Changes to passs check

R/lets_midpoint.R

@@ -25,7 +25,7 @@
 #'   centroid of the minimum convex polygon of the distribution, using the
 #'   method "MCC". This last method is useful when using a PresenceAbsence
 #'   object made from occurrence records.
-#'   @param inside logical. If TRUE the points returned are guaranteed to be
+#' @param inside logical. If TRUE the points returned are guaranteed to be
 #'     inside the polygons or on the lines, but they are not the true centroids.
 #'     True centroids may be outside a polygon, for example when a polygon is
 #'     "bean shaped", and they are unlikely to be on their line

R/summary_PresenceAbsence.R

@@ -4,15 +4,16 @@
 #' @description Summary for objects of class PresenceAbsence.
 #' 
 #' @usage 
-#' \method{summary}{PresenceAbsence}(object)
+#' \method{summary}{PresenceAbsence}(object, \dots)
 #' 
 #' @param object an object of class \code{\link{PresenceAbsence}}.
-#' 
+#' @param ... additional arguments affecting the summary produced.
+
 #' @method summary PresenceAbsence
 #' @export
 #' @import terra
 
-summary.PresenceAbsence <- function(object) {
+summary.PresenceAbsence <- function(object, ...) {
   object <- .check_pam(object)
   class <- class(object)
   Numberofspecies <- ncol(object$Pre) - 2

tests/testthat/test-TimLucas.r

@@ -12,7 +12,7 @@ test_that("Basic usage works", {
 	expect_equal(sum(PresAbMat[[1]][,3]), 5)
 	expect_equal(sum(PresAbMat[[1]][,4]), 5)
 
-	expect_true(inherits(PresAbMat[[2]], "RasterLayer"))
+	expect_true(inherits(PresAbMat[[2]], "SpatRaster"))
 
 	# Species list as factor not character
 	species <- factor(rep(c('Milvus milvus', 'Buteo buteo'), each = 5))
@@ -22,7 +22,7 @@ test_that("Basic usage works", {
 
 
 	# Check other projections
-	crsdif <- suppressWarnings(CRS("+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"))
+	crsdif <- terra::crs("+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84")
 	PresAbMat <- lets.presab.points(xy, species, crs = crsdif)
 	expect_equal(class(PresAbMat), "PresenceAbsence")
 
@@ -49,7 +49,7 @@ test_that("Single records works", {
 	species <- c('Buteo buteo', 'Milvus milvus', 'Meles meles')
 
 	PresAbMat <- lets.presab.points(xy, species, 
-                                  crs=CRS("+proj=longlat +datum=WGS84"))
+                                  crs=terra::crs("+proj=longlat +datum=WGS84"))
 	expect_equal(class(PresAbMat), "PresenceAbsence")
 
 })

tests/testthat/test-lets_rangesize.R

@@ -2,8 +2,6 @@ context("Test for lets.rangesize")
 
 data(PAM)
 data(Phyllomedusa)
-Phyllomedusa <- terra::project(Phyllomedusa, 
-                               terra::crs(PAM[[2]]))
 
 test_that("lets.rangesize works fine, geographic", {