Allow pamcrop to keep cells

DESCRIPTION

@@ -36,6 +36,6 @@ URL: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.1240
     https://github.com/macroecology/letsR,
     https://brunovilela.github.io/letsR/
 BugReports: https://github.com/macroecology/letsR/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 VignetteBuilder: knitr

R/lets_pamcrop.R

@@ -10,7 +10,8 @@
 #'   \code{terra::vect}) to crop the PresenceAbsence object.
 #' @param remove.sp Logical, if \code{TRUE} the final matrix will not contain
 #'   species that do not match any cell in the grid.
-#'
+#'@param remove.cells Logical, if \code{FALSE} the final matrix will not contain
+#'  cells in the grid with a value of zero (i.e. sites with no species present).
 #'
 #' @return The result is an object of class PresenceAbsence croped.
 #'
@@ -38,7 +39,8 @@
 #' @export
 
 
-lets.pamcrop <- function(x, shp, remove.sp = TRUE) {
+lets.pamcrop <- function(x, shp, remove.sp = TRUE,
+                         remove.cells = FALSE) {
 
   if (!methods::is(x, "PresenceAbsence")) {
     stop("x is not a PresenceAbsence object")
@@ -58,8 +60,11 @@ lets.pamcrop <- function(x, shp, remove.sp = TRUE) {
 
   # Remove cells from the matrix
   manter <- terra::extract(x[[2]], x[[1]][, 1:2])
-  x[[1]] <- x[[1]][!is.na(manter[, 1]), ]
-
+  if (remove.cells) {
+    x[[1]] <- x[[1]][!is.na(manter[, 1]), ]
+  } else {
+    x[[1]][is.na(manter[, 1]), ] <- 0
+  }
   # Remove species without presence
   if (remove.sp) {
     x[[1]] <- .removeSp(x[[1]])