update 3.1.6 issues #50 and #54

Author: rvalavi

.gitignore

@@ -1,10 +1,12 @@
-.Rproj.user
-.Rhistory
-.RData
-Meta
-cran_comments.md
-tests/testthat/Rplots.pdf
-vignettes/tutorial_1.R
-vignettes/tutorial_1.html
-vignettes/tutorial_2.R
-vignettes/tutorial_2.html
+.Rproj.user
+.Rhistory
+.RData
+Meta
+cran_comments.md
+tests/testthat/Rplots.pdf
+revdep
+revdep/*
+vignettes/tutorial_1.R
+vignettes/tutorial_1.html
+vignettes/tutorial_2.R
+vignettes/tutorial_2.html

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: blockCV
 Type: Package
 Title: Spatial and Environmental Blocking for K-Fold and LOO Cross-Validation
-Version: 3.1-5
-Date: 2024-10-31
+Version: 3.1-6
+Date: 2025-06-23
 Authors@R: c(person("Roozbeh", "Valavi", role = c("aut", "cre"),
                     email = "valavi.r@gmail.com", comment = c(ORCID = "0000-0003-2495-5277")),
              person("Jane", "Elith", role = "aut",

NEWS.md

@@ -1,3 +1,7 @@
+# version 3.1.6
+* Resolved unclear error messages; issue [#52](https://github.com/rvalavi/blockCV/issues/52) by A. Márcia Barbosa
+* Resolved ggplot testing failure; issue [#54](https://github.com/rvalavi/blockCV/issues/54) by Teun van den Brand
+
 # version 3.1.5
 * Resolved background pattern artifacts in raster plotting; issue [#50](https://github.com/rvalavi/blockCV/issues/50) by Camila Neder.
 

R/blockCV.R

@@ -22,7 +22,6 @@
 #' @references Valavi, R., Elith, J., Lahoz-Monfort, J. J., & Guillera-Arroita, G. (2019). blockCV: An R package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models. Methods in Ecology and Evolution, 10(2), 225-232. doi:10.1111/2041-210X.13107.
 #'
 #' @name blockCV
-#' @docType package
 #' @author Roozbeh Valavi, Jane Elith, José Lahoz-Monfort, Ian Flint, and Gurutzeta Guillera-Arroita
 #' @import sf
-NULL
+"_PACKAGE"

R/checks.R

@@ -6,110 +6,111 @@
 
 # check points fall within the raster layer
 .check_within <- function(x, r) {
-  bbox <- sf::st_bbox(x)
-  ex <- terra::ext(r)
+    bbox <- sf::st_bbox(x)
+    ex <- terra::ext(r)
 
-  y <- bbox[1] >= terra::xmin(ex) &
-    bbox[3] <= terra::xmax(ex) &
-    bbox[2] >= terra::ymin(ex) &
-    bbox[4] <= terra::ymax(ex)
+    y <- bbox[1] >= terra::xmin(ex) &
+        bbox[3] <= terra::xmax(ex) &
+        bbox[2] >= terra::ymin(ex) &
+        bbox[4] <= terra::ymax(ex)
 
-  if(!y) stop("The x's bounding box lies outside the raster extent.")
+    if(!y) stop("The x's bounding box lies outside the raster extent.")
 }
 
 
 # check for x
 .check_x <- function(x, name = "x"){
-  if(!methods::is(x, "sf")){
-    tryCatch(
-      {
-        x <- sf::st_as_sf(x)
-      },
-      error = function(cond) {
-        message(sprintf("'%s' is not convertible to an sf object!", name))
-        message(sprintf("'%s' must be an sf or spatial* object.", name))
-      }
-    )
-  }
-  return(x)
+    if(!methods::is(x, "sf")){
+        tryCatch(
+            {
+                x <- sf::st_as_sf(x)
+            },
+            error = function(cond) {
+                message(sprintf("'%s' is not convertible to an sf object!", name))
+                message(sprintf("'%s' must be an sf or spatial* object.", name))
+            }
+        )
+    }
+    return(x)
 }
 
