*fasterRaster* 8.4.1.1 (2025-11-18)

.Rbuildignore

@@ -12,13 +12,12 @@ CODE_OF_CONDUCT.md
 ^\.vscode
 ^README\.Rmd$
 ^.lintr$
-^fasterRaster.code-workspace
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
 ^\.github$
 ^\vignettes\^junk
 junk
-fasterRaster_workspace.code-workspace
+workspace_fasterRaster.code-workspace
 ^doc$
 ^Meta$

.Rproj.user/shared/notebooks/paths

@@ -0,0 +1,2 @@
+C:/Kaji/R/fasterRaster/DESCRIPTION="BE5F8589"
+C:/Kaji/R/fasterRaster/NEWS.md="B2E56A81"

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: fasterRaster
 Type: Package
 Title: Faster Raster and Spatial Vector Processing Using 'GRASS'
-Version: 8.4.1.0
-Date: 2025-06-19
+Version: 8.4.1.1
+Date: 2025-11-18
 Authors@R: 
 	c(
 		person(
@@ -47,4 +47,4 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
 LazyLoad: yes
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,3 +1,19 @@
+# fasterRaster 8.4.1.1 (2025-11-18)
+### New functions and functionality
+o `+` can now combine any two `GVector`s with the same geometry type (points, lines, polygons).  
+o `installAddon()` checks to see if addon is already installed, and if so, uninstalls it before re-installing.  
+o Minor documentation updates.  
+
+### Bug fixes
+o `fast()` correctly adds names to `GRaster`s loaded from disk when a `_names.csv` file exists.  
+o `geomorphons()` now works when `mode = '2'`.  
+o `rbind()` combines `GVector` data tables when each vecto has the same number of rows in its table as geometries.  
+o `scale()` and `scalepop()` work when `center` and/or `scale` are numeric.  
+o `sf` example data objects (`madCoast0`, `madCoast4`, and `madRivers`) have had their CRSs harmonized with the example raster objects. This had caused some of the examples not to work.  
+
+### Other
+o Added error checking in `fragmentation()` related to limits on size of window `w` for calculation of fragmentation indices.  
+
 # fasterRaster 8.4.1.0 (2025-06-17)
 
 ### Code-breaking changes

R/04_arithmetic.r

@@ -8,7 +8,7 @@
 #' `*` operator: Same as [intersect()]\cr
 #' `/` operator: Same as [xor()]\cr
 #' 
-#' @param e1,e2 `GRaster`s, `numeric`s, `integer`s, or `logical`s.
+#' @param e1,e2 `GRaster`s, `GVector`s, `numeric`s, `integer`s, or `logical`s.
 #'
 #' @return A `GRaster`.
 #'
@@ -428,13 +428,21 @@ methods::setMethod(
 	signature(e1 = "GVector", e2 = "GVector"),
     function(e1, e2) {
 
+		gtype1 <- geomtype(e1)
+		gtype2 <- geomtype(e2)
+		if (gtype1 != gtype2) stop("Vectors must be of the same type (polygons, lines, or points).")
+
 		compareGeom(e1, e2)
 		.locationRestore(e1)
 
 		oper <- as.vector(.Generic)[1L]
 
 		if (oper == "+") {
-			out <- union(e1, e2)
+			if (gtype1 == "polygons" & gtype2 == "polygons") {
+				out <- union(e1, e2)
+			} else {
+				out <- rbind(e1, e2)
+			}
 		} else if (oper == "-") {
 			out <- erase(e1, e2)
 		} else if (oper == "*") {

R/addons.r

@@ -36,15 +36,24 @@ addons <- function(x = NULL) {
 installAddon <- function(x, check = TRUE) {
 
 	if (check) {
+
+		# is it available?
 		avails <- rgrass::execGRASS("g.extension", flags = c("l", .quiet()), intern = TRUE)
 		if (!(x %in% avails)) {
+
 			warning("The addon is not available on the official GRASS addon repository.")
 			return(invisible(FALSE))
+
 		}
 	}
 
+	# remove addon before re-installing
+	if (addons(x)) removeAddon(x, check = FALSE)
+
 	rgrass::execGRASS("g.extension", operation = "add", extension = x, flags = .quiet())
-	invisible(TRUE)
+	success <- addons(x)
+	if (!success) warning("Addon could not be installed.")
+	invisible(success)
 
