add and use + post-process cross-validated models

Author: elgabbas

DESCRIPTION

@@ -3,7 +3,7 @@ Package: IASDT.R
 Title: Modelling the distribution of invasive alien plant species in
     Europe
 Version: 0.1.04
-Date: 2025-04-23
+Date: 2025-04-25
 Authors@R: 
     person("Ahmed", "El-Gabbas", , "ahmed.el-gabbas@ufz.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2225-088X"))

NAMESPACE

@@ -85,6 +85,7 @@ export(loaded_packages)
 export(mod_CV_evaluate)
 export(mod_CV_fit)
 export(mod_CV_postprocess_1_CPU)
+export(mod_CV_postprocess_2_CPU)
 export(mod_CV_prepare)
 export(mod_SLURM)
 export(mod_SLURM_refit)
@@ -153,6 +154,7 @@ export(source_silent)
 export(split_df_to_chunks)
 export(split_raster)
 export(split_vector)
+export(stop_ctx)
 export(system_command)
 export(text_to_coordinates)
 export(variance_partitioning_compute)

R/DWF_CHELSA_prepare.R

@@ -33,7 +33,8 @@ CHELSA_prepare <- function(
   rm(AllArgs, envir = environment())
 
   if (n_cores < 1) {
-    stop("`n_cores` must be a positive integer.", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "`n_cores` must be a positive integer.", n_cores = n_cores)
   }
 
   # # ..................................................................... ###

R/DWF_CHELSA_process.R

@@ -90,7 +90,9 @@ CHELSA_process <- function(
   rm(AllArgs, CharArgs, LogicArgs, NumericArgs, envir = environment())
 
   if (n_cores < 1 || download_n_cores < 1) {
-    stop("`n_cores` must be a positive integer.", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "`n_cores` must be a positive integer.",
+      n_cores = n_cores, download_n_cores = download_n_cores)
   }
 
   # # ..................................................................... ###
@@ -108,9 +110,8 @@ CHELSA_process <- function(
   IASDT.R::cat_time("Environment variables")
 
   if (!file.exists(env_file)) {
-    stop(
-      "Path to environment variables: ", env_file, " was not found",
-      call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path to environment variables was not found", env_file = env_file)
   }
 
   EnvVars2Read <- tibble::tribble(
@@ -189,10 +190,10 @@ CHELSA_process <- function(
         x = dplyr::pull(CHELSA_Data_Checked, "InputOkay"),
         file = IASDT.R::path(Path_CHELSA_Out, "ProblematicTiffs.txt"))
 
-      stop(
-        "Not all input tiff files are available and valid. ",
-        "Check `ProblematicTiffs.txt`", call. = FALSE
-      )
+      IASDT.R::stop_ctx(
+        paste0(
+          "Not all input tiff files are available and valid. ",
+          "Check `ProblematicTiffs.txt`"))
     }
 
     # CHELSA files that will not be processed
@@ -330,9 +331,11 @@ CHELSA_process <- function(
         x = CHELSA2Process$Path_Down,
         file = IASDT.R::path(Path_CHELSA_Out, "FailedProcessing.txt"))
 
-      stop(
-        "\n >> ", nrow(CHELSA2Process), " files failed to process.\n",
-        " >> Check `FailedProcessing.txt` for more details", call. = FALSE)
+      IASDT.R::stop_ctx(
+        paste0(
+          "\n >> ", nrow(CHELSA2Process), " files failed to process.\n",
+          " >> Check `FailedProcessing.txt` for more details"),
+        CHELSA2Process = CHELSA2Process)
     }
 
     IASDT.R::cat_time("All tiff files were processed", level = 1)

R/DWF_CHELSA_project.R

@@ -27,11 +27,15 @@ CHELSA_project <- function(
   rm(AllArgs, envir = environment())
 
   if (!inherits(metadata, "tbl_df")) {
-    stop("Input metadata has to be a tibble", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Input metadata has to be a tibble", class_metadata = class(metadata))
   }
 
   if (nrow(metadata) != 1) {
-    stop("Input metadata has to be a single-row tibble", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Input metadata has to be a single-row tibble",
+      metadata = metadata, class_metadata = class(metadata),
+      nrow_metadata = nrow(metadata))
   }
 
