Merge pull request #454 from mapme-initiative/develop

Develop

Author: zivankaraman

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mapme.biodiversity
 Title: Efficient Monitoring of Global Biodiversity Portfolios
-Version: 0.9.4.9007
+Version: 0.9.5
 Authors@R: c(person(given = "Darius A.", 
                     family = "G\u00F6rgen", 
                     role = "aut",

NEWS.md

@@ -1,16 +1,18 @@
-# mapme.biodiversity 0.9.4.9007
+# mapme.biodiversity 0.9.5
 
 ## General
 
 -   `get_gfw_treecover()` and `get_gfw_lossyear()` updated to version "GFC-2024-v1.12" ([416](https://github.com/mapme-initiative/mapme.biodiversity/issues/416))
 -   `calc_treecover_area()`, `calc_treecover_area_and_emissions()` and `calc_treecoverloss_emissions()` updated to include the year 2024 ([416](https://github.com/mapme-initiative/mapme.biodiversity/issues/416))
 -   `get_esalandcover()` has been adapted to download data from a new source in a format compatible with the previous version ([430](https://github.com/mapme-initiative/mapme.biodiversity/issues/430))
 -   modified `calc_treecover_area()` to return zero area and not NULL when tree cover \< `min_cover` ([413](https://github.com/mapme-initiative/mapme.biodiversity/issues/413))
+-   `get_teow()` now requires users to manually download the file ([450](https://github.com/mapme-initiative/mapme.biodiversity/issues/450))
 
 ## Internal
 
 -   internal function `.has_internet()` now delegates to `curl::has_internet()`
--   added function `.check_system_requirements()` that checks on package load if system requirements (GDAL and PROJ versions) are met and warns if not
+-   added function `.check_system_requirements()` that checks on package load if system requirements (GDAL and PROJ versions) are met, and warns if not
+-   use `utils::compareVersion()` instead of simple '\<' to check the GDAL system library version
 
 ## Bug fixes
 

R/get_teow.R

@@ -10,31 +10,55 @@
 #'
 #' @name teow
 #' @keywords resource
+#' @param path A character vector to the Terrestrial Ecoregions of the World (TEOW)
+#'   zip file. Note, that the file has to be downloaded manually.
 #' @returns  A function that returns an `sf` footprint object.
 #' @references Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D.,
 #' Powell, G. V. N., Underwood, E. C., D’Amico, J. A., Itoua, I., Strand, H. E.,
 #' Morrison, J. C., Loucks, C. J., Allnutt, T. F., Ricketts, T. H., Kura, Y., Lamoreux,
 #' J. F., Wettengel, W. W., Hedao, P., Kassem, K. R. 2001. Terrestrial ecoregions of
 #' the world: a new map of life on Earth. Bioscience 51(11):933-938.
 #' \doi{https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2}
-#' @importFrom utils unzip
+#' @source \url{https://files.worldwildlife.org/wwfcmsprod/files/Publication/file/6kcchn7e3u_official_teow.zip}
 #' @include register.R
 #' @export
-get_teow <- function() {
+# get_teow <- function() {
+#   function(x,
+#            name = "teow",
+#            type = "vector",
+#            outdir = mapme_options()[["outdir"]],
+#            verbose = mapme_options()[["verbose"]]) {
+#     url <- paste(
+#       "/vsizip//vsicurl/",
+#       "https://files.worldwildlife.org/wwfcmsprod/files/",
+#       "Publication/file/6kcchn7e3u_official_teow.zip/",
+#       "official/wwf_terr_ecos.shp",
+#       sep = ""
+#     )
+#     bbox <- c(xmin = -180.0, ymin = -90.0, xmax = 180.0, ymax = 84.0)
+#     tile <- st_as_sf(st_as_sfc(st_bbox(bbox, crs = "EPSG:4326")))
+#     tile[["source"]] <- url
+#     make_footprints(tile, filenames = "wwf_terr_ecos.gpkg", what = "vector")
+#   }
+# }
+
+get_teow <- function(path = NULL) {
+  if (is.null(path) || !endsWith(tolower(path), ".zip")) {
+    stop("Expecting path to point towards an existing '.zip' file.")
+  }
+
   function(x,
            name = "teow",
            type = "vector",
            outdir = mapme_options()[["outdir"]],
            verbose = mapme_options()[["verbose"]]) {
-    url <- paste(
-      "/vsizip//vsicurl/",
-      "https://files.worldwildlife.org/wwfcmsprod/files/",
-      "Publication/file/6kcchn7e3u_official_teow.zip/",
-      "official/wwf_terr_ecos.shp",
-      sep = ""
+    url <- paste0(
+      "/vsizip/",
+      path,
+      "/official/wwf_terr_ecos.shp"
     )
     bbox <- c(xmin = -180.0, ymin = -90.0, xmax = 180.0, ymax = 84.0)
-    tile <- st_as_sf(st_as_sfc(st_bbox(bbox, crs = "EPSG:4326")))
+    tile <- sf::st_as_sf(sf::st_as_sfc(sf::st_bbox(bbox, crs = "EPSG:4326")))
     tile[["source"]] <- url
     make_footprints(tile, filenames = "wwf_terr_ecos.gpkg", what = "vector")
   }