 }
 

R/backdoor.r

@@ -2,22 +2,32 @@
 #'
 #' This is a secret function to be used for faster development of **fasterRaster**. It calls [faster()] to set the install directory for **GRASS**, increases default memory, and number of cores. The function assumes development is on a Windows machine.
 #'
+#' @param start Logical: If `TRUE`, start the **GRASS** session by creating the `madElev` `GRaster`.
 #' @param ver Character: **GRASS**: e.g., "83" or "84".
 #'
 #' @returns `TRUE` (invisibly).
 #'
 #' @keywords internal
-.backdoor <- function(ver = "84") {
+.backdoor <- function(start = FALSE, ver = "84") {
 
 	verNice <- paste0(substr(ver, 1L, 1L), ".", substr(ver, 2L, 2L))
 
 	faster(
 		grassDir = paste0("C:/Program Files/GRASS GIS ", verNice),
-		addonsDir = 'C:/Users/adame/AppData/Roaming/GRASS8/addons',
+		addonsDir = "C:/Users/adame/AppData/Roaming/GRASS8/addons",
 		memory = 1024 * 8,
 		cores = 2,
 		useDataTable = TRUE,
 		verbose = TRUE
 	)
-	invisible(TRUE)
+
+	if (start) {
+		madElev <- fastData("madElev")
+		elev <- fast(madElev)
+		out <- elev
+	} else {
+		out <- TRUE
+	}
+
+	invisible(out)
 }

R/fast.r

@@ -179,7 +179,16 @@ methods::setMethod(
 
 			xRast <- terra::rast(x)
 			nLayers <- terra::nlyr(xRast)
+
 			xNames <- names(xRast)
+			fileExtension <- .fileExt(x)
+			nc <- nchar(fileExtension) + 1
+			namesFile <- substr(x, 1, nchar(x) - nc)
+			namesFile <- paste0(namesFile, '_names.csv')
+			if (file.exists(namesFile)) {
+				xNames <- utils::read.csv(namesFile)
+				xNames <- xNames$name
+			}
 
 			location <- .locationFind(xRast, match = "crs")
 

R/fastData.r

@@ -5,24 +5,24 @@
 #' @param x The name of the raster or spatial vector to get. All of these represent a portion of the eastern coast of Madagascar.
 #'
 #' Spatial vectors (objects of class `sf` from the **sf** package):
-#' * [madCoast0]: Outline of the region (polygon)
-#' * [madCoast4]: Outlines of the Fokontanies (Communes) of the region (polygons)
-#' * [madDypsis]: Records of plants of the genus *Dypsis* (points)
-#' * [madRivers]: Major rivers (lines)
+#' * [madCoast0][madCoast0]: Outline of the region (polygon)
+#' * [madCoast4][madCoast4]: Outlines of the Fokontanies (Communes) of the region (polygons)
+#' * [madDypsis][madDypsis]: Records of plants of the genus *Dypsis* (points)
+#' * [madRivers][madRivers]: Major rivers (lines)
 #'
 #' Rasters (objects of class `SpatRaster` from the **terra** package, saved as GeoTIFF files):
-#' * [madChelsa]: Bioclimatic variables
-#' * [madCover]: Land cover
-#' * [`madElev`][madElev]: Elevation
-#' * [madForest2000]: Forest cover in year 2000
-#' * [madForest2014]: Forest cover in year 2014
-#' * [madLANDSAT]: Surface reflectance in 2023
-#' * [madPpt], [madTmin], [madTmax]: Rasters of mean monthly precipitation, and minimum and maximum temperature.
+#' * [madChelsa][madChelsa]: Bioclimatic variables
+#' * [madCover][madCover]: Land cover
+#' * [madElev][madElev]: Elevation
+#' * [madForest2000][madForest2000]: Forest cover in year 2000
+#' * [madForest2014][madForest2014]: Forest cover in year 2014
+#' * [madLANDSAT][madLANDSAT]: Surface reflectance in 2023
+#' * [madPpt][madPpt], [madTmin][madTmin], [madTmax][madTmax]: Rasters of mean monthly precipitation, and minimum and maximum temperature.
 #'
 #' Data frames
-#' * [appFunsTable]: Table of functions usable by [app()]
-#' * [madCoverCats]: Land cover values and categories for [madCover]
-#' * [vegIndices]: Vegetation indices that can be calculated with [vegIndex()]
+#' * [appFunsTable][appFunsTable]: Table of functions usable by [app()]
+#' * [madCoverCats][madCoverCats]: Land cover values and categories for `madCover`
+#' * [vegIndices][vegIndices]: Vegetation indices that can be calculated with [vegIndex()]
 #'
 #' @return A `SpatRaster`, `sf` spatial vector, or a `data.frame`.
 #'

