add authors to RBGV datasets

traitecoevo · Feb 15, 2024 · 76b2a2a · 76b2a2a
1 parent 082e982
commit 76b2a2a
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Showing 7 changed files with 90,727 additions and 83,262 deletions.
diff --git a/data/ABRS_2023/metadata.yml b/data/ABRS_2023/metadata.yml
@@ -32,7 +32,6 @@ dataset:
         trait_value = ifelse(trait_name == "leaf_shape", stringr::str_replace(trait_value, "cylindrical", "terete"), trait_value),
         trait_value = ifelse(trait_name == "leaf_margin_posture", stringr::str_replace(trait_value, "recurved", "revolute"), trait_value),
         trait_value = ifelse(trait_name == "leaf_margin_posture", stringr::str_replace(trait_value, "incurved", "involute"), trait_value),
-        trait_value = ifelse(category =="rachis", NA, trait_value),
         measurement_remarks = ifelse(is.na(category), joined, paste0(joined, "; Trait value refers to ", category)),
         inferred = ifelse(stringr::str_detect(flora_value, "inferred"), flora_value, NA),
         inferred = ifelse(stringr::str_detect(flora_value, "inferred_from_species"), "inferred_from_species", inferred),

diff --git a/data/RBGV_2022/data.csv b/data/RBGV_2022/data.csv
diff --git a/data/RBGV_2022/metadata.yml b/data/RBGV_2022/metadata.yml
@@ -53,6 +53,7 @@ dataset:
   '
   collection_date: unknown/2022
   taxon_name: taxon_name
+  source_id: created_by
   description: Plant growth form data extracted from VicFlora, the Victorian online
     flora.
   basis_of_record: preserved_specimen

diff --git a/data/RBGV_2023/data.csv b/data/RBGV_2023/data.csv
diff --git a/data/RBGV_2023/metadata.yml b/data/RBGV_2023/metadata.yml
@@ -48,7 +48,7 @@ dataset:
     data %>%
       filter(!is.na(taxon_name)) %>%
       filter(str_detect(taxon_name, " ")) %>%
-      filter(!category %in% c("petiole")) %>%
+      filter(!category %in% c("petiole", "rachis")) %>%
       mutate(
         trait_value = ifelse(trait_name == "leaf_shape", stringr::str_replace(trait_value, "semi-orbicular", "orbicular"), trait_value),
         trait_value = ifelse(trait_name == "seed_shape", stringr::str_replace(trait_value, "obovate", "ovoid"), trait_value),
@@ -57,7 +57,6 @@ dataset:
         trait_value = ifelse(trait_name == "leaf_shape", stringr::str_replace(trait_value, "cylindrical", "terete"), trait_value),
         trait_value = ifelse(trait_name == "leaf_margin_posture", stringr::str_replace(trait_value, "recurved", "revolute"), trait_value),
         trait_value = ifelse(trait_name == "leaf_margin_posture", stringr::str_replace(trait_value, "incurved", "involute"), trait_value),
-        trait_value = ifelse(category =="rachis", NA, trait_value),
         measurement_remarks = ifelse(is.na(category), NA, paste0("Trait value refers to ", category)),
         inferred = ifelse(stringr::str_detect(flora_value, "inferred"), flora_value, NA),
         inferred = ifelse(stringr::str_detect(flora_value, "inferred_from_species"), "inferred_from_species", inferred),
@@ -122,6 +121,7 @@ dataset:
   trait_name: trait_name
   value: trait_value
   measurement_remarks: measurement_remarks
+  source_id: created_by
   description: Plant morphology data extracted from VicFlora, the Victorian online
     flora.
   basis_of_record: literature

diff --git a/data/RBGV_2023/raw/120224_downloaded.csv b/data/RBGV_2023/raw/120224_downloaded.csv
diff --git a/data/RBGV_2023/raw/add authors to profiles.R b/data/RBGV_2023/raw/add authors to profiles.R
@@ -0,0 +1,19 @@
+# extract authors from current RBGV download
+
+read_csv("data/RBGV_2023/raw/120224_downloaded.csv") %>%
+  select(taxon_name, created_by) %>%
+  group_by(taxon_name) %>%
+  mutate(created_by = paste0(created_by, collapse = "; ")) %>%
+  ungroup() %>% 
+  distinct() -> authors
+
+# add authors to 2 RBGV dataset
+
+read_csv("data/RBGV_2023/data.csv") %>%
+  left_join(authors) %>%
+  write_csv("data/RBGV_2023/data.csv") 
+
+read_csv("data/RBGV_2022/data.csv") %>%
+  left_join(authors) %>%
+  write_csv("data/RBGV_2022/data.csv") 
+