From ad02c87d37a6efeacf6a5ba32b099c410cd042a4 Mon Sep 17 00:00:00 2001
From: hansvancalster <hans.vancalster@inbo.be>
Date: Tue, 13 Feb 2024 11:38:13 +0100
Subject: [PATCH 1/3] improve function: also allow input to be a character
 vector

---
 source/r/check_presence.R | 50 +++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 20 deletions(-)

diff --git a/source/r/check_presence.R b/source/r/check_presence.R
index 62f4e4b..95e61be 100644
--- a/source/r/check_presence.R
+++ b/source/r/check_presence.R
@@ -1,16 +1,29 @@
-library(dplyr)
-library(purrr)
-
-# Set working directory
-setwd("YOUR_WORKING_DIRECTORY")
-
-# West-Europa
-# België, Frankrijk, Duitsland, Luxemburg, Nederland, Zwitserland, Oostenrijk
-
-
-check_presence_from_file <- function(input_file = "./EJP_inse01_species_unique.txt", countries = c("BE", "FR", "DE", "LU", "NL", "CH", "AT")) {
-  # Read scientific names from the input file
-  scientificNames <- readLines(input_file)
+#' 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
+    scientificNames <- readLines(input)
+  } else if (is.character(input)) {
+    scientificNames <- input
+  } else {
+    stop("Input must be either a character vector or a valid file path.")
+  }
 
   # Remove any empty lines
   scientificNames <- scientificNames[scientificNames != ""]
@@ -47,13 +60,10 @@ check_presence_from_file <- function(input_file = "./EJP_inse01_species_unique.t
   }
 
   # Create tibble with results
-  result_table <- tibble::tibble(present = presence, scientificName = scientificNames)
+  result_table <- tibble::tibble(
+    present = presence,
+    scientificName = scientificNames
+  )
 
   return(result_table)
 }
-
-# Example usage:
-result_WestEurope <- check_presence_from_file()
-print(result_WestEurope)
-
-write.csv(result_WestEurope, "result_WestEurope.csv")

From 1b5740ec81496c7656dd86044e1e455ad5502066 Mon Sep 17 00:00:00 2001
From: hansvancalster <hans.vancalster@inbo.be>
Date: Tue, 13 Feb 2024 11:43:55 +0100
Subject: [PATCH 2/3] use snake case

---
 source/r/check_presence.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/source/r/check_presence.R b/source/r/check_presence.R
index 95e61be..99f2bb7 100644
--- a/source/r/check_presence.R
+++ b/source/r/check_presence.R
@@ -18,18 +18,18 @@ check_presence <- function(
   require(purrr)
   if (!is.null(input) && file.exists(input)) {
     # Read scientific names from the input file
-    scientificNames <- readLines(input)
+    scientific_names <- readLines(input)
   } else if (is.character(input)) {
-    scientificNames <- input
+    scientific_names <- input
   } else {
     stop("Input must be either a character vector or a valid file path.")
   }
 
   # Remove any empty lines
-  scientificNames <- scientificNames[scientificNames != ""]
+  scientific_names <- scientific_names[scientific_names != ""]
 
   # Initialize vector to store presence results
-  presence <- logical(length(scientificNames))
+  presence <- logical(length(scientific_names))
 
   # Loop over each country
   for (country in countries) {
@@ -53,7 +53,7 @@ check_presence <- function(
     }
 
     # Map over scientific names and check occurrence data for the current country
-    country_presence <- purrr::map_lgl(scientificNames, check_occurrence)
+    country_presence <- purrr::map_lgl(scientific_names, check_occurrence)
 
     # Update presence vector with results for the current country
     presence <- presence | country_presence
@@ -62,7 +62,7 @@ check_presence <- function(
   # Create tibble with results
   result_table <- tibble::tibble(
     present = presence,
-    scientificName = scientificNames
+    scientific_name = scientific_names
   )
 
   return(result_table)

From 78dbfdc8b51685da51b801ea5cdfb013a213219f Mon Sep 17 00:00:00 2001
From: hansvancalster <hans.vancalster@inbo.be>
Date: Tue, 13 Feb 2024 11:51:23 +0100
Subject: [PATCH 3/3] fix linter

---
 source/r/check_presence.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/source/r/check_presence.R b/source/r/check_presence.R
index 99f2bb7..25f1a33 100644
--- a/source/r/check_presence.R
+++ b/source/r/check_presence.R
@@ -52,7 +52,8 @@ check_presence <- function(
       }
     }
 
-    # Map over scientific names and check occurrence data for the current country
+    # 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