R/fasterRaster.r

@@ -322,11 +322,11 @@
 #' * Vignette on **fasterRaster** hidden functions: `vignette("hidden_functions", package = "fasterRaster")`
 #'
 #' ## Classes
-#' * [`GLocation`]: Fundamental class; points to a "location/project" in **GRASS**
-#' * [`GSpatial`]: Basic class of any spatial object
-#' * [`GRegion`]: Points to a "region" of a "location/project" in **GRASS**
-#' * [`GRaster`]: Raster class
-#' * [`GVector`]: Spatial vector class
+#' * [GLocation][GLocation]: Fundamental class; points to a "location/project" in **GRASS**
+#' * [GSpatial][GSpatial]: Basic class of any spatial object
+#' * [GRegion][GRegion]: Points to a "region" of a "location/project" in **GRASS**
+#' * [GRaster][GRaster]: Raster class
+#' * [GVector][GVector]: Spatial vector class
 #'
 #' @author Adam B. Smith
 #' @name fasterRaster

R/fillNAs.r

@@ -121,4 +121,4 @@ methods::setMethod(
 	.makeGRaster(srcs, names(x))
 
 	} # EOF
-)
+)

R/fragmentation.r

@@ -13,9 +13,9 @@
 #' * 5: Undetermined (not possible to obtain when `w = 3`)
 #' * 6: Interior
 #'
-#' @param x A `SpatRaster` or `GRaster`.
+#' @param x A `SpatRaster` or `GRaster` wherein the habitat type has cell values of 1, and non-focal habitat type has cell values of 0 or `NA`
 #'
-#' @param w An odd, positive integer: Size of the window across which fragmentation is calculated (in units of "rows" and "columns"). The default is 3, meaning the function uses a 3x3 moving window to calculate fragmentation. For large rasters, compute time is ~*O*(`N`) + *O*(`N * w^2`), where `N` is the number of cells in the raster. So, even a small increase in `w` can increase compute time by a lot.
+#' @param w An odd integer between 3 and 25: Size of the window across which fragmentation is calculated (in units of "rows" and "columns"). The default is 3, meaning the function uses a 3x3 moving window to calculate fragmentation. For large rasters, compute time is ~*O*(`N`) + *O*(`N * w^2`), where `N` is the number of cells in the raster. So, even a small increase in `w` can increase compute time by a lot. Values >25 will fail. A workaround might be to use [aggregate()] with `fun = 'mode'`, apply `fragmentation()`, then `resample()` to the original resolution.
 #'
 #' @param undet Character: How to assign the "undetermined" case. Valid values are `"perforated"` (default), `"edge"`, and `"undetermined"`. Partial matching is used. If `Pf` is the proportional density raster cell value and `Pff` the proportional connectivity raster cell value, the undetermined case occurs when `Pf` > 0.6 and `Pf == Pff`.
 #'
@@ -42,7 +42,7 @@ methods::setMethod(
 	function(x, w = 3, undet = "undetermined", none = NA, na.rm = TRUE, cores = faster("cores"), verbose = TRUE) {
 
 	# errors?
-	if (!omnibus::is.wholeNumber(w) || w < 1L || w %% 2 == 0) stop("Argument `w` must be an odd, positive integer.")
+	if (w > 25 | !omnibus::is.wholeNumber(w) | w < 1L | w %% 2 == 0) stop("Argument `w` must be an odd, positive integer in the range from 3 to 25.")
 	undet <- omnibus::pmatchSafe(undet, c("undetermined", "perforated", "edge"), nmax = 1L)
 
 	# setup
@@ -307,7 +307,7 @@ methods::setMethod(
 	}
 
 	# for each layer
-	nSteps <- nLayers * (1 + length(offsets) + 6)
+	nSteps <- nLayers * (2 + length(offsets) + 6) + 1
 	if (verbose | faster("verbose")) {
 		pb <- utils::txtProgressBar(min = 0, max = nSteps, initial = 0, style = 3, width = 30)
 	}
@@ -330,13 +330,14 @@ methods::setMethod(
 		created <- c(created, srcXZeros)
 
