version 3.6-30

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: raster
 Type: Package
 Title: Geographic Data Analysis and Modeling
-Version: 3.6-26
-Date: 2023-10-12
+Version: 3.6-30
+Date: 2024-10-02
 Imports: Rcpp, methods, terra (>= 1.7-29)
 LinkingTo: Rcpp
 Depends: sp (>= 1.4-5), R (>= 3.5.0)
@@ -48,7 +48,7 @@ Authors@R: c(
 	person("Rafael", "Wueest", role = "ctb")
 	)
 NeedsCompilation: yes
-Packaged: 2023-10-12 15:29:22 UTC; rhijm
+Packaged: 2024-10-02 16:19:18 UTC; rhijm
 Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
   Jacob van Etten [ctb],
   Michael Sumner [ctb],
@@ -82,4 +82,4 @@ Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
   Rafael Wueest [ctb]
 Maintainer: Robert J. Hijmans <[email protected]>
 Repository: CRAN
-Date/Publication: 2023-10-14 13:40:12 UTC
+Date/Publication: 2024-10-02 18:10:02 UTC

MD5

@@ -1,4 +1,4 @@
-c76d096eed243669e391c2a9b2898214 *DESCRIPTION
+616a8626b5e2d29494b6911fe3901887 *DESCRIPTION
 315d9d3afd561fc33ff5c841443463cd *NAMESPACE
 8e63a09f55c46c99cf9a490c8003992f *NEWS
 8cc868c6b5aefe4c2d43d28df06ede95 *R/AAAClasses.R
@@ -51,7 +51,7 @@ a923bbded975e2e9310c9347341e5935 *R/clamp.R
 aa25fdab6a595011f6fce25d025a44fd *R/click.R
 9795a18891818eb4f1a1ba68dfe26c7e *R/clump.R
 42f4ce4c4c63b11e53075a31b0c13ceb *R/clusterR.R
-f363fcfbe6390201db7ce17d88dcae73 *R/coerce.R
+211d03d38c6df560db7394443e6b663f *R/coerce.R
 64718da05b72235575db2b4a9c5c23a7 *R/col2RGB.R
 bf4d69cac9d779c34c8ea0c35fcefec6 *R/colortable.R
 a11cba46329452f8813d48eebceefb32 *R/commonDataType.R
@@ -114,7 +114,7 @@ d9e423f2f087717358a143b3e3783182 *R/focalFun.R
 df748c28cef50ea3cbb394c0cdf37c7a *R/gdal.R
 e287001bfef2ccf762ba8bc699a472ce *R/gdalFormats.R
 1ae7377892ef1ed123d059a662685317 *R/geom.R
-ab7e6ed8eacdc7a8f394c566a904e76d *R/getData.R
+318989174d8d8f761e1b5ec13031fab9 *R/getData.R
 c5b10dfa091157a1e06cf895770d1855 *R/getValues.R
 19e6b95c32096e06597017822aa0196b *R/getValuesBlock.R
 56e8aa51ba1f14da020d9b7ca2bf3b74 *R/getValuesFocal.R
@@ -186,7 +186,7 @@ bb31c0c2988b37ade71a1dfb4ead82a4 *R/multiCore.R
 6689657ec2f6ee8f452d8518c85048f5 *R/netCDFtoRasterGMT.R
 e3d175453f106a173c6468aac9d8b221 *R/netCDFtoStack.R
 9d390903127668d44bd0e8d8a28f58fd *R/netCDFutil.R
-5ddb53419ced9c8a751cb97b5cc210e7 *R/netCDFwriteCD.R
+e47ad4d2dbf446eba4ece542c54fd519 *R/netCDFwriteCD.R
 37522b26afb24d01cfa59da00bff77be *R/newPLot.R
 a237e75cc8df7a7dd461de127c7edd3e *R/nlayers.R
 41009ec66bcfc072b8b48b2a1024b4e8 *R/notused.R
@@ -214,12 +214,12 @@ c126b01a725630014b349313fb3a8bde *R/quad.R
 95b29f77d650c98773a298f50be12238 *R/quantile.R
 e33733f012e4c0301210c3507da2b1b9 *R/randomize.R
 556aaf7db457486cb7df6897f1c8ad4e *R/range.R
-b87b7f9fa1408cdbc9710cc34956f1d3 *R/raster.R
+aa4f50e0ff7535d01d4b54208d052799 *R/raster.R
 a2055ed091243612e7808add0efca0bc *R/rasterFromASCII.R
 cc61a03d30a2ea21038f583739ef2824 *R/rasterFromBIL.R
 3d507ee8905b1d9a6ecbc693c1b00230 *R/rasterFromCells.R
 d8f4dab32e4a6c4d5e2afe0a57484155 *R/rasterFromFile.R
-0f1d508a09b3883be64f6d95504531b6 *R/rasterFromGDAL.R
+fa7b12069744eb66d8683a4f6cc362ae *R/rasterFromGDAL.R
 2185c54b649441070057362c1e74405f *R/rasterFromIDRISI.R
 0697310be1e94ae77f795174f4aa55ce *R/rasterFromRasterFile.R
 f4187c536c35a1d94c20a147ea3f522b *R/rasterFromSAGA.R
