more generic to play nice with terra

.Rbuildignore

@@ -1,6 +1,7 @@
 .gitignore
 LICENSE
 README.md
+TODO
 ^revdep$
 ^.*\.Rproj$
 ^\.Rproj\.user$

ChangeLog

@@ -1,22 +1,14 @@
---- to do
-focal for multi-layer objects
-step-size option for focal
-add equivalent to "subsWithNA" to reclassify
-add AMSR-E ice products and other raw binary products
-add orientation fixes for AVISO currents and similar NetCDFs lacking metadata on the internal CRS
-add VRT output to saveStack
-Fix lines falling between the cracks in extract (calling rasterzeLines): https://stat.ethz.ch/pipermail/r-sig-geo/2014-May/020973.html
-Better handling of NA values in 1 byte raster files
 
 --- current version
 
+
 --- 2-Nov-2018, version: 2.8-4
 Improved estimation of available RAM with contributions by Lorenzo Busetto. RAM available is now computed on windows, linux and mac. No more that 60% of available RAM is used (if the estimated RAM needed is not too low). Not more than raster:::.maxmemory() is used; but it should now be safe to set this to Inf. If canProcessInMemory() returns FALSE, chunksize is set 25% of available RAM, or raster:::.chunksize(), whichever is lower. (set options via rasterOptions())
 
 testthat unit tests introduced by Mike Sumner and Jakub Nowosad
 as.character() for Raster objects to create the R code to re-create the Raster skeleton in examples.
 
-Reading point values via GDAL has become slower in 2.7-15, reverted to previous function. 
+Reading point values via GDAL has become slower in 2.7-15, reverted to previous function. Thanks to Andrew Brown and Dylan Beaudette for identifying the problem.
 
 Bug fixes:
 fixed the link for GADM countries download. Bug reported by Loic Dutrieux
@@ -26,7 +18,7 @@ fixed problem with subs reported by Andy Craig https://github.com/rspatial/raste
 Previous version had a maxmemory value that was too high (reported by Lorenzo Busetto)
 
 --- 16-Oct-2018, version: 2.7-15
-faster extraction for points via GDAL
+faster extraction for points via GDAL (reverted to previous code in version 2.8-4)
 faster rasterization of polygons
 
 Bug fixes:
@@ -284,7 +276,7 @@ Fixed bug with RAT tables in native format (reported by Joseph Steward)
 Fixed corner case bug with extract/polygons df=TRUE (reported by Jon Olav Skoien)
 Added big.matrix as a "driver" (file format). This is experimental (and not documented).
 raster now attempts to interpret the CRS from netcdf files
-added support for the 360 day calander in netcdf files
+added support for the 360 day calendar in netcdf files
 
 
 --- 1-September-2012, version 2.0-12

DESCRIPTION

@@ -3,10 +3,10 @@ Type: Package
 Title: Geographic Data Analysis and Modeling
 Version: 2.8-5
 Date: 2018-11-02
-Depends: methods, sp (>= 1.2-0), R (>= 3.0.0)
+Depends: sp (>= 1.2-0), R (>= 3.0.0)
 Suggests: rgdal (>= 0.9-1), rgeos (>= 0.3-8), ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf, testthat
 LinkingTo: Rcpp
-Imports: Rcpp
+Imports: methods, Rcpp
 SystemRequirements: C++11
 Authors@R: c(
 	person("Robert J.", "Hijmans", role = c("cre", "aut"),  