 		### connectivities (for Pff)
-		srcConnectivities <- .makeSourceName("fragmentation_connectivities", "raster", n = length(offsets))
-		srcEither <- .makeSourceName("fragmentation_either", "raster", n = length(offsets))
-		srcBoth <- .makeSourceName("fragmentation_both", n = length(offsets))
+		n <- length(offsets)
+		srcConnectivities <- paste0('c', 1:n) # .makeSourceName("frag_connect", "raster", n = length(offsets))
+		srcEither <- paste0('e', 1:n) # .makeSourceName("frag_either", "raster", n = length(offsets))
+		srcBoth <- paste0('b', 1:n) # .makeSourceName("frag_both", n = length(offsets))
 		for (j in seq_along(offsets)) {
 
 			steps <- steps + 1
-			if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, steps)
+			if (verbose || faster("verbose")) utils::setTxtProgressBar(pb, steps)
 
 			# tally occurrences of habitat in each pair of cells		
 			y1 <- offsets[[j]][1L]
@@ -346,26 +347,25 @@ methods::setMethod(
 			x2 <- offsets[[j]][4L]
 
 			# sum of pairs of cells
-			ex <- paste0(srcConnectivities[j], " = ", srcXZeros, "[", y1, ",", x1, "] + ", srcXZeros, "[", y2, ",", x2, "]")
+			ex <- paste0(srcConnectivities[j], " = ", srcXZeros, "[", y1, ",", x1, "]+", srcXZeros, "[", y2, ",", x2, "]")
 			rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
 
 			# does either cell in a pair have habitat?
-			ex <- paste0(srcEither[j], " = if(", srcConnectivities[j], " >= 1)")
+			ex <- paste0(srcEither[j], " = if(", srcConnectivities[j], ">= 1)")
 			rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
 
 			# do both cells have habitat?
-			ex <- paste0(srcBoth[j], " = if(", srcConnectivities[j], " == 2)")
+			ex <- paste0(srcBoth[j], " = if(", srcConnectivities[j], "==2)")
 			rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
 
 		}
 		created <- c(created, srcConnectivities, srcEither, srcBoth)
 
-
 		# number of neighbor cell pairs with at least one with habitat
 		steps <- steps + 1
 		if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, steps)
 		srcNumEithers <- .makeSourceName("fragmentation_sum_eithers", "raster")
-		ex <- paste0(srcNumEithers, " = ", paste(srcEither, collapse = " + "))
+		ex <- paste0(srcNumEithers, " = ", paste(srcEither, collapse = "+"))
 		rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
 
 		created <- c(created, srcNumEithers)
@@ -486,13 +486,17 @@ methods::setMethod(
 
 		# }
 
-		srcs[i] <- src
-
+		steps <- steps + 1
+		if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, steps)
 		.rm(created, type = "raster", warn = FALSE)
 		created <- character()
 
+		srcs[i] <- src
+
 	} # next layer
 
+	steps <- steps + 1
+	if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, steps)
 	if (verbose | faster("verbose")) close(pb)
 
 	levs <- .fragmentationLevels(undet = undet, none = none)

R/geomorphons.r

@@ -50,13 +50,15 @@ methods::setMethod(
 	) {
 
 	unit <- omnibus::pmatchSafe(unit, c("cells", "meters"), nmax = 1L)
-	comparison <- omnibus::pmatchSafe(mode, c("1", "2", "2d"), nmax = 1L)
-	comparison <-if (comparison == "1") {
-		"anglev1"
-	} else if (comparison == "2") {
-		"anglev2"
-	} else if (comparison == "2d") {
-		 "anglev2_distance"
+	mode <- as.character(mode)
+	if (mode == "1") {
+		comparison <- "anglev1"
+	} else if (mode == "2") {
+		comparison <- "anglev2"
+	} else if (mode == "2d") {
+		 comparison <- "anglev2_distance"
+	} else {
+		stop("Argument `mode` can only be `1`, `2`, or `2d`.")
 	}
 
 	if (nlyr(x) > 1L) stop("This function requires `x` to have just one layer.")