@@ -303,7 +303,7 @@ d491f4a320eca9c0492159e1af236894 *R/whiches.max.R
 420475b13f5f379840dbccd46027a130 *R/writeAllGDAL.R
 a321dcb2a3233d4f4a0c2f28164b81f7 *R/writeAllRaster.R
 63056e8f9aa5e12e1756129db1622360 *R/writeRaster.R
-141ac47f36501d5fcc84e224536bbfec *R/writeStartStop.R
+6b8f3699942545055604fb07840ea82c *R/writeStartStop.R
 42ac06c70c37349c13a2f373fe3cd305 *R/writeStartStopAscii.R
 2b8cc77c4a7661ee5c2f5efd6e05494f *R/writeStartStopGDAL.R
 911c3ded9e17fddf71166fdef1de3787 *R/writeStartStopRaster.R
@@ -316,7 +316,7 @@ d9397fdb238463ae0c9929aad0347658 *R/zApply.R
 b9cc0e22fcbdd704f6199fecaf8a4382 *R/zonal.R
 227cc9e91a64d5685fc5f6eeac885ee2 *R/zoom.R
 cae0440f702e35b1a156006c63c84a0b *R/zzz.R
-2836b2c5db38c9819380bd093383d89d *build/partial.rdb
+b54db8794555342c4feee5fe0b1b8f5b *build/partial.rdb
 836fc2bffa338d9f9a721e00d9cd6078 *inst/external/countries.rds
 c85d689dcf4c7101db48cbab30338201 *inst/external/lux.dbf
 e729936bf5360b37a15365fc295a1901 *inst/external/lux.prj
@@ -401,7 +401,7 @@ a2211ba5968a68c6332a20c252057b6f *man/draw.Rd
 6925d6bc7957b6b87db4f1358a9a1587 *man/extend.Rd
 3e1812cd7ab432f6c489d0a379b71e6f *man/extension.Rd
 a62d75d75a5463b705c677bef1f9f8c6 *man/extent.Rd
-3d704c2c3008b1c2c961c0d0ddb260d4 *man/extract.Rd
+8f98c76fea3fb9a5123f93dab458c476 *man/extract.Rd
 2fb4b5d1bbd2b58d86eb07b85bd5fea0 *man/extractIndex.Rd
 4992ec4f3c4cf67fc729cfdfd14c235e *man/extremeValues.Rd
 476d2a9a163fabd07529ee6e3517d845 *man/factor.Rd
@@ -414,14 +414,14 @@ a377c61fd6a34877273a510ab4666112 *man/focal.Rd
 bf4e4b4fed61e6736bc2431c3170d7cb *man/freq.Rd
 6c9ea2d96231490cbcb98073aa0c6ab0 *man/gainoffset.Rd
 949934a51c6e89070e1fee9294f3d83f *man/geom.Rd
-6f3db4ce27959a4672feae4b0e0aad1f *man/getData.Rd
+f783eb3bd185383708e9c489cc6d3b55 *man/getData.Rd
 513b858bb6a9ab24eedd6eb2b5f75eb6 *man/getValues.Rd
 772a6d5a8788870e3d080d30b8215e65 *man/getValuesBlock.Rd
 1d2d02b7b6d01609620e99c9e4698324 *man/getValuesFocal.Rd
 1e4b75fab3932c064d4ea45eeafb28a1 *man/gridDistance.Rd
 99f6d8e81767134d112ed6cad5def120 *man/hdrFiles.Rd
 67c344771513764f6a310712cd7d8964 *man/headtail.Rd
-3d455a90e7d04c15bef11694148d8125 *man/hillShade.Rd
+a9654f73a56bd8639af3931e94d5c3ae *man/hillShade.Rd
 122e387fd0d4562d493b3c31bd1072d4 *man/hist.Rd
 163dde188853a5fb7d982077926457c6 *man/image.Rd
 79abf72046372d5e62cbdb3b1afc27bb *man/iniFile.Rd
@@ -455,7 +455,7 @@ bc10b6371999e39d3849bd647641ab57 *man/projectRaster.Rd
 1caf0fe099e717237998bc76b0197b40 *man/projection.Rd
 9cfab780186321ff86fc11a25c7ebd2c *man/properties.Rd
 11c6a58182a86dceea216a0b5043ec22 *man/quantile.Rd
-5120f5f7db664a3310dc5539a6e0af07 *man/raster-package.Rd
+10dd019a488d8f66c74af961032dea51 *man/raster-package.Rd
 dcdc942173d4152eeb736c6379f2cb55 *man/raster.Rd
 ab6c9c74ebd8d520d9e2e30d91c3cacb *man/rasterFromCells.Rd
 618d1612c39114a43c92ca22582ebec7 *man/rasterFromXYZ.Rd
@@ -501,7 +501,7 @@ f4d47f1611ebac1c4652289dd57550bb *man/stack.Rd
 e1dc88aaa384c5d14b4bbc1b393fe923 *man/subset.Rd
 03e63787f46fc69ee03cc5e3ffb5cae8 *man/summary.Rd
 7cebc3ff0f84b9b08725f6173fbf6bf9 *man/symdif.Rd
-5e711d241175aa4a10ba08aab62f7953 *man/terrain.Rd
+a14ff126872a6adced3ad700f1877769 *man/terrain.Rd
 82a3a8e9c93e600e7e377e845cae05b5 *man/text.Rd
 7a547a4dd038782eb213a0de1e7db06d *man/transpose.Rd
 29f1f18187e8d9579a43f84a8f8cbf26 *man/trim.Rd

