Merge pull request #7 from inbo/Check_occurences_GBIF

Check occurences gbif

source/r/check_presence.R

@@ -0,0 +1,70 @@
+#' Deze functie gaat na of een soort volgens GBIF voorkomt in een gekozen set
+#' van landen
+#'
+#' Default zijn West-Europese landen ingesteld: België, Frankrijk, Duitsland,
+#' Luxemburg, Nederland, Zwitserland, Oostenrijk
+#'
+#' @param input A character vector of Scientific names or a .txt file from which
+#' Scientific Names can be read.
+#' @param countries a character vector of country codes
+#'
+#' @example
+#' result_WestEurope <- check_presence_from_file()
+#' print(result_WestEurope)
+check_presence <- function(
+    input = NULL,
+    countries = c("BE", "FR", "DE", "LU", "NL", "CH", "AT")) {
+  require(dplyr)
+  require(purrr)
+  if (!is.null(input) && file.exists(input)) {
+    # Read scientific names from the input file
+    scientific_names <- readLines(input)
+  } else if (is.character(input)) {
+    scientific_names <- input
+  } else {
+    stop("Input must be either a character vector or a valid file path.")
+  }
+
+  # Remove any empty lines
+  scientific_names <- scientific_names[scientific_names != ""]
+
+  # Initialize vector to store presence results
+  presence <- logical(length(scientific_names))
+
+  # Loop over each country
+  for (country in countries) {
+    # Function to check occurrence data and handle errors
+    check_occurrence <- function(name) {
+      data <- tryCatch({
+        rgbif::occ_data(
+          scientificName = name,
+          country = country,  # Specify one country at a time
+          limit = 1
+        )
+      }, error = function(e) {
+        return(list(error = TRUE))
+      })
+
+      if (inherits(data, "error") || is.null(data$data)) {
+        return(FALSE)  # Occurrence data is not present or error occurred
+      } else {
+        return(TRUE)   # Occurrence data is present
+      }
+    }
+
+    # Map over scientific names and check occurrence data for the current
+    # country
+    country_presence <- purrr::map_lgl(scientific_names, check_occurrence)
+
+    # Update presence vector with results for the current country
+    presence <- presence | country_presence
+  }
+
+  # Create tibble with results
+  result_table <- tibble::tibble(
+    present = presence,
+    scientific_name = scientific_names
+  )
+
+  return(result_table)
+}