more pivot errors fixed (#765)

more fixes to pivoting problems:
- minor changes copied from traits.build back to austraits.build process.R file
- had to add locations to Yang_2023
- Witkowski_1991 would only recognised plant ages when I wrote them in letters after trying many many other tricks: I tried '10' and '21'; I checked metadata_check_custom_R_code("Witkowski_1991) to see how it was read in; I tried retyping the cells; I tried assigning it to a different context category; I tried adding "mutate to as.character" through custom_R_code and nothing worked. All rows in the column have a value, so it isn't being read in strangely.

R/process.R

@@ -292,11 +292,11 @@ process_create_observation_id <- function(data) {
   data <- data %>%
     dplyr::mutate(
               pop_id_segment = ifelse(
-                (!is.na(.data$location_name)|!is.na(.data$treatment_id)|!is.na(.data$plot_id)) & .data$entity_type %in% c("individual", "population"),
+                (!is.na(.data$location_name)|!is.na(.data$treatment_id)|!is.na(.data$plot_id)) & .data$entity_type %in% c("individual", "population", "metapopulation"),
                 process_generate_id(.data$population_id, "", sort = TRUE), 
                 NA),
               pop_id_segment = ifelse(is.na(.data$pop_id_segment)  & 
-                                        .data$entity_type %in% c("individual", "population"), 
+                                        .data$entity_type %in% c("individual", "population", "metapopulation"), 
                                         "pop_unk", .data$pop_id_segment),
               population_id = .data$pop_id_segment
             )
@@ -373,7 +373,7 @@ process_create_observation_id <- function(data) {
     dplyr::group_by(.data$dataset_id) %>%
     dplyr::mutate(
       observation_id = 
-        paste(.data$taxon_name, .data$population_id, .data$individual_id, .data$temporal_id, .data$entity_type, sep="-") %>%  
+        paste(.data$taxon_name, .data$population_id, .data$individual_id, .data$temporal_id, .data$entity_type, .data$life_stage, sep="-") %>%  
         process_generate_id("", sort = TRUE)
     ) %>%
     dplyr::ungroup() 
@@ -514,8 +514,8 @@ process_create_context_ids <- function(data, contexts) {
       tidyr::unite("combined", remove = FALSE) %>%
       dplyr::mutate(
         combined = ifelse(.data$combined == NAs, NA, .data$combined),  
-        id = .data$combined %>%
-          as.factor() %>% as.integer() %>% make_id()
+        id = ifelse(!is.na(.data$combined), .data$combined %>%
+                      as.factor() %>% as.integer() %>% make_id(), NA)
       ) %>%
       dplyr::select(-dplyr::all_of(c("combined")))
 

data/Witkowski_1991/data.csv

@@ -1,7 +1,7 @@
 Species,plant_age,replicates_seeds_fruit,reproductive_maturity,seed_viability_%,seed_germination_%,seed_dry_mass_mg,fire_to_flowering,fire_to_fruiting,seedset_%,fruit_set_%,post_fire_recruitment,seedling_establishment_conditions,resprouting_capacity,serotiny
-Banksia baxteri,10,15,3,98.6,41,43.4,3,5,0.9,1.2,post_fire_recruitment,establish_post_fire,fire_killed, serotiny_high
-Banksia baxteri,21,5,,99.3,31,,,,0.8,1,,,,
-Banksia speciosa,10,15,3,99.1,47,128.6,3,3,0.5,0.7,post_fire_recruitment,establish_post_fire,fire_killed, serotiny_high
-Banksia speciosa,21,5,,99.7,35,,,,0.4,0.5,,,,
-Banksia coccinea,10,15,3,99.3,21,12.8,3,3,4,8.6,post_fire_recruitment,establish_post_fire establish_anytime,fire_killed, serotiny_moderate
-Banksia coccinea,21,5,,99.2,18,,,,3.4,7.3,,,,
+Banksia baxteri,ten,15,3,98.6,41,43.4,3,5,0.9,1.2,post_fire_recruitment,establish_post_fire,fire_killed, serotiny_high
+Banksia baxteri,twentyone,5,,99.3,31,,,,0.8,1,,,,
+Banksia speciosa,ten,15,3,99.1,47,128.6,3,3,0.5,0.7,post_fire_recruitment,establish_post_fire,fire_killed, serotiny_high
+Banksia speciosa,twentyone,5,,99.7,35,,,,0.4,0.5,,,,
+Banksia coccinea,ten,15,3,99.3,21,12.8,3,3,4,8.6,post_fire_recruitment,establish_post_fire establish_anytime,fire_killed, serotiny_moderate
+Banksia coccinea,twentyone,5,,99.2,18,,,,3.4,7.3,,,,

data/Witkowski_1991/metadata.yml

@@ -70,8 +70,8 @@ contexts:
   category: entity_context
   var_in: plant_age
   values:
-  - value: 10
-  - value: 21
+  - value: ten
+  - value: twentyone
 traits:
 - var_in: reproductive_maturity
   unit_in: a

data/Yang_2023/metadata.yml

@@ -88,11 +88,13 @@ dataset:
         entity_type = "species",
         entity_type = ifelse(!is.na(fire_severity), "population", entity_type),
         entity_type = ifelse(!is.na(fire_intensity), "population", entity_type),
-        entity_type = ifelse(!is.na(habitat_conditions), "population", entity_type)
+        entity_type = ifelse(!is.na(habitat_conditions), "population", entity_type),
+        entity_type = ifelse(taxon_name %in% c("Banksia ashbyi", "Grevillea pteridifolia", "Hakea marginata", "Paraprasophyllum constrictum"), "population", entity_type)
       )
   '
   collection_date: unknown/2022
   taxon_name: taxon_name
+  location_name: site
   source_id: source_id
   description: Plant fire response and other related trait data scored from Australia's
     online state and national floras and the taxonomic literature.
@@ -113,7 +115,37 @@ dataset:
   original_file: .na
   notes: References for additional source_id's available in a column in the data.csv
     file, 'references'
-locations: .na
+locations:
+  South of Shark Bay:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  North of Carnarvon:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  QLD, NT:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Northern NT, WA:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Southern population:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Northern population:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Adelaide Hills:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Locations other than Adelaide Hills:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  Providence Ponds:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
+  NT:
+    longitude (deg): .na.character
+    latitude (deg): .na.character
 contexts:
 - context_property: fire severity
   category: plot
@@ -174,7 +206,7 @@ contexts:
     description: Time from fire to flowering measured on resprouting shoots.
   - find: fire_killed
     value: from seed
-    description: Time from fire to flowering measured on plants that germinated post-fire.
+    description: Time from fire to flowering measured on plants that germinated post-fire. 
 traits:
 - var_in: fire_response
   unit_in: .na