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rspatial · Jul 9, 2019 · 89cc846 · 89cc846
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: raster
 Type: Package
 Title: Geographic Data Analysis and Modeling
-Version: 2.9-19
-Date: 2019-07-02
+Version: 2.9-22
+Date: 2019-07-09
 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

diff --git a/R/AAgeneric_functions.R b/R/AAgeneric_functions.R
@@ -7,25 +7,21 @@ if (!isGeneric("approxNA")) {setGeneric("approxNA", function(x, ...)		standardGe
 if (!isGeneric("as.data.frame")) { setGeneric("as.data.frame", function(x, row.names = NULL, optional = FALSE, ...) standardGeneric("as.data.frame")) }	
 
 if (!isGeneric("as.factor")) {setGeneric("as.factor", function(x) standardGeneric("as.factor"))}
-
 if (!isGeneric("is.factor")) {setGeneric("is.factor", function(x) standardGeneric("is.factor"))}
-
-
 if (!isGeneric("atan2")) { setGeneric("atan2", function(y, x) standardGeneric("atan2"))}	
 if (!isGeneric("boundaries")) {	setGeneric("boundaries", function(x, ...) standardGeneric("boundaries"))}	
-
 if (!isGeneric('buffer')) {setGeneric('buffer', function(x, ...) standardGeneric('buffer'))}	
-
 if (!isGeneric("calc")) {setGeneric("calc", function(x, fun, ...) standardGeneric("calc")) }
 if (!isGeneric("clamp")) {setGeneric("clamp", function(x, ...) standardGeneric("clamp")) }	
 if (!isGeneric("cover")) {setGeneric("cover", function(x, y, ...) standardGeneric("cover"))}		
 if (!isGeneric("crop")) { setGeneric("crop", function(x, y, ...) standardGeneric("crop"))}	
 if (!isGeneric("crs")) { setGeneric("crs", function(x, ...) standardGeneric("crs")) }	
 if (!isGeneric("crs<-")) { setGeneric("crs<-", function(x, ..., value) standardGeneric("crs<-")) }	
 if (!isGeneric("disaggregate")) {setGeneric("disaggregate", function(x, ...) standardGeneric("disaggregate"))}
-
 if (!isGeneric("distance")) {setGeneric("distance", function(x, y, ...)standardGeneric("distance"))}	
 if (!isGeneric("erase")) {setGeneric("erase", function(x, y, ...) standardGeneric("erase"))}
+
+if (!isGeneric("extend")) {setGeneric("extend", function(x, y, ...) standardGeneric("extend"))}	
 if (!isGeneric("extract")) { setGeneric("extract", function(x, y, ...) standardGeneric("extract"))}	
 if (!isGeneric("flip")) { setGeneric("flip", function(x, direction, ...) standardGeneric("flip")) }
 if (!isGeneric("focal")) { setGeneric("focal", function(x, ...) standardGeneric("focal"))}
@@ -37,7 +33,7 @@ if (!isGeneric("hasValues")) { setGeneric("hasValues", function(x, ...) standard
 if (!isGeneric("ifel")) {setGeneric("ifel", function(test, yes, no, ...) standardGeneric("ifel"))}	
 if (!isGeneric("image")) {setGeneric("image", function(x,...) standardGeneric("image"))}	
 if (!isGeneric("init")) {setGeneric("init", function(x, ...) standardGeneric("init"))}	
-
+if (!isGeneric("interpolate")) { setGeneric("interpolate", function(object, ...) standardGeneric("interpolate"))}	
 if (!isGeneric("isLonLat")) { setGeneric("isLonLat", function(x, ...) standardGeneric("isLonLat"))}	
 if (!isGeneric("couldBeLonLat")) { setGeneric("couldBeLonLat", function(x, ...) standardGeneric("couldBeLonLat"))}	
 

diff --git a/R/extend.R b/R/extend.R
@@ -6,11 +6,6 @@
 
 
 
