Minor metadata fixes (#788)

A number of new tests in traits.build captured metadata inconsistencies,  that led to fixes in austraits.build metadata files and also a few refinements to the tests.

* lots of taxonomic_updates that were no longer being used - a mix of duplicates and "artifacts" from long ago, when 1) additional updates were added for a secondary fix, rather than overwriting the first one; 2) a time a while ago when fixes were made to standardised names, not truly original names; and 3) for some of the flora scraping studies the same list of taxonomic updates was used for all studies from the same flora, although some taxa didn't have any entries in one of the 2-3 datasets.
* changed process.R in traits.build such that `excluded_observations` looks for `original_name` not the standardised name, and changed those accordingly
* found a few commas delimiting values, where there should have been spaces (in basis_of_record)
* removed duplicate substitutions in ANBG_2019

In the process of removing duplicate taxonomic_updates, kept rebuilding taxon_list & checking taxonomic_updates tibble. Taxon_list changed minimally and in expected ways.

At the end:
* all original names in taxonomic_updates now match to a taxon name (first time ever!)
* `combined_table` had same number of rows as `austraits$traits` (i.e. no duplication)
* all tests pass - this also means all datasets pivot
* looked carefully at alignments in taxa table and they look good - various filtering, against different `taxon_rank`, `taxonomic_dataset` values
---------

Co-authored-by: yangsophieee <[email protected]>

data/ABRS_1981/metadata.yml

@@ -28,7 +28,7 @@ dataset:
             units = ifelse(units %in% c("m", "cm"), "mm", units),
             value = as.character(value)
       );
-      
+
     data_categorical_other <- data %>%
       filter(is.na(units) & !(trait %in% c("longevity", "flowering time start", "flowering time end"))
             ) %>%
@@ -44,14 +44,14 @@ dataset:
         left_join(filter(data, trait == "flowering time start") %>%
                     select(species_name, i), by = "species_name");
 
-    data_longevity <- data %>% 
+    data_longevity <- data %>%
       filter( !is.na(value) & trait == "longevity") %>%
       mutate(trait = "leaf_phenology",
               value = ifelse(value %in% c("EP", "E", "EAP", "EPB", "EB", "EAB", "EA"), "evergreen", value),
               value = ifelse(value %in% c("DP", "D", "DPB"), "deciduous", value)) %>%
       filter(value %in% c("evergreen", "deciduous"));
-    
-    data_lifehistory <- data %>%   
+
+    data_lifehistory <- data %>%
       filter( !is.na(value) & trait == "longevity" &
               value %in% c("EP", "P", "DP", "EDP", "A", "EA", "EB", "B","AB", "EAB", "AP", "EAP", "EPB", "DPB", "PB")) %>%
         mutate(trait = "life_history", value = ifelse(value %in% c("EP", "P", "DP", "EDP"), "perennial", value),
@@ -70,7 +70,7 @@ dataset:
           value == "HA" ~ "aquatic")
       );
 
-    bind_rows(data_numeric, data_categorical_other, data_flowering, 
+    bind_rows(data_numeric, data_categorical_other, data_flowering,
       data_longevity, data_lifehistory, data_substrate) %>%
       arrange(i) %>%
       select(-i) %>%
@@ -87,7 +87,7 @@ dataset:
       group_by(species_name, trait) %>%
         distinct(value, .keep_all = TRUE) %>%
       ungroup()
-  ' 
+  '
   collection_date: unknown/2015
   taxon_name: species_name
   trait_name: trait
@@ -517,8 +517,5 @@ taxonomic_updates:
   reason: match_14. Automatic alignment with species-level canonical name in APC accepted
     when notes are ignored (2022-11-12)
   taxonomic_resolution: species
-exclude_observations:
-- variable: taxon_name
-  find: Platanus x hispanica 'Acerifolia'
-  reason: excluding cultivars
+exclude_observations: .na
 questions: .na

data/ABRS_2022/data.csv

@@ -12250,7 +12250,7 @@ Opuntia,Opuntia microdasys," spreading shrub to 1 m high, often somewhat creepin
 Opuntia,Opuntia polyacantha var. hystricina,  ,perennial,inferred_from_family,,,shrub,inferred_from_species,,,,,,,woody,
 Opuntia,Opuntia," succulent, erect or spreading shrubs or trees, sometimes creeping, often many-branched from the base; ",perennial,inferred_from_family,,,shrub tree,shrubs trees,,,,,erect creeping spreading,erect creeping spreading,woody,
 Opuntia,Opuntia leucotricha," erect shrub 3-4 m high, to 4 m diam., trunk well-developed, to 1 m high and 15-30 cm wide in older plants. ",perennial,inferred_from_family,,,shrub,shrub,,,,,erect,erect,woody,
-Opuntia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,  ,perennial,inferred_from_family,,,herb,inferred_from_life_history,,,,,,,herbaceous,
+Opuntia,Opuntia polyacantha var. erinacea (Engelm . & J.M.Bigelow) B.D.Parfitt,  ,perennial,inferred_from_family,,,herb,inferred_from_life_history,,,,,,,herbaceous,
 Opuntia,Opuntia tomentosa," erect shrub or treelike, to 8 m high. ",perennial,inferred_from_family,,,shrub palmoid,shrub treelike,,,,,erect,erect,woody,
 Opuntia,Opuntia ficus-indica," erect shrub to 5 m high and 8 m wide, older plants with well-developed trunk to 1.2 m high and 1 m diam. ",perennial,inferred_from_family,,,shrub,shrub,,,,,erect,erect,woody,
 Oraniopsis,Oraniopsis," solitary, erect, dioecious palm. ",perennial,inferred_from_growth_form,,,palmoid,palm,,,dioecious,dioecious,erect,erect,woody,inferred_from_growth_form