 # check for column matching colnames(x)
 .check_column <- function(column, x){
-  if(!is.null(column)){
-    if(!column %in% colnames(x)){
-      warning(sprintf("There is no column named '%s' in 'x'. Column is ignored!\n", column))
-      column <- NULL
+    if(!is.null(column)){
+        if(!column %in% colnames(x)){
+            warning(sprintf("There is no column named '%s' in 'x'. Column is ignored!\n", column))
+            column <- NULL
+        }
     }
-  }
-  return(column)
+    return(column)
 }
 
 # column should be binary or categorical
 .check_classes <- function(clen, column, th = 15){
-  if(clen > th){
-    warning(
-      sprintf(
-        paste(
-          "The are too many unique values in '%s'.",
-          "Use 'column' only for binary or categorical responses (ignore this if it is).\n"
-        ),
-        column
-      )
-    )
-  }
+    if(clen > th){
+        warning(
+            sprintf(
+                paste(
+                    "The are too many unique values in '%s'.",
+                    "Use 'column' only for binary or categorical responses (ignore this if it is).\n"
+                ),
+                column
+            )
+        )
+    }
 }
 
 
 # check raster extent is valid
 .check_ext <- function(r) {
-  tryCatch(
-    {
-      e <- terra::ext(r)
-      vals <- e[1:4]
-    },
-    error = function(cond) {
-      stop("Failed to extract raster extent: ", conditionMessage(cond))
-    }
-  )
+    tryCatch(
+        {
+            e <- terra::ext(r)
+            vals <- e[1:4]
+        },
+        error = function(cond) {
+            stop("Failed to extract raster extent: ", conditionMessage(cond))
+        }
+    )
 
-  y <- all(is.finite(vals)) &&
-    (terra::xmax(e) > terra::xmin(e)) &&
-    (terra::ymax(e) > terra::ymin(e))
+    y <- all(is.finite(vals)) &&
+        (terra::xmax(e) > terra::xmin(e)) &&
+        (terra::ymax(e) > terra::ymin(e))
 
-  if (!y) stop("Invalid raster extent: values are non-finite, degenerate, or out of range.")
+    if (!y) stop("Invalid raster extent: values are non-finite or out of range.")
 }
 
 # check for r
 .check_r <- function(r, name = "r"){
-  if(!methods::is(r, "SpatRaster")){
-    tryCatch(
-      {
-        r <- terra::rast(r)
-      },
-      error = function(cond) {
-        message(sprintf("'%s' is not convertible to a terra SpatRaster object!", name))
-        message(sprintf("'%s' must be a SpatRaster, stars, Raster* object, or path to a raster file on disk.", name))
-      }
-    )
-  }
-  .check_ext(r) # check for valid extent
+    if(!methods::is(r, "SpatRaster")){
+        tryCatch(
+            {
+                r <- terra::rast(r)
+            },
+            error = function(cond) {
+                message(sprintf("'%s' is not convertible to a terra SpatRaster object!", name))
+                message(sprintf("'%s' must be a SpatRaster, stars, Raster* object, or path to a raster file on disk.", name))
+            }
+        )
+    }
+    # check for a valid extent
+    .check_ext(r)
 
-  return(r)
+    return(r)
 }
 
 # check for required packages
 .check_pkgs <- function(pkg){
-  pkgna <- names(which(sapply(sapply(pkg, find.package, quiet = TRUE), length) == 0))
-  if(length(pkgna) > 0){
-    nm <- paste(pkgna, collapse = ", ")
-    message("This function requires these packages: ", nm, "\nWould you like to install them now?\n1: yes\n2: no")
-    user <- readline(prompt = paste0("Selection: "))
-    if(tolower(user) %in% c("1", "yes", "y")){
-      utils::install.packages(pkgna)
-    } else{
-      stop("Please install these packages for function to work: ", nm)
+    pkgna <- names(which(sapply(sapply(pkg, find.package, quiet = TRUE), length) == 0))
+    if(length(pkgna) > 0){
+        nm <- paste(pkgna, collapse = ", ")
+        message("This function requires these packages: ", nm, "\nWould you like to install them now?\n1: yes\n2: no")
+        user <- readline(prompt = paste0("Selection: "))
+        if(tolower(user) %in% c("1", "yes", "y")){
+            utils::install.packages(pkgna)
+        } else{
+            stop("Please install these packages for function to work: ", nm)
+        }
     }
-  }
 }