NAMESPACE

@@ -1,11 +1,12 @@
 import(sp)
 import(Rcpp)
-importFrom("methods", "Ops", "Math", "as", ".hasSlot", "validObject")
+import(methods)
 importFrom("stats", as.formula, aggregate, predict, density, quantile, update, approx, reshape)
 importFrom("utils", stack, unstack, head, tail, download.file)
-importFrom("graphics", "hist", "lines", "image", "rect", "filled.contour", "contour", "persp", "pairs", "text", "boxplot", "points", "abline", "legend", "title", "strheight", "strwidth")
-importFrom("grDevices", "as.raster", "terrain.colors", "heat.colors", "col2rgb", "rainbow", "dev.flush", "dev.off", "dev.new", "xy.coords", "png")
+importFrom(graphics, hist, lines, image, rect, filled.contour, contour, persp, pairs, plot, text, boxplot, points, abline, legend, title, strheight, strwidth)
+importFrom(grDevices, as.raster, terrain.colors, heat.colors, col2rgb, rainbow, dev.flush, dev.off, dev.new, xy.coords, png)
 exportClasses(Extent, BasicRaster, Raster, RasterLayer, RasterBrick, RasterStack, RasterStackBrick)
-exportMethods("[", "==", '!=', '!', approxNA, as.array, as.character, as.vector, as.matrix, area, bandnr, barplot, brick, calc, clump, crop, disaggregate, distance, erase, extent, extract, extend, flip, head, intersect, is.factor, merge, mosaic, ncell, nlayers, overlay, plot, plotRGB, raster, reclassify, resample, rotate, sampleRandom, stackSelect, shift, subs, t, tail, trim, unique, unstack, union, xmin, xmax, ymin, ymax, zonal)
+exportMethods("[", "==", '!=', '!', approxNA, as.array, as.character, as.vector, as.matrix, area, bandnr, barplot, brick, calc, clump, crop, crs, "crs<-", disaggregate, distance, erase, extent, extract, extend, flip, focal, geom, head, intersect, is.factor, mask, merge, mosaic, ncell, nlayers, "nrow<-", "ncol<-", overlay, plot, plotRGB, raster, rasterize, reclassify, res, resample, rotate, sampleRandom, stackSelect, shift, subs, t, tail, trim, unique, unstack, union, xmin, xmax, xres, ymin, ymax, yres, zonal, yFromRow, xFromCol,colFromX, rowFromY, cellFromXY, cellFromRowCol, xyFromCell, yFromCell, xFromCell, rowColFromCell,rowFromCell, colFromCell, readStart, readStop, values, "values<-", writeStart, writeStop, writeValues, writeRaster)
 useDynLib(raster, .registration = TRUE)
 exportPattern("^[^\\.\\_]")
+

R/AAgeneric_functions.R

@@ -2,8 +2,17 @@ if (!isGeneric("mask")) { setGeneric("mask", function(x, mask, ...) standardGene
 if (!isGeneric("crop")) { setGeneric("crop", function(x, y, ...) standardGeneric("crop")) }	
 if (!isGeneric("trim")) { setGeneric("trim", function(x, ...) standardGeneric("trim")) }	
 if (!isGeneric("focal")) { setGeneric("focal", function(x, ...) standardGeneric("focal")) }
+if (!isGeneric("geom")) {setGeneric("geom", function(x, ...) standardGeneric("geom")) }	
+
+
 if (!isGeneric("rasterize")) {setGeneric("rasterize", function(x, y, ...) standardGeneric("rasterize"))}	
 
