Commit 1d72cdca authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.1-3+dfsg

parent 5c9f0fe2
Package: spdep
Version: 1.1-2
Date: 2019-04-05
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Version: 1.1-3
Date: 2019-09-18
Title: Spatial Dependence: Weighting Schemes, Statistics
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")), person("Micah", "Altman", role = "ctb"),
person("Luc", "Anselin", role = "ctb"),
......@@ -77,7 +77,7 @@ License: GPL (>= 2)
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-04-05 17:21:04 UTC; rsb
Packaged: 2019-09-18 12:10:34 UTC; rsb
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Micah Altman [ctb],
Luc Anselin [ctb],
......@@ -112,4 +112,4 @@ Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Repository: CRAN
Date/Publication: 2019-04-05 19:40:03 UTC
Date/Publication: 2019-09-18 13:30:02 UTC
2428ff9c8fc1c5390035b6f09bcc9b13 *ChangeLog
7cdab2fc2da85ddf80f3f84552d62b0f *DESCRIPTION
89f2c33fd3fd3733f3038ce376024f65 *DESCRIPTION
75d499ce171510f3d47cdc4219369124 *NAMESPACE
f6f0c407abbd5b20559c61858e973849 *R/AAA.R
b0e1b90e65dd7b62bdd3948361cb5237 *R/EBI.R
......@@ -24,7 +24,7 @@ e64d4fcc81be06647777c3c71fc125b3 *R/cyclical.R
bbee82cda474bd92b417bacb768fd186 *R/diffnb.R
b73f7275ce913150380ef6326f6439d5 *R/dnearneigh.R
d6b8860ef2337d9746ff5d1119f36590 *R/droplinks.R
1c7c266113c4f079d2f0c6d9ccc5141f *R/edit.nb.R
46466cb7fd75b36d3b5d8fe08cfa9f94 *R/edit.nb.R
f5741e82f0054dc0d62bea24322f658c *R/eigenw.R
20f0d53c11bba9971fb5c8dad1cbb174 *R/error.hessian.R
73cbe1921c885b77ae792f1556ef41b0 *R/error.spsarlm.R
......@@ -76,7 +76,7 @@ a63a07dadf5f8fa200f7e3c71747a403 *R/nblag.R
5f0bbb53290e57eb01a52c265f8d1806 *R/plot.mst.R
6c7e71d7f858adfff5aa9f88981647b4 *R/plot.nb.R
1062440bac3bb1409c7716a8af176a79 *R/plot.skater.R
d5acce3fda28a095de64535eb6faf6f5 *R/poly2nb.R
ad8e3dcb396629541e253193ca42643b *R/poly2nb.R
59a5f3980e8585d96ac511d4d23d669f *R/prunecost.R
58fc4f67d40bb82e24a32af9ee5ee0c2 *R/prunemst.R
72519954bdafc8521aa950d7d3b67855 *R/read.gal.R
......@@ -100,7 +100,7 @@ d10fcab9d4f11c523798dc5a222a5256 *R/summary.spsarlm.R
9cc132656403ffd40118fdb339159ec2 *R/tri2nb.R
f5c0242936707063d64cfcd44138796f *R/utils.R
6f1fcd3c6b9caaf4d4e78e0ad8028046 *R/weights-utils.R
b7a2e8f58e7fd5c318cf1d54aaddcf90 *build/vignette.rds
18492efa8af40b489d244a72ec0eac90 *build/vignette.rds
b818650dc1a3e0335a7767fe78f721f5 *data/columbus.rda
5e7e97b208f3d4a44393e668799ce382 *data/eire.rda
3c410289cf12787247a95ff858bf4a97 *data/oldcol.rda
......@@ -110,19 +110,19 @@ b818650dc1a3e0335a7767fe78f721f5 *data/columbus.rda
38a8e8aedfaa0bc14eb5edd06e09c3a7 *inst/README
