Merge pull request #453 from mapme-initiative/develop

check system requirements

Author: zivankaraman

.gitignore

@@ -53,7 +53,7 @@ rsconnect/
 ## Add any custom .gitignore items below
 
 # folder with development related stuff
-develop/
+develop
 
 # renv related files and folders
 renv.lock

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mapme.biodiversity
 Title: Efficient Monitoring of Global Biodiversity Portfolios
-Version: 0.9.4.9006
+Version: 0.9.4.9007
 Authors@R: c(person(given = "Darius A.", 
                     family = "G\u00F6rgen", 
                     role = "aut",

NEWS.md

@@ -1,4 +1,4 @@
-# mapme.biodiversity 0.9.4.9006
+# mapme.biodiversity 0.9.4.9007
 
 ## General
 
@@ -10,12 +10,14 @@
 ## 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
 
 ## Bug fixes
 
 -   internal function `.fetch_resource()` now correctly takes into account the resources that could not be retrieved and reports them ([433](https://github.com/mapme-initiative/mapme.biodiversity/issues/433))
 -   fixed messages from the `check_namespace()` function
--   fixed the way `normalizePath()` is ised so it works correctly on Windows ([446](https://github.com/mapme-initiative/mapme.biodiversity/issues/446))
+-   fixed the way `normalizePath()` is used so it works correctly on Windows ([446](https://github.com/mapme-initiative/mapme.biodiversity/issues/446))
+-   fixed `calc_treecover_area()` to correctly handle the full tree cover (100%) ([451](https://github.com/mapme-initiative/mapme.biodiversity/issues/451))
 
 # mapme.biodiversity 0.9.4
 

R/calc_treecover_area.R

@@ -155,7 +155,7 @@ calc_treecover_area <- function(years = 2000:2024,
   data[data[["patches"]] %in% keep_patches, ]
 }
 
-.sum_gfw <- function(data, what = "coverage_area", max_year = 2023) {
+.sum_gfw <- function(data, what, max_year) {
   # calculate loss area by year
   df <- data.frame(years = 2000:max_year, var = 0)
   names(df)[2] <- what
@@ -243,7 +243,8 @@ calc_treecover_area <- function(years = 2000:2024,
   # binarize the treecover layer based on min_cover argument
   rcl<- matrix(c(NA, NA, 0,
                  0, cover, 0,
-                 cover, 100, 1), ncol = 3, byrow = TRUE)
+                 cover, 100.001, 1), ncol = 3, byrow = TRUE)
+  # need value > 100 to include 100 with 'right = FALSE'
   binary_treecover <- terra::classify(treecover,
                                       rcl = rcl,
                                       right = FALSE, others = NA)

R/calc_treecover_area_and_emissions.R

@@ -102,7 +102,7 @@ calc_treecover_area_and_emissions <- function(years = 2000:2024,
         data <- .prep_gfw_data(data, min_size)
         losses <- .sum_gfw(data, "coverage_area", max_year)
         names(losses)[2] <- "loss"
-        emissions <- .sum_gfw(data, "emissions")
+        emissions <- .sum_gfw(data, "emissions", max_year)
 
         org_coverage <- sum(data[["coverage_area"]])
 

R/register.R

@@ -14,6 +14,7 @@
     log_dir = NULL,
     verbose = TRUE
   )
+  .check_system_requirements()
   invisible()
 }
 
@@ -312,3 +313,17 @@ available_indicators <- function(indicators = NULL) {
 .clear_resources <- function() {
   .pkgenv$avail_resources <- list()
 }
+
+.check_system_requirements <- function() {
+  chk <- mapply(.compare_sf_version, c("GDAL", "PROJ"), c("3.7.0", "4.8.0"))
+  invisible()
+}
+
+.compare_sf_version <- function(lib, target) {
+  installed_version <- sf::sf_extSoftVersion()[[lib]]
+  if (utils::compareVersion(installed_version, target) < 0) {
+    msg <- sprintf("%s system library version (%s) < %s", lib, installed_version, target)
+    warning(msg, call. = FALSE)
+  }
+}
+

tests/testthat/_snaps/calc_treecover_area.md

@@ -3,5 +3,5 @@
     Code
       result$value
     Output
-      [1] 2050.641 2050.348 2048.659 2017.076 2008.575 2004.666
+      [1] 2057.330 2056.816 2055.127 2021.265 2011.870 2007.594
 

tests/testthat/_snaps/calc_treecover_area_and_emissions.md

@@ -3,6 +3,6 @@
     Code
       result$value
     Output
-       [1]     0.0000  2050.6413   120.3610  2050.3477   619.3609  2048.6594
-       [7] 11905.1140  2017.0757  3297.2784  2008.5752  1590.3710  2004.6661
+       [1]     0.0000  2057.3295   212.5268  2056.8158   619.3609  2055.1275
+       [7] 12932.7655  2021.2651  3676.1357  2011.8703  1731.4164  2007.5943
 

tests/testthat/_snaps/calc_treecoverloss_emissions.md

@@ -3,5 +3,5 @@
     Code
       result$value
     Output
-      [1]     0.0000   120.3610   619.3609 11905.1140  3297.2784  1590.3710
+      [1]     0.0000   212.5268   619.3609 12932.7655  3676.1357  1731.4164
 

tests/testthat/test-calc_carbon.R

@@ -1,4 +1,6 @@
 test_that("calc_irr_carbon works", {
+  # CRAN checks fail on some platforms, not reproducible
+  skip_on_cran()
   x <- read_sf(system.file("extdata", "shell_beach_protected_area_41057_B.gpkg",
     package = "mapme.biodiversity"
   ))
@@ -32,6 +34,8 @@ test_that("calc_irr_carbon works", {
 
 
 test_that("calc_vul_carbon works", {
+  # CRAN checks fail on some platforms, not reproducible
+  skip_on_cran()
   x <- read_sf(system.file("extdata", "shell_beach_protected_area_41057_B.gpkg",
     package = "mapme.biodiversity"
   ))
@@ -64,6 +68,8 @@ test_that("calc_vul_carbon works", {
 })
 
 test_that("calc_man_carbon works", {
+  # CRAN checks fail on some platforms, not reproducible
+  skip_on_cran()
   x <- read_sf(system.file("extdata", "shell_beach_protected_area_41057_B.gpkg",
     package = "mapme.biodiversity"
   ))