diff --git a/DESCRIPTION b/DESCRIPTION index d1ab828..6207cf9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: spatialreg -Version: 1.3-3 -Date: 2024-05-31 +Version: 1.3-4 +Date: 2024-06-10 Title: Spatial Regression Analysis Encoding: UTF-8 Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), email = "Roger.Bivand@nhh.no", comment=c(ORCID="0000-0003-2392-6140")), @@ -25,7 +25,7 @@ Authors@R: c(person("Roger", "Bivand", role = c("cre", "aut"), email = "Roger.Bi person(given = "Mauricio", family = "Sarrias", role = c("ctb"), email = "mauricio.sarrias@ucn.cl"), person(given = "JuanTomas", family = "Sayago", role = c("ctb"), email = "juantomas.sayago@gmail.com"), person("Michael", "Tiefelsdorf", role = "ctb")) -Depends: R (>= 3.3.0), spData, Matrix, sf +Depends: R (>= 3.3.0), spData (>= 2.3.1), Matrix, sf Imports: spdep (>= 1.3-1), coda, methods, MASS, boot, splines, LearnBayes, nlme, multcomp Suggests: parallel, RSpectra, tmap, foreign, spam, knitr, lmtest, expm, diff --git a/NEWS.md b/NEWS.md index 0214ed7..5510430 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,8 @@ -# Version 1.3-3 (development) +# Version 1.3-4 (development) + +* migrate from ESRI Shapefile to GeoPackage #50 + +# Version 1.3-3 (2024-05-31) * protect `errorsarlm` against missing `Durbin=` if only intercept diff --git a/man/ME.Rd b/man/ME.Rd index 5de00f8..5d5eb4d 100644 --- a/man/ME.Rd +++ b/man/ME.Rd @@ -65,7 +65,7 @@ coef(summary(glmME)) anova(glmbase, glmME, test="Chisq") \dontrun{ require("sf", quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require("spdep", quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) lw <- spdep::nb2listw(col.gal.nb) @@ -96,7 +96,7 @@ COL.ME.NA <- ME(CRIME ~ INC + HOVAL, data=NA.columbus, family="gaussian", COL.ME.NA$na.action summary(lm(CRIME ~ INC + HOVAL + fitted(COL.ME.NA), data=NA.columbus, na.action=na.exclude)) -nc.sids <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE) +nc.sids <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE) rn <- as.character(nc.sids$FIPS) ncCC89_nb <- spdep::read.gal(system.file("weights/ncCC89.gal", package="spData")[1], region.id=rn) diff --git a/man/SpatialFiltering.Rd b/man/SpatialFiltering.Rd index 0081984..f1aa340 100644 --- a/man/SpatialFiltering.Rd +++ b/man/SpatialFiltering.Rd @@ -55,7 +55,7 @@ SpatialFiltering(formula, lagformula=NULL, data=list(), na.action=na.fail, \seealso{\code{\link[stats]{lm}}, \code{\link[base]{eigen}}, \code{\link{nb2listw}}, \code{\link{listw2U}}} \examples{ require("sf", quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require("spdep", quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) lmbase <- lm(CRIME ~ INC + HOVAL, data=columbus) diff --git a/man/aple.Rd b/man/aple.Rd index 314b18c..f32ebd5 100644 --- a/man/aple.Rd +++ b/man/aple.Rd @@ -27,7 +27,7 @@ aple(x, listw, override_similarity_check=FALSE, useTrace=TRUE) \seealso{\code{\link[spdep]{nb2listw}}, \code{\link{aple.mc}}, \code{\link{aple.plot}} } \examples{ -wheat <- st_read(system.file("shapes/wheat.shp", package="spData")[1], quiet=TRUE) +wheat <- st_read(system.file("shapes/wheat.gpkg", package="spData")[1], quiet=TRUE) library(spdep) nbr1 <- spdep::poly2nb(wheat, queen=FALSE) nbrl <- spdep::nblag(nbr1, 2) diff --git a/man/aple.mc.Rd b/man/aple.mc.Rd index cb533c1..ec9fab4 100644 --- a/man/aple.mc.Rd +++ b/man/aple.mc.Rd @@ -26,7 +26,7 @@ aple.mc(x, listw, nsim, override_similarity_check=FALSE, useTrace=TRUE) \seealso{\code{\link{aple}}, \code{\link[boot]{boot}}} \examples{ \dontrun{ -wheat <- st_read(system.file("shapes/wheat.shp", package="spData")[1], quiet=TRUE) +wheat <- st_read(system.file("shapes/wheat.gpkg", package="spData")[1], quiet=TRUE) nbr1 <- spdep::poly2nb(wheat, queen=FALSE) nbrl <- spdep::nblag(nbr1, 2) nbr12 <- spdep::nblag_cumul(nbrl) diff --git a/man/aple.plot.Rd b/man/aple.plot.Rd index 7f96bfb..70914aa 100644 --- a/man/aple.plot.Rd +++ b/man/aple.plot.Rd @@ -35,7 +35,7 @@ localAple(x, listw, override_similarity_check=FALSE, useTrace=TRUE) \seealso{\code{\link{aple}}} \examples{ \dontrun{ -wheat <- st_read(system.file("shapes/wheat.shp", package="spData")[1], quiet=TRUE) +wheat <- st_read(system.file("shapes/wheat.gpkg", package="spData")[1], quiet=TRUE) nbr1 <- spdep::poly2nb(wheat, queen=FALSE) nbrl <- spdep::nblag(nbr1, 2) nbr12 <- spdep::nblag_cumul(nbrl) diff --git a/man/impacts.Rd b/man/impacts.Rd index 858275b..06628d1 100644 --- a/man/impacts.Rd +++ b/man/impacts.Rd @@ -95,7 +95,7 @@ Roger Bivand, Gianfranco Piras (2015). Comparing Implementations