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rspatial · Nov 11, 2023 · 83ef6f9 · 83ef6f9
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Showing 8 changed files with 12 additions and 7 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,8 @@
 https://stackoverflow.com/questions/77304534/rspatial-terraflip-error-when-flipping-a-multi-layer-spatrast-object) 
 - SpatRaster now correctly handles `NA & FALSE` and `NA | TRUE` [#1316](https://github.com/rspatial/terra/issues/1316) by John Baums
 - `set.names` wasn't working properly for SpatRasterDataset or SpatRasterCollection [#1333](https://github.com/rspatial/terra/pull/1333) by Derek Friend
+- `extract` with argument "layer" not NULL shifted the layers [#1332](https://github.com/rspatial/terra/issues/1332) by Ewan Wakefield
+
 
 ## enhancements
 

diff --git a/R/RGB.R b/R/RGB.R
@@ -140,7 +140,7 @@ rgb2col <- function(x, value, stretch=NULL, grays=FALSE, NAzero=FALSE, filename=
 	}
 
 	v <- cbind(id=1:ncell(x), values(x))
-	v <- terra:::median_cut(stats::na.omit(v))
+	v <- median_cut(stats::na.omit(v))
 
 	a <- aggregate(v[,-c(1:2)], list(v[,1]), median)
 #	if (n==3) {

diff --git a/R/coerce.R b/R/coerce.R
@@ -396,7 +396,7 @@ as.data.frame.SpatRaster <- function(x, row.names=NULL, optional=FALSE, xy=FALSE
 			if (xy) idv <- c("x", "y", idv)
 			if (cells) idv <- c("cell", idv)
 			nms <- names(x)
-			d <- reshape(d, direction="long", idvar=idv, varying=nms, v.names="values")
+			d <- stats::reshape(d, direction="long", idvar=idv, varying=nms, v.names="values")
 			d$time <- nms[d$time]
 			names(d)[names(d) == "time"] <- "layer"
 		}

diff --git a/R/k_means.R b/R/k_means.R
@@ -11,7 +11,7 @@ setMethod("k_means", signature(x="SpatRaster"),
 		if (ncell(x) <= maxcell) {
 			v <- na.omit(as.matrix(x))
 			omit <- as.vector(attr(v, "na.action"))
-			km <- kmeans(v, centers=centers, ...)
+			km <- stats::kmeans(v, centers=centers, ...)
 			out <- rast(x, nlyr=1)
 			if (is.null(omit)) {
 				values(out) <- km$cluster
@@ -34,8 +34,8 @@ setMethod("k_means", signature(x="SpatRaster"),
 				}
 				vec
 			}			
-			v <- na.omit(spatSample(x, maxcell, "regular"))
-			km <- kmeans(v, centers=centers, ...)$centers		
+			v <- unique(na.omit(spatSample(x, maxcell, "regular")))
+			km <- stats::kmeans(v, centers=centers, ...)$centers		
 			out <- predict(x, km, fun=pkmeans, filename=filename, overwrite=overwrite, wopt=wopt)
 		}
 		out

diff --git a/R/plot_raster.R b/R/plot_raster.R
@@ -579,7 +579,7 @@ prettyNumbs <- function(x, digits) {
 	if (ncell(x) > 1.1 * maxcell) {
 		if (inherits(alpha, "SpatRaster")) {
 			if (nlyr(alpha) > 1) {
-				alpha <- alpha[[y]]
+				alpha <- alpha[[1]]
 			}
 			alpha <- spatSample(alpha, maxcell, method="regular", as.raster=TRUE, warn=FALSE)
 		}

diff --git a/R/zonal.R b/R/zonal.R
@@ -189,7 +189,7 @@ setMethod("zonal", signature(x="SpatRaster", z="SpatVector"),
 				}
 				if (as.polygons | wide) {
 					nms <- names(v)
-					v <- reshape(v, direction="wide", idvar=nms[1], timevar=nms[2])
+					v <- stats::reshape(v, direction="wide", idvar=nms[1], timevar=nms[2])
 					names(v) <- gsub("count.", "", names(v))
 					v[is.na(v)] <- 0
 					rownames(v) <- NULL

diff --git a/man/distance.Rd b/man/distance.Rd
@@ -8,6 +8,8 @@
 \alias{distance,SpatVector,SpatVector-method}
 \alias{distance,matrix,matrix-method}
 \alias{distance,matrix,missing-method}
+\alias{distance,data.frame,data.frame-method}
+\alias{distance,data.frame,missing-method}
 
 \title{Geographic distance}
 

diff --git a/man/time.Rd b/man/time.Rd
@@ -5,6 +5,7 @@
 \alias{time<-}
 \alias{time<-,SpatRaster-method}
 \alias{time<-,SpatRasterDataset-method}
+\alias{has.time,SpatRasterDataset-method}
 \alias{time,SpatRaster-method}
 \alias{time,SpatRasterDataset-method}
 \alias{timeInfo}