-if (!isGeneric("extend")) {
-	setGeneric("extend", function(x, y, ...)
-		standardGeneric("extend"))
-}	
-
 setMethod('extend', signature(x='Extent'), 
 # function by Etienne B. Racine
 function(x, y, ...) {

diff --git a/R/geom.R b/R/geom.R
@@ -93,13 +93,19 @@ setMethod("geom", signature(x="data.frame"),
 	function(x, d, gt, crs, ...) {	
 		if (gt == "polygons") {
 			sp <- as(x, "SpatialPolygons")
-			sp <- sp::SpatialPolygonsDataFrame(sp, d)
+			if (NROW(d) > 0) {
+				sp <- sp::SpatialPolygonsDataFrame(sp, d)
+			}
 		} else if (gt == "lines") {
 			sp <- as(x, "SpatialLines")		
-			sp <- sp::SpatialLinesDataFrame(sp, d)
+			if (NROW(d) > 0) {
+				sp <- sp::SpatialLinesDataFrame(sp, d)
+			}
 		} else {
-			sp <- as(x, "SpatialPoints")
-			sp <- sp::SpatialPointsDataFrame(sp, d)
+			sp <- sp::SpatialPoints(x[,c("x", "y")])
+			if (NROW(d) > 0) {
+				sp <- sp::SpatialPointsDataFrame(sp, d)
+			}
 		}
 		crs(sp)<- crs
 		sp

diff --git a/R/ifelse.R b/R/ifelse.R
@@ -3,8 +3,9 @@
 # Version 1.0
 # Licence GPL v3
 
-setMethod("ifel", signature(test="Raster", yes="ANY", no="ANY"), 
-	function(test, yes, no, filename="", ...) {
+#setMethod("ifel", signature(test="Raster", yes="ANY", no="ANY"), 
+
+.ifel <- function(test, yes, no, filename="", ...) {
 		if (!inherits(no, "Raster")) {
 			stopifnot(is.numeric(no))
 			if (length(no) > 1) warning('only the first element of "no" is used')
@@ -19,4 +20,4 @@ setMethod("ifel", signature(test="Raster", yes="ANY", no="ANY"),
 		}
 		cover(no, yes, filename=filename)
 	}
-)
+#)
diff --git a/R/interpolate.R b/R/interpolate.R
@@ -1,8 +1,4 @@
 
-if (!isGeneric("interpolate")) {
-	setGeneric("interpolate", function(object, ...)
-		standardGeneric("interpolate"))
-}	
 
 # to do: should allow index to be a vector
 

diff --git a/man/cluster.Rd b/man/cluster.Rd
@@ -81,10 +81,10 @@ values(r) <- runif(ncell(r))
 m <- c(0, 0.25, 1,  0.25, 0.5, 2,  0.5, 1, 3)
 m <- matrix(m, ncol=3, byrow=TRUE)
 rc1 <- clusterR(r, reclassify, args=list(rcl=m, right=FALSE), 
-               filename='rcltest.grd', datatype='INT2S', overwrite=TRUE)
+               filename=rasterTmpFile(), datatype='INT2S', overwrite=TRUE)
 
 # equivalent to:
-rc2 <- reclassify(r, rcl=m, right=FALSE, filename='rcltest.grd', datatype='INT2S', overwrite=TRUE)
+rc2 <- reclassify(r, rcl=m, right=FALSE, filename=rasterTmpFile(), datatype='INT2S', overwrite=TRUE)
 
 
 # example with the calc function

diff --git a/man/datasource.Rd b/man/datasource.Rd
@@ -49,9 +49,9 @@ fromDisk(rs)
 rs <- setValues(rs, 1:ncell(rs))
 inMemory(rs)
 fromDisk(rs)
-rs <- writeRaster(rs, filename='test', overwrite=TRUE)
-inMemory(rs)
-fromDisk(rs)
+#rs <- writeRaster(rs, filename=rasterTmpFile(), overwrite=TRUE)
+#inMemory(rs)
+#fromDisk(rs)
 }
 
 \keyword{ spatial }
diff --git a/man/factor.Rd b/man/factor.Rd
@@ -104,8 +104,8 @@ i
 factorValues(r, i)
 
 # write to file:
-rr <- writeRaster(r, 'test.grd', overwrite=TRUE)
-rr
+# rr <- writeRaster(r, rasterTmpFile(), overwrite=TRUE)
+# rr
 
 # create a single-layer factor 
 x <- deratify(r, 'landcover')

diff --git a/man/ifelse.Rd b/man/ifelse.Rd
diff --git a/man/init.Rd b/man/init.Rd
@@ -39,8 +39,8 @@ y <- init(r, fun=runif)
 
 # there are different ways to set all values to 1 
 # for large rasters:
-set1f <- function(x){rep(1, x)}
-z1 <- init(r, fun=set1f, filename='test.grd', overwrite=TRUE)
+# set1f <- function(x){rep(1, x)}
+# z1 <- init(r, fun=set1f, filename=rasterTmpFile(), overwrite=TRUE)
 
