldir, boot (>= 1.3-1), graphics, utils, grDevices, units, s2, e1071, sp (>= 1.0) Suggests: spatialreg (>= 1.2-1), Matrix, parallel, dbscan, RColorBrewer, lattice, xtable, foreign, igraph, RSpectra, knitr, classInt, tmap, spam, ggplot2, rmarkdown, tinytest, rgeoda URL: https://github.com/r-spatial/spdep/, https://r-spatial.github.io/spdep/ diff --git a/vignettes/nb.Rmd b/vignettes/nb.Rmd index 2c58030f..396aa465 100644 --- a/vignettes/nb.Rmd +++ b/vignettes/nb.Rmd @@ -45,7 +45,14 @@ read into R. ```{r} library(spdep) -NY8 <- as(sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData")), "Spatial") +if (packageVersion("spData") >= "2.3.2") { + NY8a <- sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData")) +} else { + NY8a <- sf::st_read(system.file("shapes/NY8_bna_utm18.gpkg", package="spData")) + sf::st_crs(NY8a) <- "EPSG:32618" + NY8a$Cases <- NY8a$TRACTCAS +} +NY8 <- as(NY8a, "Spatial") NY_nb <- read.gal(system.file("weights/NY_nb.gal", package="spData"), region.id=as.character(as.integer(row.names(NY8))-1L)) ``` @@ -57,8 +64,8 @@ to the full data set. We retrieve the part of the neighbour list in Syracuse using the `subset` method. ```{r} -Syracuse <- NY8[NY8$AREANAME == "Syracuse city",] -Sy0_nb <- subset(NY_nb, NY8$AREANAME == "Syracuse city") +Syracuse <- NY8[!is.na(NY8$AREANAME) & NY8$AREANAME == "Syracuse city",] +Sy0_nb <- subset(NY_nb, !is.na(NY8$AREANAME) & NY8$AREANAME == "Syracuse city") summary(Sy0_nb) ``` diff --git a/vignettes/nb_sf.Rmd b/vignettes/nb_sf.Rmd index dc207b0f..ac0cda17 100644 --- a/vignettes/nb_sf.Rmd +++ b/vignettes/nb_sf.Rmd @@ -111,7 +111,13 @@ spdep::poly2nb uses two heuristics, first to find candidate neighbours from inte Next, we explore a further possible source of differences in neighbour object reproduction, using the original version of the tract boundaries used in ASDAR, but with some invalid geometries as mentioned earlier: ```{r, echo=dothis, eval=dothis} -NY8_sf_old <- st_read(system.file("shapes/NY8_utm18.gpkg", package="spData"), quiet=TRUE) +if (packageVersion("spData") >= "2.3.2") { + NY8_sf_old <- sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData")) +} else { + NY8_sf_old <- sf::st_read(system.file("shapes/NY8_bna_utm18.gpkg", package="spData")) + sf::st_crs(NY8_sf_old) <- "EPSG:32618" + NY8_sf_old$Cases <- NY8_sf_old$TRACTCAS +} table(st_is_valid(NY8_sf_old)) ```