Update functions and examples

R/get_range.R

@@ -20,15 +20,15 @@
 #' @param bioreg  'SpatialPolygonsDataFrame', 'SpatVector' or 'sf' object containg different
 #' ecoregions (convex hulls will be classified on a bioreg basis) and of CRS WGS84. Note
 #' that this parameter may be fed with an external, generated (function make_ecoregion) or
-#' in-house ecoregion shapefile. Four shapefiles can be downloaded with the library (function get_bioreg
+#' in-house ecoregion shapefile. Four shapefiles can be downloaded with the library (see functions get_bioreg
 #' and others): eco_terra' (for terrestrial species; Nature conservancy version adapted from Olson & al. 2001),
 #' 'eco_marine' and 'eco_hd_marine' (for marine species; Spalding & al. 2007, 2012) and 'eco_fresh' (for freshwater
 #' species; Abell & al. 2008). For marine species, 'eco_terra' may also be used if the user wants to represent
 #' the terrestrial range of species that also partially settle on mainland. For fresh water species, same may be
 #' done if the user considers that terrestrial ecoregions should be more representative of the species ecology.
-#' @param bioreg_name Character. How is the shapefile attribute containing the ecoregion names called?
-#' E.g., very detailed level of 'eco_terra' is 'ECO_NAME'. Note that 'EcoRegion' (default) must always be supplied when
-#' using a make_ecoregion() output. See details.
+#' @param bioreg_name Character. One ecoregion level/category name from the 'bioreg' polygon must be supplied.
+#' E.g., very detailed level of 'eco_terra' is 'ECO_NAME'. Note that default applies if a make_ecoregion()
+#' polygon is provided as 'bioreg'.
 #' @param degrees_outlier Numeric. Distance threshold (degrees) for outlier classification.
 #' If the nearest minimal distance to the next point is larger than this threshold, it will be
 #' considered as an outlier.
@@ -123,7 +123,7 @@
 get_range <- function (sp_name = NULL, 
                        occ_coord = NULL, 
                        bioreg = NULL, 
-                       bioreg_name = "EcoRegion", 
+                       bioreg_name = NULL, 
                        degrees_outlier = 3,
                        clustered_points_outlier = 2,
                        buffer_width_point = 4, 
@@ -138,9 +138,11 @@ get_range <- function (sp_name = NULL,
   ### =========================================================================
 
   # bioreg
+   if (names(bioreg)[1]%in%"CLARA") {
+    bioreg_name = "EcoRegion"
+  } 
   if (methods::is(bioreg_name,"NULL")) {
-    stop("An ecoregion polygon should be supplied; if unavailable see command 'bioreg_list' and
-      internal functions get_bioreg(), read_bioreg() and check_and_get_bioreg()")
+    stop("Name of the desired ecoregion level/category ('bioreg_name' parameter) is missing, please provide one...")
   } 
 
   # occ_coord