9c3f16bf1ed12822b432c8d7a6c6dbea *inst/doc/CO69.R
7385c8721943d8d2ce34b91214d0dd37 *inst/doc/CO69.Rmd
b47e7dd5f59bad14d6aba1ea413ef205 *inst/doc/CO69.html
14059711bf981b3de0ca12bb25f211e5 *inst/doc/CO69.html
e12b7288630644ee28894e5b04cea06c *inst/doc/nb.R
96bd583488e35a9e980cbe5b79f57d46 *inst/doc/nb.Rnw
adf001daaeceae7f188c6cbfa893ec02 *inst/doc/nb.pdf
67043118005a3cd623d785b650cdaba3 *inst/doc/nb.pdf
4710739a7ea0586a2fbd90815a11f3d6 *inst/doc/nb_igraph.R
0926f15bb77b188af892e3a93fc70197 *inst/doc/nb_igraph.Rmd
abd2d5f91d2696d479f7879be7760552 *inst/doc/nb_igraph.html
73a9899efed28e55b1c86c2860cf7cd5 *inst/doc/nb_igraph.html
522b2484fbd34290eaa545c19089dd77 *inst/doc/nb_sf.R
941aa1849341d87ce66e36c168b8ad7f *inst/doc/nb_sf.Rmd
71f76a76ca7e7bc56ee6b6ec215d1f23 *inst/doc/nb_sf.html
6bf66c0ee6e6d2bc4262855c83bdd34b *inst/doc/nb_sf.Rmd
ccf2737aa9b22fa5d01be5e02325106e *inst/doc/nb_sf.html
7a2777c88700eb99f2057ed2e9ac023d *inst/doc/sids.R
9a5886447fc9eef2843f9d6875453644 *inst/doc/sids.Rmd
d5dee234166641c8825fdbe125cfd384 *inst/doc/sids.html
fd295235cde2bdd9407aa9b9011f44a2 *inst/doc/sids.Rmd
61aea9f1983a013bbc1377d84dc47e07 *inst/doc/sids.html
68a52b4a10480b4a2adedb18494c7deb *inst/etc/backstore/boot_res.RData
3889914095150cc9ed13c578b5f51a73 *inst/etc/backstore/nyME_res.RData
53178ac43dd150bbb835b63e018f0cd4 *inst/etc/misc/geary_eire.txt
......@@ -167,7 +167,7 @@ f9199ce993af1de9e4d302b6beb79f31 *man/choynowski.Rd
5dc8467be5c40ab177ed1f75be3b5737 *man/diffnb.Rd
6f38c2878b23dcc1b5bb763b95dfd2f5 *man/dnearneigh.Rd
ab9d1a7b4f443b31a4c1fa58a57da7aa *man/droplinks.Rd
c7dec0e79dd39617f378efce3347582d *man/edit.nb.Rd
2034afb6d33f32ebbf9bc84cf22cf3ff *man/edit.nb.Rd
c28e1263be5dbd60f5da17b124efc534 *man/eire.Rd
25e1a53cd6d9cbbb7bea0c1fea3e1ef0 *man/geary.Rd
e5e5f9840a79014d86c7758de589b0f9 *man/geary.mc.Rd
......@@ -178,7 +178,7 @@ e5e5f9840a79014d86c7758de589b0f9 *man/geary.mc.Rd
5b794b4e7a14903192df556d3724eab6 *man/include.self.Rd
dddcf9d4b16463e9c6b76c514cc5a587 *man/invIrM.Rd
3a5aa076bb3c12d7c608a5d57eae9fb7 *man/joincount.mc.Rd
3ef157b0a852acb019081ea67d9b3c0c *man/joincount.multi.Rd
fc9cab3ab103f4790a80cf438dd51e8a *man/joincount.multi.Rd
3ca8dd3ff7a52d1c2fa8ce590e66fe70 *man/joincount.test.Rd
082bcc3cc78a644bf16b67589bffdce3 *man/knearneigh.Rd
7f29dba937768cacca71f38982ded409 *man/knn2nb.Rd
......@@ -191,7 +191,7 @@ ab1776c96e814381f2428a84cb19bec1 *man/lm.LMtests.Rd
bf22c7dc637db3a45d7a63839a7269a8 *man/lm.morantest.Rd
5c1c2888e6b6cd0c47219c6291eb77f0 *man/lm.morantest.exact.Rd
64d60b3c6fca61752ed89237a50ea7ad *man/lm.morantest.sad.Rd