R/coerce.R

@@ -30,6 +30,9 @@ setAs("SpatRaster", "Raster",
 			if ((length(usid) == 1) & (b$source[1] != "")) {
 				if ((nl == nrow(b)) && (b$bands[1] == 1) && (all(diff(b$bands) == 1))) {
 					r <- raster::brick(b$source[1])
+					if (nlayers(r) != nl) {
+						r <- r[[b$bands]]
+					}
 				} else {
 					r <- raster::stack(b$source[1], bands=b$bands)
 				}

R/getData.R

@@ -4,14 +4,20 @@
 # Version 0.9
 # October 2008
 
+getData <- function(...) {
+
+	stop("getData has been removed. Please use the geodata package instead.")
+
+}
 
-getData <- function(name='GADM', download=TRUE, path='', ...) {
 
-#	w <- getOption('rasterGetDataWarningGiven')
-#	if (is.null(w)) {
-		warning("getData will be removed in a future version of raster\n. Please use the geodata package instead")
-#		options(rasterGetDataWarningGiven=TRUE)
-#	}
+.getData <- function(name='GADM', download=TRUE, path='', ...) {
+
+	message("getData will stop working soon!\n. 
+			Please use the geodata package instead.\n
+			Going to sleep for 15 seconds...")
+
+	Sys.sleep(15)
 
 	path <- .getDataPath(path)
 

R/netCDFwriteCD.R

@@ -160,12 +160,18 @@
 }
 
 
-.stopWriteCDF <-  function(x) {
+.writeRangeCDF <- function(x) {
+
 	nc <- ncdf4::nc_open(x@file@name, write=TRUE)
 	on.exit( ncdf4::nc_close(nc) )
 	ncdf4::ncatt_put(nc, x@title, 'min', as.numeric(x@data@min))
 	ncdf4::ncatt_put(nc, x@title, 'max', as.numeric(x@data@max))
+}
+
+
+.stopWriteCDF <-  function(x) {
 
+        .writeRangeCDF(x)
 	if (inherits(x, 'RasterBrick')) {
 		r <- brick(x@file@name)
 	} else {

R/raster.R

@@ -221,12 +221,12 @@ setMethod('raster', signature(x='RasterBrick'),
 				r <- raster(extent(x), nrows=nrow(x), ncols=ncol(x), crs=.getCRS(x))	
 				r@file <- x@file
 
-				r@file@blockrows <- x@file@blockrows
-				r@file@blockcols <- x@file@blockcols
+				r@file@blockrows <- x@file@blockrows[dindex]
+				r@file@blockcols <- x@file@blockcols[dindex]
 				r@file@nbands <- nlayers(x)
 
