Merge branch 'master' of github.com:traitecoevo/saltbush

traitecoevo · Nov 18, 2024 · c9a7d00 · c9a7d00
2 parents f0cecc1 + b599c8d
commit c9a7d00
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Showing 3 changed files with 24 additions and 3 deletions.
diff --git a/R/calculate_spectral_metrics.R b/R/calculate_spectral_metrics.R
@@ -22,7 +22,7 @@
 #'   red = runif(20000, min = 0, max = 1),
 #'   red_edge = runif(20000, min = 0, max = 1),
 #'   nir = runif(20000, min = 0, max = 1))
-#' spectral_metrics <- calculate_cv(df,
+#' spectral_metrics <- calculate_spectral_metrics(df,
 #'    wavelengths = c('blue','green','red','red_edge','nir'),
 #'    rarefaction = TRUE, min_points = 5000, n = 999)
 
@@ -183,7 +183,7 @@ calculate_spectral_metrics <- function(pixel_values_df,
     sv <- calculate_sv(site_pixel_values, wavelengths = wavelengths)
     chv <- calculate_chv_nopca(site_pixel_values, wavelengths, rarefaction = rarefaction, n = n, min_points = min_points)
 
-    results <- list(CV = cv, SV = sv, CHV = chv)
+    results[[site]] <- list(CV = cv, SV = sv, CHV = chv)
   }
 
   combined_cv <- dplyr::bind_rows(lapply(results, function(x) x$CV), .id = 'site')

diff --git a/man/calculate_cv.Rd b/man/calculate_cv.Rd
diff --git a/tests/testthat/test-test_spectral.R b/tests/testthat/test-test_spectral.R
@@ -16,6 +16,27 @@ test_that("calculate_cv works", {
   expect_true(pixelvalues$aoi_id==1)
 })
 
+test_that("calculate_spectral_metrics works", {
+  set.seed(123)
+  df <- data.frame(
+    site_name = rep(c("site_one", "site_two", "site_three", "site_four"), each = 5000),
+    aoi_id = 1,
+    blue = runif(20000, min = 0, max = 1),
+    green = runif(20000, min = 0, max = 1),
+    red = runif(20000, min = 0, max = 1),
+    red_edge = runif(20000, min = 0, max = 1),
+    nir = runif(20000, min = 0, max = 1))
+  spectral_metrics <- calculate_spectral_metrics(df,
+                              wavelengths = c('blue','green','red','red_edge','nir'),
+                              rarefaction = TRUE, min_points = 5000, n = 999)
+  expect_type(spectral_metrics,"data.frame")
+  expect_true(spectral_metrics$CV<0.6)
+  expect_true(spectral_metrics$SV<0.42)
+  expect_true(spectral_metrics$CHV_nopca<0.87)
+  expect_true(spectral_metrics$aoi_id==1)
+  expect_true(spectral_metrics$image_type=='masked')
+})
+
 test_that("extract_pixel_values works", {
   aoi_files <- list.files(
     system.file("extdata/fishnet", package = "saltbush"),