5cd317c04724ebf7ab35ae2ea482079e *man/localG.Rd
dfc81e018981e123eac55583f868590a *man/localG.Rd
cd402b48f08dddff07c0bcb2b081154a *man/localmoran.Rd
6c204aa004f48a99f7d41cb459c28c31 *man/localmoran.exact.Rd
ece85e85fa53184277c9ed4d8c32efa2 *man/localmoran.sad.Rd
......@@ -219,7 +219,7 @@ c4be5e2e8828f7d6e041e5ae093a0c2c *man/plot.skater.Rd
2cb371e39e65b81677b1cb65c4ee1192 *man/probmap.Rd
09b2776bb47f80cdbe5562d88b36ef18 *man/prunecost.Rd
f592261ce51e820587da92afaa7cd853 *man/prunemst.Rd
f8dc0b0518d2badebbd7f93e552a3f73 *man/read.gal.Rd
26743a89777691183c840eb3e421b4c9 *man/read.gal.Rd
fe86bf830f291a16d60102c52bfdf01e *man/read.gwt2nb.Rd
feb42a50dc7b72cc991066c40fb4d75f *man/rotation.Rd
d4ec4879830f577619f8194ac46d2876 *man/set.mcOption.Rd
......@@ -227,7 +227,7 @@ d4ec4879830f577619f8194ac46d2876 *man/set.mcOption.Rd
ecbbf3db33c5dc31f965c5ddaefb87e5 *man/skater.Rd
a784863084158161a533f13353bea08d *man/sp.correlogram.Rd
cc5b6792ef98679cb5ec9fe4623df4f4 *man/sp.mantel.mc.Rd
cbdb07679c13eda199bbd23595b6534c *man/spdep-deprecated.Rd
85b932eb4b1b0fb2a4bbe1b0c948f1c1 *man/spdep-deprecated.Rd
487249a672c9c93ffa4370cbd5d23810 *man/spdep.Rd
bca044be46d29893de136d50dfc28c34 *man/spweights.constants.Rd
c2198571e7ff56c757ddbc1f90b56cb2 *man/ssw.Rd
......@@ -264,6 +264,6 @@ d5188a82abbb16aac83bf280b8110355 *src/symtest.c
7385c8721943d8d2ce34b91214d0dd37 *vignettes/CO69.Rmd
96bd583488e35a9e980cbe5b79f57d46 *vignettes/nb.Rnw
0926f15bb77b188af892e3a93fc70197 *vignettes/nb_igraph.Rmd
941aa1849341d87ce66e36c168b8ad7f *vignettes/nb_sf.Rmd
6bf66c0ee6e6d2bc4262855c83bdd34b *vignettes/nb_sf.Rmd
b62da117254a0b1cc824f482bba57137 *vignettes/refs.bib
9a5886447fc9eef2843f9d6875453644 *vignettes/sids.Rmd
fd295235cde2bdd9407aa9b9011f44a2 *vignettes/sids.Rmd
......@@ -2,6 +2,8 @@
#
edit.nb <- function(name, coords, polys=NULL, ..., use_region.id=FALSE) {
if (.Platform$GUI == "RStudio")
stop("do not use in RStudio, use an R console session")
nb <- name
cnb <- card(nb)
# class to inherits Jari Oksanen 080603
......
# Copyright 2001-2010 by Roger Bivand
# Copyright 2001-2019 by Roger Bivand
#
#
# Modified by Micah Altman 2010
......@@ -19,8 +19,10 @@ poly2nb <- function(pl, row.names=NULL, snap=sqrt(.Machine$double.eps),
pl <- sf::st_geometry(pl)
}
if (inherits(pl, "sfc")) {
if (length(grep("POLYGON", class(pl))) == 0L)
stop("Polygon geometries required")
if (length(grep("POLYGON", class(pl)[1])) == 0L)
pl <- try(st_cast(pl, "MULTIPOLYGON"), silent=TRUE)
if (class(pl)[1] == "try-error")
stop("Polygon geometries required")
if (attr(pl, "n_empty") > 0L)
stop("Empty geometries found")
sf <- TRUE
......