+if (!isGeneric("as.data.frame")) { setGeneric("as.data.frame", function(x, row.names = NULL, optional = FALSE, ...) standardGeneric("as.data.frame")) }	
+
+
+if (!isGeneric("nrow<-")) { setGeneric("nrow<-", function(x, ..., value) standardGeneric("nrow<-")) }	
+if (!isGeneric("ncol<-")) { setGeneric("ncol<-", function(x, ..., value) standardGeneric("ncol<-")) }	
+
 if (!isGeneric("crs")) { setGeneric("crs", function(x, ...) standardGeneric("crs")) }	
 if (!isGeneric("crs<-")) { setGeneric("crs<-", function(x, ..., value) standardGeneric("crs<-")) }	
 if (!isGeneric("ncell")) { setGeneric("ncell", function(x) standardGeneric("ncell")) }	
@@ -13,17 +22,13 @@ if (!isGeneric("yres")) { setGeneric("yres", function(x) standardGeneric("yres")
 if (!isGeneric("values")) { setGeneric("values", function(x, ...) standardGeneric("values")) }	
 if (!isGeneric("values<-")) { setGeneric("values<-", function(x, value) standardGeneric("values<-"))}	
 if (!isGeneric('writeRaster')) {setGeneric('writeRaster', function(x, filename, ...) standardGeneric('writeRaster'))}
-
-
 if (!isGeneric("yFromRow")) { setGeneric("yFromRow", function(object, row) standardGeneric("yFromRow")) }
 if (!isGeneric("xFromCol")) { setGeneric("xFromCol", function(object, col) standardGeneric("xFromCol")) }                  
 if (!isGeneric("colFromX")) { setGeneric("colFromX", function(object, x) standardGeneric("colFromX")) }                  
 if (!isGeneric("rowFromY")) { setGeneric("rowFromY", function(object, y) standardGeneric("rowFromY")) }                  
 if (!isGeneric("cellFromXY")) { setGeneric("cellFromXY", function(object, xy) standardGeneric("cellFromXY")) }
 if (!isGeneric("cellFromRowCol")) { setGeneric("cellFromRowCol", function(object, row, col) standardGeneric("cellFromRowCol")) }
-
 if (!isGeneric("xyFromCell")) { setGeneric("xyFromCell", function(object, cell, ...) standardGeneric("xyFromCell")) } 
-
 if (!isGeneric("yFromCell")) { setGeneric("yFromCell", function(object, cell) standardGeneric("yFromCell")) }             
 if (!isGeneric("xFromCell")) { setGeneric("xFromCell", function(object, cell) standardGeneric("xFromCell")) }               
 if (!isGeneric("rowColFromCell")) { setGeneric("rowColFromCell", function(object, cell) standardGeneric("rowColFromCell")) }

R/as.data.frame.R

@@ -3,10 +3,6 @@
 # Version 1.0
 # Licence GPL v3
 
-if (!isGeneric("as.data.frame")) {
-	setGeneric("as.data.frame", function(x, row.names = NULL, optional = FALSE, ...)
-		standardGeneric("as.data.frame"))
-}	
 
 
 .insertColsInDF <- function(x, y, col, combinenames=TRUE) {

R/cellRowCol.R

@@ -4,13 +4,23 @@
 # Licence GPL v3
 
 
-
-rowFromCell <- function(object, cell) {
-	object <- raster(object)
-	cell <- round(cell)
-	cell[cell < 1 | cell > ncell(object)] <- NA
-	trunc((cell-1)/ncol(object)) + 1
-}
+setMethod(rowFromCell, signature(object="BasicRaster", cell="numeric"), 	
+	function(object, cell) {
+		object <- raster(object)
+		cell <- round(cell)
+		cell[cell < 1 | cell > ncell(object)] <- NA
+		trunc((cell-1)/ncol(object)) + 1
+	}
+)
+
+#rowFromCell <- function(object, cell) {
+#	object <- raster(object)
+#	cell <- round(cell)
+#	cell[cell < 1 | cell > ncell(object)] <- NA
+#	trunc((cell-1)/ncol(object)) + 1
+#}
+
+
 
 .rowFromCell <- function(object, cell) {
 	trunc((cell-1)/ncol(object)) + 1
@@ -57,35 +67,65 @@ cellFromRowColCombine <- function(object, rownr, colnr) {
 	as.vector(t(cols))
 }
 
-
-colFromCell <- function(object, cell) {
-	object <- raster(object)
-	cell <- round(cell)
-	cell[cell < 1 | cell > ncell(object)] <- NA	
-	rownr <- trunc((cell-1)/object@ncols) + 1
-	as.integer(cell - ((rownr-1) * object@ncols))
-}
+setMethod(colFromCell, signature(object="BasicRaster", cell="numeric"), 	
+	function(object, cell) {
+		object <- raster(object)
+		cell <- round(cell)
+		cell[cell < 1 | cell > ncell(object)] <- NA	
+		rownr <- trunc((cell-1)/object@ncols) + 1
+		as.integer(cell - ((rownr-1) * object@ncols))
+	}
+)
+
+#colFromCell <- function(object, cell) {
+#	object <- raster(object)
+#	cell <- round(cell)
+#	cell[cell < 1 | cell > ncell(object)] <- NA	
+#	rownr <- trunc((cell-1)/object@ncols) + 1
+#	as.integer(cell - ((rownr-1) * object@ncols))
+#}
 
