fix bug in habitat codes for resident distributions

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aoh
 Type: Package
-Version: 0.0.2.11
+Version: 0.0.2.12
 Title: Create Area of Habitat Data
 Description: Create Area of Habitat data to characterize species distributions.
     Data are produced following procedures outlined by Brooks et al. (2019)

NEWS.md

@@ -1,3 +1,19 @@
+# aoh 0.0.2.12
+
+- Fix bug in `create_spp_info_data()` in assigning habitat types for resident
+  distributions of migratory and non-migratory species. This bug meant that (i)
+  habitat types for resident distributions of migratory species would include
+  those exclusively affiliated with the species' passage distributions and (ii)
+  habitat types for resident distributions of non-migratory species would not
+  include those exclusively affiliated with the species' passage distributions.
+  Thanks to Jianqiao Zhao for bug report.
+- Update built-in testing data to include multiple migratory species.
+- Update internal R script for creating test dataset
+  (i.e., `inst/scripts/test-data.R`) to be compatible with current version of
+  the package.
+- Update `is_gdal_calc_available()` to be more robust.
+- Fix URLs.
+
 # aoh 0.0.2.11
 
 - Fix bug in `create_spp_info_data()` so that the IUCN Red List API key can be

R/collate_spp_info_data.R

@@ -199,34 +199,63 @@ collate_spp_info_data <- function(x,
   spp_habitat_data <- spp_habitat_data[idx, , drop = FALSE]
   ## if exact matches for habitat codes should not be used then...
   if (isTRUE(adjust_habitat_codes)) {
-    ### create new data by merging habitat codes following KBA guidelines
+    ### create new data by merging habitat codes based on KBA guidelines
+    ### and personal communications with Busana M. and Butchart S.H.M. at
+    ### BirdLife International
     spp_habitat_data <- dplyr::bind_rows(
       list(
         ### resident (non-migratory species)
+        #### NOTE: we include habitat types listed for all seasonal
+        #### distributions. although non-migratory
+        #### species should not have any habitat types affiliated with
+        #### non-residential distributions, this can happen due to
+        #### errors/discrepancies in the IUCN Red List data
         prepare_habitat_codes(
-          dplyr::filter(spp_habitat_data, .data$seasonal %in% migratory_ids),
+          dplyr::filter(spp_habitat_data, !.data$id_no %in% migratory_ids),
           focal_seasonal = 1L,
           extra_seasonal = c(2L, 3L, 4L, 5L, NA_integer_)
         ),
         ### resident (migratory species)
+        #### NOTE: we do not include passage (code 4) habitat types here
+        #### for migratory bird species because these might be substantially
+        #### different from resident distributions
         prepare_habitat_codes(
-          dplyr::filter(spp_habitat_data, !.data$seasonal %in% migratory_ids),
+          dplyr::filter(spp_habitat_data, .data$id_no %in% migratory_ids),
           focal_seasonal = 1L,
           extra_seasonal = c(2L, 3L, 5L, NA_integer_)
         ),
         ### breeding
+        #### NOTE: we include habitat types listed for resident (code 1),
+        #### breeding (code 2) and seasonality uncertain (code 5) when
+        #### mapping the breeding distributions, per KBA guidelines
         prepare_habitat_codes(
           spp_habitat_data,
           focal_seasonal = 2L,
           extra_seasonal = c(1L, 5L, NA_integer_)
         ),
         ### non-breeding
+        #### NOTE: we include habitat types listed for resident (code 1),
+        #### non-breeding (code 2) and seasonality uncertain (code 5) when
+        #### mapping the non-breeding distributions, per KBA guidelines
         prepare_habitat_codes(
           spp_habitat_data,
           focal_seasonal = 3L,
           extra_seasonal = c(1L, 5L, NA_integer_)
         ),
         ### passage
+        #### NOTE: we include habitat types listed for resident (code 1),
+        #### passage (code 24 and seasonality uncertain (code 5) when
+        #### mapping the passage distributions, following a similar
+        #### rationale for the breeding and non-breeding distributions.
+        #### although the resident distribution for migratory species
+        #### does not consider habitat types listed for passage
+        #### distributions (based on the rationale that species might
+        #### have habitat types unique to their passage distribution),
+        #### we include habitat types for resident distributions here
+        #### since (i) many species are missing habitat types for their
+        #### passage distributions and (ii) if the habitat types are
+        #### used during the resident distribution, then they are
+        #### likely used during passage (but not vice versa)
         prepare_habitat_codes(
           spp_habitat_data,
           focal_seasonal = 4L,