of Estimation M } \examples{ require("sf", quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require("spdep", quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) listw <- spdep::nb2listw(col.gal.nb) diff --git a/man/sarlm_tests.Rd b/man/sarlm_tests.Rd index 2681193..e9d053b 100644 --- a/man/sarlm_tests.Rd +++ b/man/sarlm_tests.Rd @@ -76,7 +76,7 @@ Dordrecht: Kluwer, pp. 121--122. \examples{ require("sf", quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require("spdep", quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) lm.mod <- lm(CRIME ~ HOVAL + INC, data=columbus) diff --git a/man/sparse_mat.Rd b/man/sparse_mat.Rd index 1e41927..738a511 100644 --- a/man/sparse_mat.Rd +++ b/man/sparse_mat.Rd @@ -46,7 +46,7 @@ powerWeights(W, rho, order=250, X, tol=.Machine$double.eps^(3/5)) \examples{ \dontrun{ require(sf, quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require(spdep, quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) col.listw <- spdep::nb2listw(col.gal.nb) diff --git a/man/spautolm.Rd b/man/spautolm.Rd index 60f4b4f..0d675a6 100644 --- a/man/spautolm.Rd +++ b/man/spautolm.Rd @@ -199,7 +199,7 @@ summary(ecar1wM) } \dontrun{ require("sf", quietly=TRUE) -nc.sids <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE) +nc.sids <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE) ft.SID74 <- sqrt(1000)*(sqrt(nc.sids$SID74/nc.sids$BIR74) + sqrt((nc.sids$SID74+1)/nc.sids$BIR74)) lm_nc <- lm(ft.SID74 ~ 1) diff --git a/man/trW.Rd b/man/trW.Rd index 0ce5798..5243f32 100644 --- a/man/trW.Rd +++ b/man/trW.Rd @@ -38,7 +38,7 @@ A numeric vector of \code{m} traces, with \dQuote{timings} and \dQuote{type} att } \examples{ require("sf", quietly=TRUE) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE) #require(spdep, quietly=TRUE) col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1]) listw <- spdep::nb2listw(col.gal.nb) diff --git a/vignettes/SpatialFiltering.Rmd b/vignettes/SpatialFiltering.Rmd index 15c0ca9..11d9534 100644 --- a/vignettes/SpatialFiltering.Rmd +++ b/vignettes/SpatialFiltering.Rmd @@ -54,7 +54,13 @@ by Pedro Peres-Neto and is discussed in @dray+legendre+peres-neto:06 and ```{r echo=TRUE} library(spdep) require("sf", quietly=TRUE) -NY8 <- st_read(system.file("shapes/NY8_utm18.shp", package="spData")) +if (packageVersion("spData") >= "2.3.2") { + NY8 <- sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData")) +} else { + NY8 <- sf::st_read(system.file("shapes/NY8_bna_utm18.gpkg", package="spData")) + sf::st_crs(NY8) <- "EPSG:32618" + NY8$Cases <- NY8$TRACTCAS +} NY_nb <- read.gal(system.file("weights/NY_nb.gal", package="spData"), override.id=TRUE) ``` @@ -89,22 +95,18 @@ set.seed(111) ``` ```{r, echo=TRUE} -nyME <- ME(Cases~PEXPOSURE+PCTAGE65P+PCTOWNHOME, data=NY8, offset=log(POP8), family="poisson", listw=NYlistwW, alpha=0.44) +nyME <- ME(Cases~PEXPOSURE+PCTAGE65P+PCTOWNHOME, data=NY8, offset=log(POP8), family="poisson", listw=NYlistwW, alpha=0.46) ``` ```{r, echo=TRUE} nyME -NY8$eigen_24 <- fitted(nyME)[,1] -NY8$eigen_223 <- fitted(nyME)[,2] +NY8$eigen_1 <- fitted(nyME)[,1] +NY8$eigen_2 <- fitted(nyME)[,2] ``` -```{r, results='asis',echo=FALSE, eval=FALSE} -.iwidth <- 6 -.iheight <- 4 -.ipointsize <- 10 -library(RColorBrewer) +```{r, echo=TRUE} #gry <- brewer.pal(9, "Greys")[-1] -spplot(NY8, c("eigen_24", "eigen_223"), col.regions=grey.colors(6, 0.95, 0.55, 2.2), cuts=5) +plot(NY8[,c("eigen_1", "eigen_2")]) ``` ```{r, echo=TRUE} diff --git a/vignettes/nb_igraph.Rmd b/vignettes/nb_igraph.Rmd index bd680a5..c1dbcf8 100644 --- a/vignettes/nb_igraph.Rmd +++ b/vignettes/nb_igraph.Rmd @@ -50,7 +50,7 @@ if (dothis) { ``` ```{r, echo=dothis, eval=dothis} library(sf) -columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1]) +columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1]) row.names(columbus)[1:10] ``` diff --git a/vignettes/sids_models.Rmd b/vignettes/sids_models.Rmd index a431c80..d975482 100644 --- a/vignettes/sids_models.Rmd +++ b/vignettes/sids_models.Rmd @@ -49,8 +49,8 @@ data set in **spData**. The actual data, included in a shapefile of the county b ```{r echo=TRUE,eval=TRUE} library(spdep) -nc <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE) -st_crs(nc) <- "+proj=longlat +datum=NAD27" +nc <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE) +#st_crs(nc) <- "+proj=longlat +datum=NAD27" row.names(nc) <- as.character(nc$FIPSNO) ``` @@ -175,4 +175,4 @@ plot(ll ~ lambda, ecarIawll$llprof, type="l") ## 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.