Merge branch 'martin' into dev

DESCRIPTION

@@ -21,6 +21,7 @@ Imports:
   terra
 Suggests:
   gdalUtilities,
+  stars,
   testthat (>= 3.0.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -2,3 +2,4 @@
 
 export(misc_sanitizeNames)
 export(sp_resampleRas)
+export(sp_replaceGriddedNA)

R/spl_replaceGriddedNA.R

@@ -0,0 +1,49 @@
+#' Replace NA values in gridded layers with a fixed value.
+#'
+#' @description
+#' This function replaces all NA values in a spatial gridded layer with
+#' a fixed value such as for example \code{0}. Accepted input layers are for [`SpatRaster`] from
+#' the \code{"terra"} R-package and [`stars`] from the \code{"stars"} R-package.
+#'
+#' @details
+#' Required inputs are a single \code{"obj"} gridded data object and a numeric value.
+#' In addition an optional mask layer can be provided that to use a mask. In this case
+#' all no-data values a replaced with the value in this mask.
+#'
+#' @param obj A [`SpatRaster`], [`SpatRasterDataset`] or [`stars`] object.
+#' @param value A fixed numeric value of which all \code{NA} values are to be replaced with (Default: \code{0}).
+#' @param mask An optional [`SpatRaster`] object used instead of the value.
+#' @param verbose Be chatty about what is processed (Default: \code{FALSE}).
+#'
+#' @examples
+#' # Example
+#' s <- rast(system.file("ex/logo.tif", package="terra"))
+#' s[sample(1:terra::ncell(s), 100)] <- NA
+#' sfill <- sp_replaceGriddedNA(s, value = 100)
+#' plot(sfill)
+#'
+#' @returns A object of the same type as the input but with no-data values replaced with \code{'value'}.
+#' @author Martin Jung
+#' @keywords internal, utils
+#' @export
+sp_replaceGriddedNA <- function(obj, value = 0, mask, verbose = FALSE){
+  assertthat::assert_that(
+    inherits(obj, "stars") || inherits(obj, "SpatRaster"),
+    is.numeric(value) || length(value)==1,
+    missing(mask) || (inherits(mask, "stars") || inherits(mask, "SpatRaster")),
+    is.logical(verbose),
+    msg = "Input data or parameters wrong set?"
+  )
+
+  # Process
+  if(missing(mask)){
+    if(verbose) message("Replacing no data values with value: ", value)
+    # Set all NA to the value
+    obj[is.na(obj)] <- value
+  } else {
+    if(verbose) message("Masking obj with mask values.")
+    # Mask the layer by template
+    obj[is.na(obj)] <- mask[is.na(obj)]
+  }
+  return(obj)
+}

tests/testthat/test-spl_tests.R

@@ -0,0 +1,27 @@
+test_that("Spatial object modifications", {
+
+  suppressWarnings(requireNamespace("terra", quietly = TRUE))
+
+  # Dummy layers
+  r1 <- terra::rast(nrows = 10, ncols = 10, res = 0.05, xmin = -1.5, xmax = 1.5, ymin = -1.5, ymax = 1.5, vals = rnorm(3600,mean = .5,sd = .1))
+  r2 <- terra::rast(nrows = 10, ncols = 10, res = 0.05, xmin = -1.5, xmax = 1.5, ymin = -1.5, ymax = 1.5, vals = rnorm(3600,mean = .5,sd = .5))
+  expect_s4_class(r1, "SpatRaster")
+  expect_s4_class(r2, "SpatRaster")
+
+  # --- #
+  # NA replacements #
+  r1[sample(1:terra::ncell(r1),100)] <- NA
+  expect_no_error(
+    r1_filled <- sp_replaceGriddedNA(r1, value = 0)
+  )
+  expect_s4_class(r1_filled, "SpatRaster")
+  expect_equal(terra::global(r1_filled,"min")[,1], 0) # Should be 0
+  # Use layer 2 for masking instead
+  expect_no_error(
+    r1_filled2 <- sp_replaceGriddedNA(r1,mask = r2)
+  )
+  expect_s4_class(r1_filled2, "SpatRaster")
+  # --- #
+
+
+})