No preview for this file type
No preview for this file type
......@@ -33,7 +33,7 @@ This is a summary of the results below:
## Data set
We'll use the whole NY 8 county set of boundaries, as they challenge the implementations more than just the Syracuse subset. The description of the input geometries from ADSAR is: New York leukemia: used and documented extensively in Waller and Gotway (2004) and with data made available in Chap. 9 of [http://web1.sph.emory.edu/users/lwaller/ch9index.htm]
(http://web1.sph.emory.edu/users/lwaller/ch9index.htm); the data import process is described in the help file of NY_data in spdep; geometries downloaded from the CIESIN server at [ftp.ciesin.columbia.edu](ftp.ciesin.columbia.edu), file /pub/census/usa/tiger/ny/bna_st/t8_36.zip, and extensively edited; a zip archive NY_data.zip of shapefiles and a GAL format neighbours list is on the book website. Further, the zipfile is now at: [a new location requiring login]
(http://web1.sph.emory.edu/users/lwaller/ch9index.htm); the data import process is described in the help file of NY_data in spdep; geometries downloaded from the CIESIN server at [https://sedac.ciesin.columbia.edu/data/set/acrp-boundary-1992/data-download](https://sedac.ciesin.columbia.edu/data/set/acrp-boundary-1992/data-download), file /pub/census/usa/tiger/ny/bna_st/t8_36.zip, and extensively edited; a zip archive NY_data.zip of shapefiles and a GAL format neighbours list is on the book website. Further, the zipfile is now at: [a new location requiring login]
(http://sedac.ciesin.columbia.edu/ftpsite/pub/census/usa/tiger/ny/bna_st/t8_36.zip). The object listw_NY is directly imported from nyadjwts.dbf on the Waller & Gotway (2004) chapter 9 website.
The version of the New York 8 counties geometries used in ASDAR and included as a shapefile in spdep was converted from the original BNA file using an external utility program to convert to MapInfo format and converted on from there using GDAL 1.4.1 (the OGR BNA driver was not then available; it entered OGR at 1.5.0, release at the end of 2007), and contains invalid geometries. What was found in mid-2007 was that included villages were in/excluded by in-out umbilical cords to the boundary of the enclosing tract, when the underlying BNA file was first converted to MapInfo (holes could not exist then).
......
......@@ -249,7 +249,7 @@ tm_shape(nc) + tm_fill(c("low", "high"), palette="Set1", title="p-values") +
```
For more complicated thematic maps, it may be helpful to use ColorBrewer
(<http://colorbrewer.org>) colour palettes. Here we use
(<http://colorbrewer2.org>) colour palettes. Here we use
palettes accessed through **tmap**, available in R in the **RColorBrewer** package.
While the [`choynowski()`]{} function only provides the probability map
......
......@@ -8,6 +8,8 @@ allow unneeded links to be deleted, and missing links to be inserted. It uses \c
endpoints of the link to be deleted or added, and asks for confirmation before
committing. If the result is not assigned to a new object, the editing
will be lost - as in \code{edit}.
This method relies on direct contact with the graphics device. Do not use in RStudio.
}
\usage{
\method{edit}{nb}(name, coords, polys=NULL, ..., use_region.id=FALSE)
......
......@@ -25,7 +25,7 @@ joincount.multi(fx, listw, zero.policy = FALSE,
\value{
A matrix with class \code{jcmulti} with row and column names for observed and expected counts, variance, and z-value.
}
\references{Cliff, A. D., Ord, J. K. 1981 Spatial processes, Pion, p. 20; Upton, G., Fingleton, B. 1985 Spatial data analysis by example: point pattern and quatitative data, Wiley, pp. 158--170.}
\references{Cliff, A. D., Ord, J. K. 1981 Spatial processes, Pion, p. 20; Upton, G., Fingleton, B. 1985 Spatial data analysis by example: point pattern and qualitative data, Wiley, pp. 158--170.}
\author{Roger Bivand \email{Roger.Bivand@nhh.no}}
\note{The derivation of the test (Cliff and Ord, 1981, p. 18) assumes that the weights matrix is symmetric. For inherently non-symmetric matrices, such as k-nearest neighbour matrices, \code{listw2U()} can be used to make the matrix symmetric. In non-symmetric weights matrix cases, the variance of the test statistic may be negative.
}
......
......@@ -51,6 +51,13 @@ International), 261--277; Bivand RS, Wong DWS 2018 Comparing implementations of
\examples{
data(getisord, package="spData")
# spData 0.3.2 changes x, y, xyz object names to go_x, go_y, go_xyz to
# avoid putting these objects into the global environment via lazy loading
if (exists("go_xyz") && packageVersion("spData") >= "0.3.2") {
xyz <- go_xyz
x <- go_x
y <- go_y
}
xycoords <- cbind(xyz$x, xyz$y)
nb30 <- dnearneigh(xycoords, 0, 30)
G30 <- localG(xyz$val, nb2listw(nb30, style="B"))
......