R/internal.R

@@ -44,6 +44,9 @@ normalize_path <- function(path, winslash = "\\", mustWork = NA) {
   if (identical(.Platform$OS.type, "unix")) {
     # if on a Unix platform, then we just need to use normalizePath()
     out <- normalizePath(path, winslash = winslash, mustWork = mustWork)
+    # if on a macOS system, this sometimes results in file paths
+    # that contain "//" instead of "/" for a folder separator
+    out <- gsub("//", "/", out, fixed = TRUE)
   } else {
     # if on a Windows platform, then things get a bit more complicated...
     if (!grepl("~", path, fixed = TRUE)) {

R/is_available.R

@@ -138,11 +138,21 @@ is_gdal_calc_available <- function() {
       return(FALSE)
     }
   }
-  v <- try(
-    system(python_gdal_calc("--help"), intern = TRUE),
-    silent = TRUE
+  v <- suppressWarnings(
+    try(
+      system(python_gdal_calc("--help"), intern = TRUE),
+      silent = TRUE
+    )
   )
+  # return FALSE if system command executed with error
   if (inherits(v, "try-error")) return(FALSE)
+  # return FALSE if system command executed with non-zero status
+  if (!is.null(attr(v, "status"))) {
+    if (!identical(attr(v, "status"), 0L)) {
+      return(FALSE)
+    }
+  }
+  # otherwise, return TRUE
   TRUE
 }
 

R/read_spp_range_data.R

@@ -19,7 +19,7 @@ NULL
 #' (see https://www.iucnredlist.org/resources/spatial-data-download).
 #' Data for birds can be obtained by requesting data from
 #' [BirdLife International](https://www.birdlife.org/)
-#' (see <http://datazone.birdlife.org/species/requestdis>).
+#' (see <https://datazone.birdlife.org/species/requestdis>).
 #' To standardize data from the IUCN Red List and BirdLife International,
 #' the `"SISID"` and `"SISRecID"` columns are renamed as `"id_no"`.
 #'

R/terra_gdal_calc.R

@@ -229,6 +229,8 @@ terra_gdal_calc <- function(x, expr,
   if (isTRUE(verbose)) {
     cli::cli_alert_info(paste("System command:", cmd))
   }
+
+  # run gdal_calc via system command
   system(cmd, intern = !verbose)
 
   # clean up
@@ -246,6 +248,15 @@ terra_gdal_calc <- function(x, expr,
     unlink(f3, force = TRUE)
   }
 
+  # verify output file exists
+  assertthat::assert_that(
+    file.exists(filename),
+    msg = paste0(
+      "failed to run `gdal_calc.py` script: output file \"",
+      filename, "\" does not exist"
+    )
+  )
+
   # return result
   if (output_raster) {
     return(stats::setNames(terra::rast(filename), nms))

README.Rmd

@@ -180,7 +180,7 @@ print(spp_aoh_rasters)
 
 Finally, let's create some maps to compare the range data with the Area of habitat data.
 
-```{r "map", message = FALSE, warning = FALSE, dpi = 200, fig.width = 5.5, fig.height = 4, out.width = ifelse(isTRUE(knitr::is_html_output(excludes = c("markdown"))), "60%", "90%")}
+```{r "map", message = FALSE, warning = FALSE, results = "hide", dpi = 200, fig.width = 5.5, fig.height = 4, out.width = ifelse(isTRUE(knitr::is_html_output(excludes = c("markdown"))), "60%", "90%")}
 # create maps
 ## N.B. you might need to install the ggmap package
 map <-

README.md

@@ -366,15 +366,15 @@ produce Area of Habitat data.
     relevant data using:
 
       Hanson JO (2024) aoh: Create Area of Habitat Data. R package version
-      0.0.2.11. Available at https://github.com/prioritizr/aoh.
+      0.0.2.12. Available at https://github.com/prioritizr/aoh.
 
       IUCN [insert year] IUCN Red List of Threatened Species. Version
       [insert version]. Available at www.iucnredlist.org.
 
       BirdLife International and Handbook of the Birds of the World
       ([insert year]) Bird species distribution maps of the world. Version
       [insert version]. Available at
-      http://datazone.birdlife.org/species/requestdis.
+      https://datazone.birdlife.org/species/requestdis.
 
       Jung M, Dahal PR, Butchart SHM, Donald PF, De Lamo X, Lesiv M, Kapos
       V, Rondinini C, Visconti P (2020). "A global map of terrestrial