Merge branch 'main' into allow-geographic-coordinate-systems

R/disp.R

@@ -73,7 +73,7 @@
 #' # disp
 #' disp_output <- disp(
 #'   N_t = sim_data$n1_map,
-#'   id = sim_data$id,
+#'   id = unwrap(sim_data$id),
 #'   id_matrix = as.matrix(sim_data$id, wide = TRUE),
 #'   data_table = sim_data$data_table,
 #'   kernel = sim_data$kernel,

R/initialise.R

@@ -359,12 +359,12 @@ initialise <- function(
   # output list ---------------------------------------------
   out <- list(
     n1_map = as.matrix(n1_map, wide = TRUE),
-    id = id,
+    id = wrap(id),
     dist_bin = dist_bin,
     dist_resolution = dist_resolution,
     r = r,
     r_sd = r_sd,
-    K_map = K_map,
+    K_map = wrap(K_map),
     K_sd = K_sd,
     growth = growth,
     A = A,

R/print.sim_data.R

@@ -32,7 +32,7 @@ print.sim_data <- function(x, ...) {
 
   # prepare output
   n1_sm <- summary(as.numeric(x$n1_map))
-  K_sm <- x$K_map
+  K_sm <- unwrap(x$K_map)
 
   names <- names(x)
   names <- names[(names %in% c(

R/sim.R

@@ -188,14 +188,14 @@ sim <- function(
   on.exit(pboptions(pbo))
 
   # Extract data from the sim_data object
-  K_map <- obj$K_map # carrying capacity
+  K_map <- unwrap(obj$K_map) # carrying capacity
   K_sd <- obj$K_sd # sd of carrying capacity (additional cell specific variation) #nolint
   dynamics <- obj$dynamics # population growth function
   n1_map <- obj$n1_map # population numbers at the first time step
   r <- obj$r # intrinsic population growth rate
   r_sd <- obj$r_sd # sd of intrinsic growth rate (time specific variation)
   A <- obj$A # Allee effect coefficient
-  id <- obj$id # grid cells identifiers as raster
+  id <- unwrap(obj$id) # grid cells identifiers as raster
   id_matrix <- as.matrix(id, wide = TRUE) # grid cells identifiers as matrix
   ncells <- obj$ncells # number of cells in the study area
   data_table <- obj$data_table

R/summary.sim_data.R

@@ -33,7 +33,7 @@ summary.sim_data <- function(object, ...) {
 
   # prepare summaries
   n1_sm <- summary(as.numeric(object$n1_map))
-  K_sm <- summary(as.numeric(as.matrix(object$K_map)))
+  K_sm <- summary(as.numeric(as.matrix(unwrap(object$K_map))))
 
   names <- c(
     "growth", "r", "A", "kernel_fun", "dens_dep", "border",

R/update.sim_data.R

@@ -98,6 +98,11 @@ update.sim_data <- function(object, ..., evaluate = TRUE) {
       }
     }
 
+    # unwrap K_map if not updated
+    if(!"K_map" %in% names(extras)) {
+      call$K_map <- unwrap(object$K_map)
+    }
+
     # transform call to call object
     call <- as.call(call)
 

tests/testthat/test-initialise.R

@@ -558,6 +558,6 @@ test_that("K_add_stochasticity works", {
   )
 
 
-  expect_s4_class(test_sim_data_1$K_map, "SpatRaster")
-  expect_s4_class(test_sim_data_2$K_map, "SpatRaster")
+  expect_s4_class(test_sim_data_1$K_map, "PackedSpatRaster")
+  expect_s4_class(test_sim_data_2$K_map, "PackedSpatRaster")
 })