 .colFromCell <- function(object, cell) {
 	nc <- object@ncols
 	rownr <- trunc((cell-1)/nc) + 1
 	cell - ((rownr-1) * nc)
 }
 
-rowColFromCell <- function(object, cell) {
-	object <- raster(object)
-	cell <- round(cell)
-	cell[cell < 1 | cell > ncell(object)] <- NA
-	row <- as.integer(trunc((cell-1)/object@ncols) + 1)
-	col <- as.integer(cell - ((row-1) * object@ncols))
-	return(cbind(row, col))
-}
 
-cellFromRowCol <- function(object, rownr, colnr) {
-	rows <- object@nrows
-	cols <- object@ncols
-	.doCellFromRowCol(rows, cols, rownr, colnr)
-}
+setMethod(rowColFromCell, signature(object="BasicRaster", cell="numeric"), 
+	function(object, cell) {
+		object <- raster(object)
+		cell <- round(cell)
+		cell[cell < 1 | cell > ncell(object)] <- NA
+		row <- as.integer(trunc((cell-1)/object@ncols) + 1)
+		col <- as.integer(cell - ((row-1) * object@ncols))
+		return(cbind(row, col))
+	}	
+)
+
+#rowColFromCell <- function(object, cell) {
+#	object <- raster(object)
+#	cell <- round(cell)
+#	cell[cell < 1 | cell > ncell(object)] <- NA
+#	row <- as.integer(trunc((cell-1)/object@ncols) + 1)
+#	col <- as.integer(cell - ((row-1) * object@ncols))
+#	return(cbind(row, col))
+#}
+
+
+setMethod(cellFromRowCol, signature(object="BasicRaster", row="numeric", col="numeric"), 
+	function(object, row, col) {
+		rows <- object@nrows
+		cols <- object@ncols
+		.doCellFromRowCol(rows, cols, row, col)
+	}
+)
+
+#cellFromRowCol <- function(object, rownr, colnr) {
+#	rows <- object@nrows
+#	cols <- object@ncols
+#	.doCellFromRowCol(rows, cols, rownr, colnr)
+#}
 
 
 

R/geom.R

@@ -1,8 +1,4 @@
 
-if (!isGeneric("geom")) {
-	setGeneric("geom", function(x, ...)
-		standardGeneric("geom"))
-}	
 
 setMethod('geom', signature(x='SpatialPolygons'), 
 	function(x, sepNA=FALSE, ...) {

R/projection.R

@@ -13,11 +13,24 @@ setMethod("crs", signature('ANY'),
 )
 
 
-'crs<-' <- function(x, value) {
-	projection(x) <- value
-	x
-}
+#'crs<-' <- function(x, value) {
+#	projection(x) <- value
+#	x
+#}
+
+setMethod("crs<-", signature('BasicRaster', 'ANY'), 
+	function(x, ..., value) {
+		projection(x) <- value
+		x
+	}
+)
 
+setMethod("crs<-", signature('Spatial', 'ANY'), 
+	function(x, ..., value) {
+		projection(x) <- value
+		x
+	}
+)
 
 setMethod('is.na', signature(x='CRS'), 
 	function(x) {

R/replaceProperties.R

@@ -4,16 +4,29 @@
 # Licence GPL v3
 
 
+setMethod("ncol<-", signature('BasicRaster', 'numeric'), 
+	function(x, ..., value) {
+		dim(x) <- c(nrow(x), value)
+		return(x)
+	}
+)
 
-'ncol<-' <- function(x, value) {
-	dim(x) <- c(nrow(x), value)
-	return(x)
-}	
+setMethod("nrow<-", signature('BasicRaster', 'numeric'), 
+	function(x, ..., value) {
+		dim(x) <- c(value, ncol(x))
+		return(x)
+	}
+)
 