-				r@data@offset <- x@data@offset
-				r@data@gain <- x@data@gain
+				r@data@offset <- x@data@offset[dindex]
+				r@data@gain <- x@data@gain[dindex]
 				r@data@inmemory <- FALSE
 				r@data@fromdisk <- TRUE
 				r@data@haveminmax <- x@data@haveminmax
@@ -253,8 +253,6 @@ setMethod('raster', signature(x='RasterBrick'),
 					attr(r@data, "level") <- x@data@level
 				}
 
-				r@data@offset <- x@data@offset
-				r@data@gain <- x@data@gain
 				r@file@nodatavalue <- x@file@nodatavalue
 
 			} else {

R/rasterFromGDAL.R

@@ -73,6 +73,11 @@
 		r@data@min <- minv[band]
 		r@data@max <- maxv[band]
 
+		sc <- scoff(x)
+		r@data@gain <- sc[band,1]
+		r@data@offset <- sc[band,2]
+
+
 		if (is.factor(x)[1]) {
 			cts <- cats(x)[[1]]
 			if (!is.null(cts)) {
@@ -83,6 +88,9 @@
 	} else {
 		r@data@min <- minv
 		r@data@max <- maxv
+		sc <- scoff(x)
+		r@data@gain <- sc[,1]
+		r@data@offset <- sc[,2]
 	}
 
 	return(r)

R/writeStartStop.R

@@ -31,9 +31,9 @@ function(x, filename, options=NULL, format, prj=FALSE, ...) {
 	}		
 
 	if (prj) {
-		crs <-.getCRS(x)
-		if (crs != "") {
-			writeLines(wkt(x), extension(filename, "prj") )
+		wk <- wkt(x)
+		if (wk != "") {
+			writeLines(wk, extension(filename, "prj") )
 		}
 	}
 	return(x)

man/extract.Rd

@@ -44,7 +44,7 @@ It is also possible to extract values for point locations from SpatialPolygons.
 \arguments{
 \item{x}{Raster* object}
 
-\item{y}{points represented by a two-column matrix or data.frame, or \code{\link{SpatialPoints}*}; \code{\link{SpatialPolygons}*}; \code{\link[sp]{SpatialLines}}; \code{sf} spatial vector objects; \code{\link{Extent}}; or a numeric vector representing cell numbers}
+\item{y}{points represented by a two-column matrix or data.frame, or \code{\link[sp]{SpatialPoints}*}; \code{\link[sp]{SpatialPolygons}*}; \code{\link[sp]{SpatialLines}}; \code{sf} spatial vector objects; \code{\link{Extent}}; or a numeric vector representing cell numbers}
 
 \item{method}{character. \code{'simple'} or \code{'bilinear'}. If \code{'simple'} values for the cell a point falls in are returned. If \code{'bilinear'} the returned values are interpolated from the values of the four nearest raster cells.}
 

man/getData.Rd

@@ -5,72 +5,15 @@
 \title{Get geographic data }
 
 \description{
-Get geographic data for anywhere in the world. Data are read from files that are first downloaded if necessary. Function \code{ccodes} returns country names and the ISO codes
-
-See the geodata package for access to more recent versions of the data available through this function, and for many other datasets.
+This function has been deprecated and does not work anymore.
 }
 
 \usage{
-getData(name, download=TRUE, path="", ...)
+getData(...)
 ccodes()
 }
 
 \arguments{
-  \item{name}{Data set name, currently supported are 'GADM', 'countries', 'SRTM', 'alt', and 'worldclim'. See Details for more info}
-  \item{download}{Logical. If \code{TRUE} data will be downloaded if not locally available}
-  \item{path}{Character. Path name indicating where to store the data. Default is the current working directory }
-  \item{...}{ Additional required (!) parameters. These are data set specific. See Details}   
+  \item{...}{arguments}   
 }
 
