Speedup loop_ecology that was too slow for the evol simulation

R/ecology.R

@@ -99,12 +99,16 @@ loop_ecology <- function(config, data, vars) {
       chars <- as.character(die_sure)
     } #end of check if any die_sure
   } #end loop over ids with at least one species...
-  species_list <- list()
-  for (species in data$all_species) {
-    cells <- names(species[["abundance"]])[species[["abundance"]] != 0]
-    updated_species <- limit_species_to_cells(species, cells)
-    species_list <- append(species_list, list(updated_species))
-  }
+  # species_list <- list()
+  # for (species in data$all_species) {
+  #   cells <- names(species[["abundance"]])[species[["abundance"]] != 0]
+  #   updated_species <- limit_species_to_cells(species, cells)
+  #   species_list <- append(species_list, list(updated_species))
+  # }
+  species_list <- vector(mode = "list", length = length(data$all_species))
+  species_list <- lapply(1:length(data$all_species), function(i) {
+  append(species_list[[i]], limit_species_to_cells(data$all_species[[i]], names(data$all_species[[i]][["abundance"]])[data$all_species[[i]][["abundance"]] != 0]))
+  })
   data$all_species <- species_list
 
   if(config$gen3sis$general$verbose>=3){