data/ABRS_2022/metadata.yml

@@ -24,9 +24,9 @@ dataset:
     data %>%
       filter(str_detect(taxon_name, " ")) %>%
       mutate(
-        woodiness_a = stringr::str_replace(woodiness_a, "soft_wood","semi_woody")
+        woodiness_a = stringr::str_replace(woodiness_a, "soft_wood", "semi_woody")
       )
-  '
+    '
   collection_date: unknown/2022
   taxon_name: taxon_name
   description: Plant growth form data extracted from the Flora of Australia online
@@ -139,10 +139,6 @@ taxonomic_updates:
   replace: Aristida ramosa x Aristida vagans
   reason: Manual alignment with canonical species name in APC (Elizabeth Wenk, 2022-11-22)
   taxonomic_resolution: species
-- find: Blechnum pennamarina subsp. alpina
-  replace: Blechnum penna-marina subsp. alpina
-  reason: Manual alignment with canonical  species name in APC (Elizabeth Wenk, 2022-11-21)
-  taxonomic_resolution: subspecies
 - find: Brassica juncea
   replace: Brassica x juncea
   reason: match_14. Automatic alignment with species-level canonical name in APC accepted
@@ -173,10 +169,6 @@ taxonomic_updates:
   reason: match_05. Automatic alignment with scientific name in APC accepted list
     (2022-11-22)
   taxonomic_resolution: species
-- find: Crepidomanes aphleboides
-  replace: Crepidomanes aphlebioides
-  reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21)
-  taxonomic_resolution: species
 - find: Dactyliophora novaeguineae
   replace: Dactyliophora novae-guineae
   reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22)
@@ -327,10 +319,6 @@ taxonomic_updates:
   replace: Lindsaea terrae-reginae
   reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21)
   taxonomic_resolution: species
-- find: Marsdenia hemi-ptera
-  replace: Marsdenia hemiptera
-  reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-21)
-  taxonomic_resolution: species
 - find: Melicytus novae-zelandae subsp. centurionis
   replace: Melicytus novae-zelandiae subsp. centurionis
   reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22)
@@ -339,15 +327,6 @@ taxonomic_updates:
   replace: Mesua sp. (Boonjee)
   reason: match_08. Automatic alignment with synonymous name in APNI (2022-11-22)
   taxonomic_resolution: species
-- find: Monimiaceae Q3 (Mt. Hemmant)
-  replace: Monimiaceae Q3 (Mt. Hemmant) sp. Q1 (Mt. Hemmant)
-  reason: match_12. Automatic alignment with infraspecific canonical name in APC known
-    names when notes are ignored (2022-11-21)
-  taxonomic_resolution: species
-- find: Myrsine maccomishii
-  replace: Myrsine mccomishii
-  reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-21)
-  taxonomic_resolution: species
 - find: Neoalsomitra sp. A ( B.Hyland 10923)
   replace: Neoalsomitra sp. A (B.Hyland 10923)
   reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-22)
@@ -356,12 +335,7 @@ taxonomic_updates:
   replace: Oligochaetochilus macrocalymma
   reason: match_07_fuzzy. Fuzzy alignment with known canonical name in APC (2022-11-22)
   taxonomic_resolution: species
-- find: Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt
-  replace: Opuntia polyacantha
-  reason: match_14. Automatic alignment with species-level canonical name in APC accepted
-    when notes are ignored (2022-11-22)
-  taxonomic_resolution: species
-- find: Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt
+- find: Opuntia polyacantha var. erinacea (Engelm . & J.M.Bigelow) B.D.Parfitt
   replace: Opuntia polyacantha
   reason: Exact match of the first two words of the taxon name to an APC-accepted
     canonical name (2023-11-02)
@@ -401,10 +375,6 @@ taxonomic_updates:
   replace: Pterostylis x ralphcranei
   reason: match_07_fuzzy. Fuzzy alignment with accepted canonical name in APC (2022-11-22)
   taxonomic_resolution: species
-- find: Rubiaceae Gen. Nov. sp. (Shute Harbour DAH Q811)
-  replace: Gynochthodes retropila
-  reason: Manual alignment with APC accepted name (E. Wenk, 2023-06-16)
-  taxonomic_resolution: species
 - find: Salvinia molesta
   replace: Salvinia x molesta
   reason: match_14. Automatic alignment with species-level canonical name in APC accepted
@@ -481,21 +451,6 @@ taxonomic_updates:
   reason: match_14. Automatic alignment with species-level canonical name in APC accepted
     when notes are ignored (2022-11-22)
   taxonomic_resolution: species
-- find: x Cynochloris macivorii
-  replace: x Cynochloris macivorii
-  reason: match_06. Automatic alignment with synonymous term among accepted canonical
-    names in APC (2022-11-22)
-  taxonomic_resolution: species
-- find: x Cynochloris reynoldensis
-  replace: x Cynochloris reynoldensis
-  reason: match_06. Automatic alignment with synonymous term among accepted canonical
-    names in APC (2022-11-22)
-  taxonomic_resolution: species
-- find: x Glossadenia x tutelata
-  replace: Glossodia x tutelata
-  reason: match_06. Automatic alignment with synonymous term among known canonical
-    names APC (2022-11-21)
-  taxonomic_resolution: species
 - find: xCyanthera glossodioides
   replace: x Cyanthera glossodioides
   reason: Manual alignment with canonical species name in APC (E. Wenk, 2023-11-02)
@@ -505,28 +460,11 @@ taxonomic_updates:
   reason: Manual alignment with canonical species name in APC (E. Wenk, 2023-11-02)
   taxonomic_resolution: species
 exclude_observations:
-- variable: taxon_name
-  find: Acacioides Group, Adenotricha Group, Aethiopicum Group, Agrifolia Group, Aspera
-    Group, Bulbiferum Group, Buxifolia Group, Capitisyork Group, Ceratophylla Group,
-    Cirsiifolia Group, Clavata Group, Cristata Group, Cucullata Group, Eriantha Group,
-    Eryngioides Group, Goodii Group, Hakeoides Group, Heliosperma Group, Hilliana
-    Group, Huegelii Group, Incrassata Group, Integrifolia Group, Linearifolia Group,
-    Linearis Group, Lissocarpha Group, Longistyla Group, Lorea Group, Marriottii Group,
-    Megalosperma Group, Microcarpa Group, Multilineata Group, Nodosa Group, Obliqua
-    Group, Obtusatum Group, Oncogyne Group, Parvum Group, Petiolaris Group, Petrophiloides
-    Group, Polyodon Group, Pteridifolia Group, Pythara Group, Quercifolia Group, Robusta
-    Group, Rudis Group, Ruscifolia Group, Salicifolia Group, Shiressii Group, Simplicifrons
-    Group, Strumosa Group, Thelemanniana Group, Trifida Group, Trifurcata Group, Triloba
-    Group, Trineura Group, Ulicina Group, Undulata Group, Wickhamii Group
-  reason: not species in APC/APNI
-- variable: taxon_name
-  find: Platanus xhispanica 'Acerifolia'
-  reason: excluding cultivars
 - variable: taxon_name
   find: Asplenium lobulatum Mett. ex Kuhn, Cerastium pyrenaicum J.Gay, Passiflora miniata, Quercus ilex,
     Selenicereus undatus, Silene gracilis DC.
   reason: excluding non-native, non-naturalised species
 - variable: taxon_name
-  find: Anacolosa sp., x Cynochloris, Sphaerocionium
+  find: Anacolosa sp., x Cynochloris
   reason: excluding genera
 questions: .na