-\value{
-A spatial object (Raster* or Spatial*)
-} 
-
-\details{  
-'alt' stands for altitude (elevation); the data were aggregated from SRTM 90 m resolution data between -60 and 60 latitude. 'GADM' is a database of global administrative boundaries. 'worldclim' is a database of global interpolated climate data. 'SRTM' refers to the hole-filled CGIAR-SRTM (90 m resolution). 'countries' has polygons for all countries at a higher resolution than the 'wrld_simpl' data in the maptools package . 
-
-If \code{name} is 'alt' or 'GADM' you must provide a 'country=' argument. Countries are specified by their 3 letter ISO codes. Use getData('ISO3') to see these codes. In the case of GADM you must also provide the level of administrative subdivision (0=country, 1=first level subdivision). In the case of alt you can set 'mask' to FALSE. If it is TRUE values for neighbouring countries are set to NA. For example:
-
-\code{getData('GADM', country='FRA', level=1)}
-
-\code{getData('alt', country='FRA', mask=TRUE)}
-
-
-If \code{name} is 'SRTM' you must provide 'lon' and 'lat' arguments (longitude and latitude). These should be single numbers somewhere within the SRTM tile that you want.
-
-\code{getData('SRTM', lon=5, lat=45)}
-
-If \code{name='worldclim'} you must also provide arguments \code{var}, and a resolution \code{res}. Valid variables names are 'tmin', 'tmax', 'prec' and 'bio'. Valid resolutions are 0.5, 2.5, 5, and 10 (minutes of a degree). In the case of \code{res=0.5}, you must also provide a \code{lon} and \code{lat} argument for a tile; for the lower resolutions global data will be downloaded. In all cases there are 12 (monthly) files for each variable except for 'bio' which contains 19 files.
-
-\code{getData('worldclim', var='tmin', res=0.5, lon=5, lat=45)}
-
-\code{getData('worldclim', var='bio', res=10)}
-
-
-To get (projected) future climate data (CMIP5), you must provide arguments \code{var} and \code{res} as above. Only resolutions 2.5, 5, and 10 are currently available. In addition, you need to provide \code{model}, \code{rcp} and \code{year}. For example,
-
-\code{getData('CMIP5', var='tmin', res=10, rcp=85, model='AC', year=70)}
-
-function (var, model, rcp, year, res, lon, lat, path, download = TRUE) 
-
-'model' should be one of "AC", "BC", "CC", "CE", "CN", "GF", "GD", "GS", "HD", "HG", "HE", "IN", "IP", "MI", "MR", "MC", "MP", "MG", or  "NO".
-
-'rcp' should be one of 26, 45, 60, or 85.
-
-'year' should be 50 or 70
-
-Not all combinations are available. See www.worldclim.org for details.
-}
-
-\references{
-\url{https://www.worldclim.org}
-
-\url{https://gadm.org}
-
-https://srtm.csi.cgiar.org/
-
-\url{https://diva-gis.org/gdata}
-}
-
-
-\keyword{ spatial }

man/hillShade.Rd

@@ -35,16 +35,5 @@ Horn, B.K.P., 1981. Hill shading and the reflectance map. Proceedings of the IEE
 }
 
 
-\examples{
-\dontrun{
-alt <- getData('alt', country='CHE')
-slope <- terrain(alt, opt='slope')
-aspect <- terrain(alt, opt='aspect')
-hill <- hillShade(slope, aspect, 40, 270)
-plot(hill, col=grey(0:100/100), legend=FALSE, main='Switzerland')
-plot(alt, col=rainbow(25, alpha=0.35), add=TRUE)
-}
-}
-
 \keyword{spatial}
 

man/raster-package.Rd

@@ -335,7 +335,6 @@ Some of these functions are in the \code{sp} package. The name in \bold{bold} is
 
 \tabular{ll}{
     \code{\link{rasterOptions}} \tab Show, set, save or get session options \cr
-    \code{\link{getData}} \tab Download and geographic data\cr
     \code{\link{pointDistance}} \tab Distance between points \cr
     \code{\link{readIniFile}} \tab Read a (windows) 'ini' file \cr
     \code{\link{hdr}} \tab Write header file for a number of raster formats \cr

man/terrain.Rd

@@ -72,22 +72,4 @@ Wilson, M.F.J., O'Connell, B., Brown, C., Guinan, J.C., Grehan, A.J., 2007. Mult
 }
 
 
-\examples{
-\dontrun{
-elevation <- getData('alt', country='CHE')
-x <- terrain(elevation, opt=c('slope', 'aspect'), unit='degrees')
-plot(x)
-
-
-# TPI for different neighborhood size:
-tpiw <- function(x, w=5) {
-	m <- matrix(1/(w^2-1), nc=w, nr=w)
-	m[ceiling(0.5 * length(m))] <- 0
-	f <- focal(x, m)
-	x - f
-}
-tpi5 <- tpiw(elevation, w=5)
-}
-}
-
 \keyword{spatial}