   # # ..................................................................... ###
@@ -43,11 +47,12 @@ CHELSA_project <- function(
   # # ..................................................................... ###
 
   if (is.null(metadata)) {
-    stop("Input metadata can not be `NULL`", call. = FALSE)
+    IASDT.R::stop_ctx("Input metadata can not be `NULL`", metadata = metadata)
   }
 
   if (!file.exists(metadata$Path_Down)) {
-    stop("Input file does not exist: ", metadata$Path_Down, call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Input file does not exist", path = metadata$Path_Down)
   }
 
   # Set `GTIFF_SRS_SOURCE` configuration option to EPSG to use
@@ -72,8 +77,8 @@ CHELSA_project <- function(
 
   GridR <- IASDT.R::path(Path_Grid, "Grid_10_Land_Crop.RData")
   if (!file.exists(GridR)) {
-    stop(
-      "Path for the Europe boundaries does not exist: ", GridR, call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path for the Europe boundaries does not exist", GridR = GridR)
   }
   GridR <- terra::unwrap(IASDT.R::load_as(GridR))
 

R/DWF_CLC_plot.R

@@ -38,9 +38,12 @@ CLC_plot <- function(
 
   if (is.null(CLC_name) || is.null(EU_map) || is.null(crosswalk) ||
       is.null(path_JPEG) || is.null(path_JPEG_free)) {
-    stop(
-      "`CLC_name`, `EU_map`, `crosswalk`, `path_JPEG`, and ",
-      "`path_JPEG_free` can not be empty", call. = FALSE)
+    IASDT.R::stop_ctx(
+      paste0(
+        "`CLC_name`, `EU_map`, `crosswalk`, `path_JPEG`, and ",
+        "`path_JPEG_free` can not be empty"),
+      CLC_name = CLC_name, EU_map = EU_map, crosswalk = crosswalk,
+      path_JPEG = path_JPEG, path_JPEG_free = path_JPEG_free)
   }
 
   CLC_MapR <- dplyr::filter(CLC_map, Name == CLC_name) %>%
@@ -261,11 +264,11 @@ CLC_plot <- function(
 
   # nolint start
   CommonLegend <- cowplot::get_legend(
-    (ggplot2::ggplot() + 
+    (ggplot2::ggplot() +
       tidyterra::geom_spatraster(
         data = terra::rast(CLC_MapR[[1]]), maxcell = terra::ncell(CLC_MapR)) +
       paletteer::scale_fill_paletteer_c(
-        na.value = "transparent", palette = "viridis::plasma", 
+        na.value = "transparent", palette = "viridis::plasma",
         limits = c(0, 100)) +
       ggplot2::theme(
         legend.box.margin = ggplot2::margin(0, 0, 0, 0),

R/DWF_CLC_process.R

@@ -30,7 +30,7 @@
 #' <https://doi.org/10.2909/960998c1-1870-4e82-8051-6485205ebbac>
 
 CLC_process <- function(
-  env_file = ".env", min_land_percent = 15, plot_CLC = TRUE) {
+    env_file = ".env", min_land_percent = 15, plot_CLC = TRUE) {
   # # ..................................................................... ###
 
   .StartTime <- lubridate::now(tzone = "CET")
@@ -46,21 +46,19 @@ CLC_process <- function(
     EU_Bound <- Value <- Country <- Country2 <- NULL
 
   if (is.null(env_file)) {
-    stop("env_file can not be empty", call. = FALSE)
+    IASDT.R::stop_ctx("env_file can not be empty", env_file = env_file)
   }
 
   if (!is.numeric(min_land_percent) ||
       !dplyr::between(min_land_percent, 0, 100)) {
-    stop(
+    IASDT.R::stop_ctx(
       "`min_land_percent` must be a numeric value between 0 and 100.",
-      call. = FALSE)
+      min_land_percent = min_land_percent)
   }
 
   if (!file.exists(env_file)) {
-    stop(
-      "Path to environment variables (`env_file`): ", env_file,
-      " was not found",
-      call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path to environment variables was not found", env_file = env_file)
   }
 
