Updates docs and files

8Ginette8 · Feb 4, 2025 · aa7c89b · aa7c89b
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Showing 28 changed files with 10 additions and 10 deletions.
diff --git a/R/evaluate_range.R b/R/evaluate_range.R
@@ -11,7 +11,7 @@
 #' region (see 'mask') and aggregations of the input maps to different resolutions,
 #' given the importance of these factors for specific applications (Pinkert et al., 2023).
 #' @param root_dir Character. Working directory to load and save target files.
-#' @param valData_dir Numeric. Directory to validation data.
+#' @param valData_dir Numeric. Directory to validation spatial data (must have same name as data in ecoRM_dir)
 #' @param ecoRM_dir  Numeric. Directory to range maps (generated with get_range).
 #' @param valData_type Character. Type of valData - either "SHP" or "TIFF".
 #' @param verbose Logical (optional). Report details while running.

diff --git a/inst/examples/evaluate_range_help.R b/inst/examples/evaluate_range_help.R
@@ -2,7 +2,7 @@
 # EcoRM evaluation at different resolutions (>4min runtime)
 root.dir  <- list.files(system.file(package = "gbif.range"), pattern = "extdata", full.names = TRUE)
 
-res1km <- evaluate_range(root_dir = root.dir, 
+res5km <- evaluate_range(root_dir = root.dir, 
            valData_dir = "SDM", 
            ecoRM_dir = "EcoRM",
            verbose = TRUE, 
@@ -18,7 +18,7 @@ res10km <- evaluate_range(root_dir = root.dir,
                    print_map = TRUE,
                    valData_type = "TIFF", 
                    mask = NULL, 
-                   res_fact = 10)
+                   res_fact = 2)
 
 
 # Extract and plot a specific overlay map
@@ -48,12 +48,12 @@ legend("bottomright",
 
 ## Compare sensitivity and precision outputs ##
 # Calculate overall performance (e.g. mean sensitivity & precision)
-res1km$df_eval$Mean_SenPrec <- (res1km$df_eval$Sen_ecoRM + res1km$df_eval$Prec_ecoRM) / 2
+res5km$df_eval$Mean_SenPrec <- (res5km$df_eval$Sen_ecoRM + res5km$df_eval$Prec_ecoRM) / 2
 res10km$df_eval$Mean_SenPrec <- (res10km$df_eval$Sen_ecoRM + res10km$df_eval$Prec_ecoRM) / 2
 
 # Combine the data frames and add a Resolution column
 combined_df <- rbind(
-  cbind(res1km$df_eval, Resolution = "1km"),
+  cbind(res5km$df_eval, Resolution = "1km"),
   cbind(res10km$df_eval, Resolution = "10km")
 )
 

diff --git a/inst/extdata/EcoRM/Arctostaphylos_alpinus.tif b/inst/extdata/EcoRM/Arctostaphylos_alpinus.tif
diff --git a/inst/extdata/EcoRM/Atropa_bella-donna.tif b/inst/extdata/EcoRM/Atropa_bella-donna.tif
diff --git a/inst/extdata/EcoRM/Centaurea_montana.tif b/inst/extdata/EcoRM/Centaurea_montana.tif
diff --git a/inst/extdata/EcoRM/Cirsium_rivulare.tif b/inst/extdata/EcoRM/Cirsium_rivulare.tif
diff --git a/inst/extdata/EcoRM/Cupressus_sempervirens.tif b/inst/extdata/EcoRM/Cupressus_sempervirens.tif
diff --git a/inst/extdata/EcoRM/Pinus_nigra.tif b/inst/extdata/EcoRM/Pinus_nigra.tif
diff --git a/inst/extdata/EcoRM/Plantago_alpina.tif b/inst/extdata/EcoRM/Plantago_alpina.tif
diff --git a/inst/extdata/EcoRM/Plantago_media.tif b/inst/extdata/EcoRM/Plantago_media.tif
diff --git a/inst/extdata/EcoRM/Prunella_vulgaris.tif b/inst/extdata/EcoRM/Prunella_vulgaris.tif
diff --git a/inst/extdata/EcoRM/Salvia_pratensis.tif b/inst/extdata/EcoRM/Salvia_pratensis.tif
diff --git a/inst/extdata/EcoRM/Salvia_pratensis_pratensis.tif b/inst/extdata/EcoRM/Salvia_pratensis_pratensis.tif
diff --git a/inst/extdata/EcoRM/Tragopogon_dubius.tif b/inst/extdata/EcoRM/Tragopogon_dubius.tif
diff --git a/inst/extdata/SDM/Arctostaphylos_alpinus.tif b/inst/extdata/SDM/Arctostaphylos_alpinus.tif
diff --git a/...xtdata/SDM/Salvia_pratensis_pratensis.tif → inst/extdata/SDM/Salvia_pratensis.tif b/...xtdata/SDM/Salvia_pratensis_pratensis.tif → inst/extdata/SDM/Salvia_pratensis.tif
diff --git a/inst/extdata/eval_output/Evaluation_map_Arctostaphylos_alpinus.pdf b/inst/extdata/eval_output/Evaluation_map_Arctostaphylos_alpinus.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Atropa_bella-donna.pdf b/inst/extdata/eval_output/Evaluation_map_Atropa_bella-donna.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Centaurea_montana.pdf b/inst/extdata/eval_output/Evaluation_map_Centaurea_montana.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Cirsium_rivulare.pdf b/inst/extdata/eval_output/Evaluation_map_Cirsium_rivulare.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Cupressus_sempervirens.pdf b/inst/extdata/eval_output/Evaluation_map_Cupressus_sempervirens.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Pinus_nigra.pdf b/inst/extdata/eval_output/Evaluation_map_Pinus_nigra.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Plantago_alpina.pdf b/inst/extdata/eval_output/Evaluation_map_Plantago_alpina.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Plantago_media.pdf b/inst/extdata/eval_output/Evaluation_map_Plantago_media.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Prunella_vulgaris.pdf b/inst/extdata/eval_output/Evaluation_map_Prunella_vulgaris.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Salvia_pratensis.pdf b/inst/extdata/eval_output/Evaluation_map_Salvia_pratensis.pdf
diff --git a/inst/extdata/eval_output/Evaluation_map_Tragopogon_dubius.pdf b/inst/extdata/eval_output/Evaluation_map_Tragopogon_dubius.pdf
diff --git a/man/evaluate_range.Rd b/man/evaluate_range.Rd