From b9af2d874c182d0617bdb01a6c3e6b4cab60145e Mon Sep 17 00:00:00 2001
From: Daniel Falster <daniel.falster@unsw.edu.au>
Date: Wed, 26 Jul 2023 12:59:56 +1000
Subject: [PATCH] Reducing duplication

---
 R/clean_names.R | 27 +++++++++++----------------
 1 file changed, 11 insertions(+), 16 deletions(-)

diff --git a/R/clean_names.R b/R/clean_names.R
index b0d7705f..6c286dd6 100644
--- a/R/clean_names.R
+++ b/R/clean_names.R
@@ -569,24 +569,19 @@ get_updated_species_list <-
       aligned_data$aligned_name %>% update_taxonomy(resources = resources, output = output)
     
     if (one_to_many %in% c("return_all", "collapse_to_higher_taxon")) {
-      aligned_data %>%
-        dplyr::select(original_name, aligned_name, aligned_reason) %>%
-        dplyr::left_join(aligned_species_list_tmp,
-                         by = c("aligned_name"),
-                         multiple = "all") %>%
-        dplyr::filter(!is.na(taxonIDClean)) %>%
-        dplyr::mutate(genus = stringr::word(canonicalName, 1, 1)) %>%
-        dplyr::rename(canonical_name = canonicalName)
+      multiple = "all"
     } else {
-      aligned_data %>%
-        dplyr::select(original_name, aligned_name, aligned_reason) %>%
-        dplyr::left_join(aligned_species_list_tmp,
-                         by = c("aligned_name"),
-                         multiple = "first") %>%
-        dplyr::filter(!is.na(taxonIDClean)) %>%
-        dplyr::mutate(genus = stringr::word(canonicalName, 1, 1)) %>%
-        dplyr::rename(canonical_name = canonicalName)
+      multiple = "first"
     }
+
+    aligned_data %>%
+      dplyr::select(original_name, aligned_name, aligned_reason) %>%
+      dplyr::left_join(aligned_species_list_tmp,
+                        by = c("aligned_name"),
+                        multiple = multiple) %>%
+      dplyr::filter(!is.na(taxonIDClean)) %>%
+      dplyr::mutate(genus = stringr::word(canonicalName, 1, 1)) %>%
+      dplyr::rename(canonical_name = canonicalName)
   }