   # # ..................................................................... ###
@@ -106,7 +104,7 @@ CLC_process <- function(
     .x = requiredPaths,
     .f = function(path) {
       if (!file.exists(path)) {
-        stop("Required path does not exist: ", path, call. = FALSE)
+        IASDT.R::stop_ctx("Required path does not exist: ", path = path)
       }
     }
   )
@@ -627,15 +625,19 @@ CLC_get_percentage <- function(
 
   if (is.null(CLC_type) || is.null(CLC_crossWalk) || is.null(CLC_fracs_r) ||
       is.null(path_tif) || is.null(path_RData)) {
-    stop("None of the input parameters can be empty", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "None of the input parameters can be empty",
+      CLC_type = CLC_type, CLC_crossWalk = CLC_crossWalk,
+      CLC_fracs_r = CLC_fracs_r, path_tif = path_tif, path_RData = path_RData)
   }
 
   if (!(
     CLC_type %in% c("SynHab", "CLC_L1", "CLC_L2", "CLC_L3", "EUNIS_2019"))) {
-    stop(
-      "CLC_type has to be one of SynHab, CLC_L1, CLC_L2, ",
-      "CLC_L3, and EUNIS_2019",
-      call. = FALSE)
+    IASDT.R::stop_ctx(
+      paste0(
+        "CLC_type has to be one of SynHab, CLC_L1, CLC_L2, ",
+        "CLC_L3, and EUNIS_2019"),
+      CLC_type = CLC_type)
   }
   # # ..................................................................... ###
 
@@ -721,15 +723,21 @@ CLC_get_majority <- function(
   if (is.null(CLC_type) || is.null(CLC_majority) || is.null(path_tif) ||
       is.null(path_tif_crop) || is.null(path_RData) || is.null(Grid_10_Land) ||
       is.null(Grid_10_Land_Crop)) {
-    stop("None of the input parameters can be empty", call. = FALSE)
+    IASDT.R::stop_ctx(
+      "None of the input parameters can be empty",
+      CLC_type = CLC_type, CLC_majority = CLC_majority,
+      path_tif = path_tif, path_tif_crop = path_tif_crop,
+      path_RData = path_RData, Grid_10_Land = Grid_10_Land,
+      Grid_10_Land_Crop = Grid_10_Land_Crop)
   }
 
   if (!(
     CLC_type %in% c("SynHab", "CLC_L1", "CLC_L2", "CLC_L3", "EUNIS_2019"))) {
-    stop(
-      "CLC_type has to be one of SynHab, CLC_L1, CLC_L2, ",
-      "CLC_L3, and EUNIS_2019",
-      call. = FALSE)
+    IASDT.R::stop_ctx(
+      paste0(
+        "CLC_type has to be one of SynHab, CLC_L1, CLC_L2, ",
+        "CLC_L3, and EUNIS_2019"),
+      CLC_type = CLC_type)
   }
 
   # # ..................................................................... ###

R/DWF_EASIN_download.R

@@ -16,7 +16,7 @@ EASIN_download <- function(
   # # ..................................................................... ###
 
   if (is.null(species_key)) {
-    stop("species_key cannot be NULL", call. = FALSE)
+    IASDT.R::stop_ctx("species_key cannot be NULL", species_key = species_key)
   }
 
   Path_EASIN <- NULL

R/DWF_EASIN_plot.R

@@ -74,11 +74,9 @@ EASIN_plot <- function(env_file = ".env") {
   SummaryMapsMissing <- !file.exists(PathSummaryMaps)
 
   if (any(SummaryMapsMissing)) {
-    stop(
-      "The following input files are missing: \n",
-      paste0(
-        " >> ", PathSummaryMaps[which(SummaryMapsMissing)], collapse = "\n") ,
-      call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Missing summary input files",
+      missing_files = PathSummaryMaps[which(SummaryMapsMissing)])
   }
 
   # # |||||||||||||||||||||||||||||||||||

R/DWF_EASIN_process.R

@@ -150,21 +150,23 @@ EASIN_process <- function(
   ## Grid - raster ----
   GridR <- IASDT.R::path(Path_Grid, "Grid_10_Land_Crop.RData")
   if (!file.exists(GridR)) {
-    stop("Path for the reference grid does not exist: ", GridR, call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path for the reference grid does not exist", GridR = GridR)
   }
 
   ## Grid - sf ----
   GridSf <- IASDT.R::path(Path_Grid_Ref, "Grid_10_sf.RData")
   if (!file.exists(GridSf)) {
-    stop("Path for the reference grid does not exist: ", GridSf, call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path for the reference grid does not exist", GridSf = GridSf)
   }
 
   ## Grid - sf - study area ----
   # Grid ID overlapping with study area
   LandGrids <- IASDT.R::path(Path_Grid, "Grid_10_Land_sf.RData")
   if (!file.exists(LandGrids)) {
-    stop(
-      "Path for the reference grid does not exist: ", LandGrids, call. = FALSE)
+    IASDT.R::stop_ctx(
+      "Path for the reference grid does not exist", LandGrids = LandGrids)
   }
 
   ## Species list ----