-'nrow<-' <- function(x, value) {
-	dim(x) <- c(value, ncol(x))
-	return(x)
-}	
+#'ncol<-' <- function(x, value) {
+#	dim(x) <- c(nrow(x), value)
+#	return(x)
+#}	
+
+#'nrow<-' <- function(x, value) {
+#	dim(x) <- c(value, ncol(x))
+#	return(x)
+#}	
 
 
 'xmin<-' <- function(x, value) {

R/xyCell.R

@@ -92,11 +92,12 @@ setMethod("cellFromXY", signature(object="BasicRaster", xy="ANY"),
 	}
 )
 
-setMethod("colFromX", signature(object="Raster", x="numeric"), 
+setMethod("colFromX", signature(object="BasicRaster", x="numeric"), 
 	function ( object, x )	{
-		if (inherits(x, 'Spatial')) { 
-			x <- x@coords[,1] 
-		}
+# from pre-generic
+#		if (inherits(x, 'Spatial')) { 
+#			x <- x@coords[,1] 
+#		}
 		if (rotated(object)) {
 			stop('this function is not supported for rotated rasters')
 		}
@@ -108,11 +109,12 @@ setMethod("colFromX", signature(object="Raster", x="numeric"),
 )
 
 
-setMethod("rowFromY", signature(object="Raster", y="numeric"), 
+setMethod("rowFromY", signature(object="BasicRaster", y="numeric"), 
 	function(object, y)	{
-		if (inherits(y, 'Spatial')) {
-			y <- y@coords[,2] 
-		}
+# from pre-generic
+#		if (inherits(y, 'Spatial')) {
+#			y <- y@coords[,2] 
+#		}
 		if (rotated(object)) {
 			stop('this function is not supported for rotated rasters')
 		}

TODO

@@ -0,0 +1,9 @@
+--- to do
+focal for multi-layer objects
+step-size option for focal
+add equivalent to "subsWithNA" to reclassify
+add AMSR-E ice products and other raw binary products
+add orientation fixes for AVISO currents and similar NetCDFs lacking metadata on the internal CRS
+add VRT output to saveStack
+Fix lines falling between the cracks in extract (calling rasterzeLines): https://stat.ethz.ch/pipermail/r-sig-geo/2014-May/020973.html
+Better handling of NA values in 1 byte raster files

man/cellFrom.Rd

@@ -1,11 +1,11 @@
 \name{cellFrom}
 
 \alias{cellFromRowCol}
-\alias{cellFromRowCol,Raster,numeric,numeric-method}
+\alias{cellFromRowCol,BasicRaster,numeric,numeric-method}
 \alias{colFromX}
-\alias{colFromX,Raster,numeric-method}
+\alias{colFromX,BasicRaster,numeric-method}
 \alias{rowFromY}
-\alias{rowFromY,Raster,numeric-method}
+\alias{rowFromY,BasicRaster,numeric-method}
 \alias{cellFromXY}
 \alias{cellFromXY,BasicRaster-method}
 
@@ -27,7 +27,7 @@ The last cell number equals the number of cells of the Raster* object.
 }
 
 \usage{
-cellFromRowCol(object, rownr, colnr)
+cellFromRowCol(object, row, col)
 cellFromRowColCombine(object, rownr, colnr)
 cellFromRow(object, rownr)
 cellFromCol(object, colnr)
@@ -43,6 +43,8 @@ fourCellsFromXY(object, xy, duplicates=TRUE)
   \item{object}{Raster* object (or a SpatialPixels* or SpatialGrid* object)}
   \item{colnr}{column number; or vector of column numbers}
   \item{rownr}{row number; or vector of row numbers}
+  \item{col}{column number; or vector of column numbers}
+  \item{row}{row number; or vector of row numbers}
   \item{x}{x coordinate(s)}
   \item{y}{y coordinate(s)}
   \item{xy}{matrix of x and y coordinates, or a SpatialPoints or SpatialPointsDataFrame object}