action & coverage

.github/workflows/R-CMD-check.yaml

@@ -18,7 +18,7 @@ jobs:
         config:
              - {os: macos-latest,   r: 'release'}
              - {os: windows-latest, r: 'release'}
-             - {os: ubuntu-latest,   r: 'release'}
+             #- {os: ubuntu-latest,   r: 'release'}
              #- {os: windows-latest, r: '3.6'}
              #- {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
              #- {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -29,7 +29,7 @@ jobs:
       CRAN: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -38,7 +38,7 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/test-coverage.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

R/nm_boyce.R

@@ -32,15 +32,14 @@
 #' presence_predicted <- sqrt(runif(100))
 #' contrast <- runif(1000)
 #' nm_boyce(presence_predicted, contrast)
-#' contBoyce2x(presence_predicted, contrast)
 #' presence_weight <- c(rep(1, 10), rep(0.5, 90))
 #' nm_boyce(presence_predicted, contrast, presence_weight=presence_weight)
 #'
 
 nm_boyce <- function(
     presence_predicted,
     contrast,
-    numBins = 101,
+    num_bins = 101,
     bin_width = 0.1,
     presence_weight = rep(1, length(presence_predicted)),
     contrast_weight = rep(1, length(contrast)),

tests/testthat/test-nm_find_hcv.R

@@ -6,9 +6,19 @@ testthat::test_that("Test find highly correlated variables", {
   weigth <- abs(rnorm(150, 56.2, 11.4))
   glucose_rate <- runif(150, .2, .6)
 
-  test_data <- data.frame(age, heigth, weigth, glucose_rate) %>%
-    cor()
+  samp_data <- data.frame(age, heigth, weigth, glucose_rate)
+  test_cor <- samp_data%>% cor()
 
   # highly correlated variables
-  testthat::expect_equal(class(nm_find_hcv(x = test_data)), "character")
+  testthat::expect_equal(class(nm_find_hcv(x = test_cor)), "character")
+  testthat::expect_equal(class(nm_find_hcv(x = test_cor, verbose = TRUE)), "character")
+
+
+  samp_data$na_v <- sample(x = rep(c(1, NA, 5, 2, 5,9), 200), size = 150)
+  test_cor <- samp_data%>% cor()
+
+  expect_error(nm_find_hcv(x = test_cor))
+  expect_error(nm_find_hcv(x = c(12, 45, 6)))
+
+  rm(samp_data, test_cor)
 })

tests/testthat/test-nm_match_raster.R

@@ -2,18 +2,37 @@ test_that("test for nm_match_raster", {
   library(terra)
 
   env_layers_path <- paste0(system.file("extdata", package = "nimo"), "/env_layers")
-  env_layers_path <- list.files(env_layers_path, full.names = TRUE)[1:2]
+  env_layers_path <- list.files(env_layers_path, pattern = ".tif$", full.names = TRUE)[1:2]
 
   target <- terra::rast(env_layers_path[1]) # reference raster to get properties from
   to_match <- terra::rast(env_layers_path[2]) # raster that will inherit properties
-
+  #
   new_dnw <- nm_match_raster(to_match = to_match, target = target)
-
   expect_true(class(new_dnw) == "SpatRaster")
   expect_error(
     nm_match_raster(to_match = to_match, target = target, method = "linear")
     )
 
+  expect_error(
+    nm_match_raster(to_match = to_match, target = "", method = "linear")
+  )
+
+  #
+  new_dnw <- nm_match_raster(to_match = to_match, target = target,
+                             save_file = T, file_name = "test.tif")
+  expect_true(file.exists(paste0(getwd(), "/test.tif")))
+  unlink(paste0(getwd(), "/test.tif"), recursive = T)
+
+  #
+  new_dnw <- nm_match_raster(to_match = to_match, target = target,
+                             save_file = T)
+  save_path <- paste0(
+    dirname(terra::sources(to_match)), "/",
+    gsub("\\..*$", "", basename(terra::sources(to_match))), "_matched.tif"
+  )
+  expect_true(file.exists(save_path))
+  unlink(save_path, recursive = T)
+
 
-  rm(env_layers_path, target, to_match, new_dnw)
+  rm(env_layers_path, target, to_match, new_dnw, save_path)
 })