 # This is equivalent to (but not memory safe):
 z2 <- setValues(r, rep(1, ncell(r)))

diff --git a/man/metadata.Rd b/man/metadata.Rd
@@ -31,18 +31,20 @@ Raster* object or list
 
 \examples{ 
 r <- raster(nc=10, nr=10)
-r[] <- 1:ncell(r)
+values(r) <- 1:ncell(r)
 
 m <- list(wave=list(a=1, b=2, c=c('cool', 'important')), that=list(red='44', blue=1:5,
        days=as.Date(c('2014-1-15','2014-2-15'))), this='888 miles from here', today=NA)
 
 metadata(r) <- m
-x <- writeRaster(r, 'test.grd', overwrite=TRUE)
+
+\dontrun{
+
+x <- writeRaster(r, rasterTmpFile(), overwrite=TRUE)
 metax <- metadata(x)
 
 identical(metax, m)
 
-\dontrun{
 # nested too deep
 badmeta1 <- list(wave=list(a=1, b=2, c='x'), that=list(red='4', blue=list(bad=5)))
 metadata(r) <- badmeta1

diff --git a/man/update.Rd b/man/update.Rd
@@ -36,9 +36,10 @@ RasterLayer or RasterBrick
 }
 
 \examples{
+\dontrun{
 # setting up an example RasterLayer with file
 r <- raster(nrow=5, ncol=10, vals=0)
-r <- writeRaster(r, 'test', overwrite=TRUE, datatype='INT2S')
+r <- writeRaster(r, rasterTmpFile(), overwrite=TRUE, datatype='INT2S')
 as.matrix(r)
 
 # update with a vector starting a cell
@@ -52,10 +53,11 @@ r <- update(r, v=5:1, cell=c(5,15,25,35,45))
 as.matrix(r)
 
 # updating with a marix, anchored at a cell number
-m = matrix(1:10, ncol=2)
+m <- matrix(1:10, ncol=2)
 r <- update(r, v=m, cell=2)
 as.matrix(r)
 }
+}
 
 \keyword{methods}
 \keyword{spatial}

diff --git a/src/distance.cpp b/src/distance.cpp
@@ -2,16 +2,14 @@
 
 */
 
-#ifndef M_PI
-#define M_PI (3.14159265358979323846)
-#endif
 
 #include <Rcpp.h>
 using namespace Rcpp;
 using namespace std;
 #include <vector>
 #include "geodesic.h"
 #include <math.h>
+#include "util.h"
 
 
 double distance_lonlat(double lon1, double lat1, double lon2, double lat2, double a, double f) {
@@ -92,16 +90,6 @@ std::vector<double> distanceToNearest_plane(std::vector<double> x1, std::vector<
 
 
 
-// Convert degrees to radians 
-double toRad(double deg) {
-	return( deg * 0.0174532925199433 );
-}
-
-double toDeg(double rad) {
-	return( rad * 57.2957795130823 );
-}
-
-
 
 double direction_lonlat(double lon1, double lat1, double lon2, double lat2, bool degrees, double a, double f) {
 	double s12, azi1, azi2;

diff --git a/src/rcpp_aggregate.cpp → src/raster_aggregate.cpp b/src/rcpp_aggregate.cpp → src/raster_aggregate.cpp
diff --git a/src/rcpp_distance.cpp → src/raster_distance.cpp b/src/rcpp_distance.cpp → src/raster_distance.cpp
diff --git a/src/r_terrain.cpp → src/terrain.cpp b/src/r_terrain.cpp → src/terrain.cpp
diff --git a/src/util.c → src/util.cpp b/src/util.c → src/util.cpp
@@ -1,9 +1,14 @@
-#include    <R.h>
-#include	<stdio.h>
-#include	<stdlib.h>
-#include	<math.h>
+
+#ifndef RASTERUTIL_GUARD
+#define RASTERUTIL_GUARD
+
+
+#include <math.h>
 #include "Rmath.h"
 
+#ifndef M_PI
+#define M_PI (3.14159265358979323846)
+#endif
 
 
 double mod(double x, double n) {
@@ -30,3 +35,6 @@ double toDeg(double rad) {
 
 
 
+
+#endif
+
diff --git a/src/wirth.c b/src/wirth.c
diff --git a/src/rcpp_xyCell.cpp → src/xyCell.cpp b/src/rcpp_xyCell.cpp → src/xyCell.cpp