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address #50 #51

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Jun 10, 2024
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2a8b258
address #50
rsbivand Jun 8, 2024
8e36886
fixes #50
rsbivand Jun 10, 2024
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6 changes: 3 additions & 3 deletions DESCRIPTION
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@@ -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 = "[email protected]", comment=c(ORCID="0000-0003-2392-6140")),
Expand All @@ -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 = "[email protected]"),
person(given = "JuanTomas", family = "Sayago", role = c("ctb"), email = "[email protected]"),
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,
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6 changes: 5 additions & 1 deletion NEWS.md
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@@ -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

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4 changes: 2 additions & 2 deletions man/ME.Rd
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Expand Up @@ -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)
Expand Down Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/SpatialFiltering.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/aple.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/aple.mc.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/aple.plot.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/impacts.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/sarlm_tests.Rd
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion man/sparse_mat.Rd
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Expand Up @@ -46,7 +46,7 @@ powerWeights(W, rho, order=250, X, tol=.Machine$double.eps^(3/5))
\examples{
\dontrun{
require(sf, quietly=TRUE)
columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE)
columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE)
#require(spdep, quietly=TRUE)
col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1])
col.listw <- spdep::nb2listw(col.gal.nb)
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2 changes: 1 addition & 1 deletion man/spautolm.Rd
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Expand Up @@ -199,7 +199,7 @@ summary(ecar1wM)
}
\dontrun{
require("sf", quietly=TRUE)
nc.sids <- st_read(system.file("shapes/sids.shp", package="spData")[1], quiet=TRUE)
nc.sids <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE)
ft.SID74 <- sqrt(1000)*(sqrt(nc.sids$SID74/nc.sids$BIR74) +
sqrt((nc.sids$SID74+1)/nc.sids$BIR74))
lm_nc <- lm(ft.SID74 ~ 1)
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2 changes: 1 addition & 1 deletion man/trW.Rd
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Expand Up @@ -38,7 +38,7 @@ A numeric vector of \code{m} traces, with \dQuote{timings} and \dQuote{type} att
}
\examples{
require("sf", quietly=TRUE)
columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE)
columbus <- st_read(system.file("shapes/columbus.gpkg", package="spData")[1], quiet=TRUE)
#require(spdep, quietly=TRUE)
col.gal.nb <- spdep::read.gal(system.file("weights/columbus.gal", package="spData")[1])
listw <- spdep::nb2listw(col.gal.nb)
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22 changes: 12 additions & 10 deletions vignettes/SpatialFiltering.Rmd
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Expand Up @@ -54,7 +54,13 @@ by Pedro Peres-Neto and is discussed in @dray+legendre+peres-neto:06 and
```{r echo=TRUE}
library(spdep)
require("sf", quietly=TRUE)
NY8 <- st_read(system.file("shapes/NY8_utm18.shp", package="spData"))
if (packageVersion("spData") >= "2.3.2") {
NY8 <- sf::st_read(system.file("shapes/NY8_utm18.gpkg", package="spData"))
} else {
NY8 <- sf::st_read(system.file("shapes/NY8_bna_utm18.gpkg", package="spData"))
sf::st_crs(NY8) <- "EPSG:32618"
NY8$Cases <- NY8$TRACTCAS
}
NY_nb <- read.gal(system.file("weights/NY_nb.gal", package="spData"), override.id=TRUE)
```

Expand Down Expand Up @@ -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}
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2 changes: 1 addition & 1 deletion vignettes/nb_igraph.Rmd
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Expand Up @@ -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]
```

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6 changes: 3 additions & 3 deletions vignettes/sids_models.Rmd
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Expand Up @@ -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)
```

Expand Down Expand Up @@ -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.
[sal.agecon.uiuc.edu/datasets/sids.zip]; see also [GeoDa Center](https://geodacenter.github.io/data-and-lab/) for a contemporary source.
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