Deprecate get_species()

Fix #343

NEWS.md

@@ -5,6 +5,7 @@ This is a major release that updates the internal data model to Camtrap DP 1.0 a
 - `read_camtrap_dp()` (with underscore) is now deprecated. Use `read_camtrapdp()`, which reexports the read functionality from [camtrapdp](https://inbo.github.io/camtrapdp/reference/read_camtrapdp.html) (#298) (#298).
 - Function `get_record_table()` is now deprecated. Use `camtrapR_recordTable()` (#240).
 - Function `get_cam_op()` is now deprecated. Use `camtrapR_cameraOperation()` (#239).
+- Function `get_species()` is now deprecated. Use `taxa()` (#343).
 - Function `get_n_species()` is now deprecated. Use `n_species()` (#243).
 - Function `map_dep()` is now deprecated. Use `map_deployments()` (#231).
 - Filter predicates (`apply_filter_predicate()`, `pred()` `pred_not()` `pred_gt()`, `pred_and()`, `pred_or()`, etc.) are now defunct. Use `filter_deployments()` (#316).

R/get_species.R

@@ -1,45 +1,17 @@
 #' Get species
 #'
-#' Gets all identified species.
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#' 
+#' This function is deprecated. Please use [taxa()] instead.
 #'
-#' @param x Camera trap data package object, as returned by
-#'   [camtrapdp::read_camtrapdp()].
-#' @return A tibble data frame with all scientific names and vernacular names of
-#'   the identified species.
-#' @family exploration functions
+#' @inheritParams taxa
 #' @export
-#' @examples
-#' x <- example_dataset()
-#' get_species(x)
 get_species <- function(x) {
-  # Get taxonomic information from metadata
-  if (!"taxonomic" %in% names(x)) {
-    return(NULL)
-  } else {
-    taxonomy <- x$taxonomic
-    if ("vernacularNames" %in% names(taxonomy[[1]])) {
-      # Get all languages used in vernacularNames
-      langs <- purrr::map(taxonomy, function(x) {
-        vernacular_languages <- NULL
-        if ("vernacularNames" %in% names(x)) {
-          vernacular_languages <- names(x$vernacularNames)
-        }
-      })
-      langs <- unique(unlist(langs))
-
-      # Fill empty vernacular names with NA
-      taxonomy <- purrr::map(taxonomy, function(x) {
-        missing_langs <- langs[!langs %in% names(x$vernacularNames)]
-        for (i in missing_langs) {
-          x$vernacularNames[[i]] <- NA_character_
-        }
-        x
-      })
-    }
-    # flatten list and transform to data.frame
-    purrr::map_dfr(taxonomy, function(x) {
-      purrr::list_flatten(x, name_spec = "{outer}.{inner}")
-      }
-    )
-  }
+  lifecycle::deprecate_warn(
+    when = "1.0.0",
+    what = "get_species()",
+    with = "taxa()"
+  )
+  taxa(x)
 }