......@@ -19,7 +19,7 @@ read.geoda(file, row.names=NULL, skip=0)
\item{skip}{skip number of lines, as in \code{read.csv()}}
}
\details{
Luc Anselin (2003): Spatial Analysis Laboratory, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, \url{http://www.csiss.org/gispopsci/workshops/2011/PSU/readings/W15_Anselin2007.pdf}; Luc Anselin (2003) \emph{GeoDa 0.9 User's Guide}, pp. 80--81, Spatial Analysis Laboratory, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, \url{https://s3.amazonaws.com/geoda/software/docs/geoda093.pdf}; GAL - Geographical Algorithms Library, University of Newcastle}
Luc Anselin (2003): Spatial Analysis Laboratory, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, now dead link: http://www.csiss.org/gispopsci/workshops/2011/PSU/readings/W15_Anselin2007.pdf; Luc Anselin (2003) \emph{GeoDa 0.9 User's Guide}, pp. 80--81, Spatial Analysis Laboratory, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, \url{https://s3.amazonaws.com/geoda/software/docs/geoda093.pdf}; GAL - Geographical Algorithms Library, University of Newcastle}
\value{
The function \code{read.gal()} returns an object of class \code{nb} with a list of integer vectors containing neighbour region number ids. The function \code{read.geoda} returns a data frame, and issues a warning if the returned object has only one column.
......
......@@ -141,7 +141,7 @@
lextrB(lw, zero.policy = TRUE, control = list())
lextrW(lw, zero.policy=TRUE, control=list())
lextrS(lw, zero.policy=TRUE, control=list())
i#l_max(lw, zero.policy=TRUE, control=list())
#l_max(lw, zero.policy=TRUE, control=list())
griffith_sone(P, Q, type="rook")
subgraph_eigenw(nb, glist=NULL, style="W", zero.policy=NULL, quiet=NULL)
mom_calc(lw, m)
......
......@@ -33,7 +33,7 @@ This is a summary of the results below:
## Data set
We'll use the whole NY 8 county set of boundaries, as they challenge the implementations more than just the Syracuse subset. The description of the input geometries from ADSAR is: New York leukemia: used and documented extensively in Waller and Gotway (2004) and with data made available in Chap. 9 of [http://web1.sph.emory.edu/users/lwaller/ch9index.htm]
(http://web1.sph.emory.edu/users/lwaller/ch9index.htm); the data import process is described in the help file of NY_data in spdep; geometries downloaded from the CIESIN server at [ftp.ciesin.columbia.edu](ftp.ciesin.columbia.edu), file /pub/census/usa/tiger/ny/bna_st/t8_36.zip, and extensively edited; a zip archive NY_data.zip of shapefiles and a GAL format neighbours list is on the book website. Further, the zipfile is now at: [a new location requiring login]
(http://web1.sph.emory.edu/users/lwaller/ch9index.htm); the data import process is described in the help file of NY_data in spdep; geometries downloaded from the CIESIN server at [https://sedac.ciesin.columbia.edu/data/set/acrp-boundary-1992/data-download](https://sedac.ciesin.columbia.edu/data/set/acrp-boundary-1992/data-download), file /pub/census/usa/tiger/ny/bna_st/t8_36.zip, and extensively edited; a zip archive NY_data.zip of shapefiles and a GAL format neighbours list is on the book website. Further, the zipfile is now at: [a new location requiring login]
(http://sedac.ciesin.columbia.edu/ftpsite/pub/census/usa/tiger/ny/bna_st/t8_36.zip). The object listw_NY is directly imported from nyadjwts.dbf on the Waller & Gotway (2004) chapter 9 website.
The version of the New York 8 counties geometries used in ASDAR and included as a shapefile in spdep was converted from the original BNA file using an external utility program to convert to MapInfo format and converted on from there using GDAL 1.4.1 (the OGR BNA driver was not then available; it entered OGR at 1.5.0, release at the end of 2007), and contains invalid geometries. What was found in mid-2007 was that included villages were in/excluded by in-out umbilical cords to the boundary of the enclosing tract, when the underlying BNA file was first converted to MapInfo (holes could not exist then).
......
......@@ -249,7 +249,7 @@ tm_shape(nc) + tm_fill(c("low", "high"), palette="Set1", title="p-values") +
```
For more complicated thematic maps, it may be helpful to use ColorBrewer
(<http://colorbrewer.org>) colour palettes. Here we use
(<http://colorbrewer2.org>) colour palettes. Here we use
palettes accessed through **tmap**, available in R in the **RColorBrewer** package.
While the [`choynowski()`]{} function only provides the probability map
......
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