R/spatial-utils.R

@@ -47,7 +47,8 @@ spds_exists <- function(path, oo = character(0), what = c("vector", "raster")) {
     ),
     raster = c("-json", "-nomd", "-norat", "-noct", oo)
   )
-  if (what == "vector" && sf::sf_extSoftVersion()[["GDAL"]] < "3.7.0") {
+  if (what == "vector" &&
+      (utils::compareVersion(sf::sf_extSoftVersion()[["GDAL"]], "3.7.0") < 0)) {
     util <- "gdalinfo"
     opts <- oo
   }

man/teow.Rd

@@ -8,7 +8,7 @@ test_that("biome computation works", {
   outdir <- file.path(tempdir(), "mapme.data")
   .copy_resource_dir(outdir)
   mapme_options(outdir = outdir, verbose = FALSE)
-  get_resources(x, get_teow())
+  get_resources(x, get_teow("test.zip"))
   teow <- prep_resources(x)[["teow"]]
 
   cb <- calc_biome()

tests/testthat/test-calc_biome.R

@@ -9,7 +9,7 @@ test_that("ecoregion computation works", {
   outdir <- file.path(tempdir(), "mapme.data")
   .copy_resource_dir(outdir)
   mapme_options(outdir = outdir, verbose = FALSE)
-  get_resources(x, get_teow())
+  get_resources(x, get_teow("test.zip"))
   teow <- prep_resources(x)[["teow"]]
 
   ce <- calc_ecoregion()

tests/testthat/test-calc_ecoregion.R

@@ -1,7 +1,7 @@
 test_that(".get_teow works", {
   skip_on_cran()
 
-  gteow <- get_teow()
+  gteow <- get_teow("test.zip")
   expect_silent(.check_resource_fun(gteow))
   fps <- gteow()
   expect_silent(.check_footprints(fps))

tests/testthat/test-get_teow.R

@@ -112,7 +112,9 @@ test_that(".read_raster works correctly", {
 })
 
 test_that(".read_vector works", {
-  if (sf::sf_extSoftVersion()[["GDAL"]] < "3.7.0") skip()
+  if (utils::compareVersion(sf::sf_extSoftVersion()[["GDAL"]], "3.7.0") < 0) {
+    skip("GDAL < 3.7.0")
+  }
 
   # copy to directory with w permissions, as ogrinfo otherwise fails on CRAN
   org <- system.file("extdata", "burundi.gpkg", package = "mapme.biodiversity")
@@ -133,7 +135,9 @@ test_that(".read_vector works", {
 })
 
 test_that("can get info from zipped vector resource", {
-  if (sf::sf_extSoftVersion()[["GDAL"]] < "3.7.0") skip("GDAL < 3.7.0")
+  if (utils::compareVersion(sf::sf_extSoftVersion()[["GDAL"]], "3.7.0") < 0) {
+    skip("GDAL < 3.7.0")
+  }
   if (packageVersion("sf") == "1.0.18") skip("sf == '1.0.18'")
   f <- system.file("extdata", "gfw_sample.gpkg",
     package = "mapme.biodiversity"