data/ABRS_2023/data.csv

@@ -8878,7 +8878,7 @@ Flora_of_Australia,Opuntia microdasys,fruit_dehiscence,,indehiscent,inferred_fro
 Flora_of_Australia,Opuntia monacantha,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
 Flora_of_Australia,Opuntia polyacantha,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
 Flora_of_Australia,Opuntia polyacantha var. hystricina,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
-Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
+Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
 Flora_of_Australia,Opuntia puberula,fruit_dehiscence,,dehiscent,splitting,,mode
 Flora_of_Australia,Opuntia robusta,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
 Flora_of_Australia,Opuntia schickendantzii,fruit_dehiscence,,indehiscent,inferred_from_genus,,mode
@@ -43769,7 +43769,7 @@ Flora_of_Australia,Opuntia microdasys,leaf_arrangement,,spiral,inferred_from_fam
 Flora_of_Australia,Opuntia monacantha,leaf_arrangement,,spiral,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha,leaf_arrangement,,spiral,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha var. hystricina,leaf_arrangement,,spiral,inferred_from_family,,mode
-Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_arrangement,,spiral,inferred_from_family,,mode
+Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_arrangement,,spiral,inferred_from_family,,mode
 Flora_of_Australia,Opuntia puberula,leaf_arrangement,,spiral,inferred_from_family,,mode
 Flora_of_Australia,Opuntia robusta,leaf_arrangement,,spiral,inferred_from_family,,mode
 Flora_of_Australia,Opuntia schickendantzii,leaf_arrangement,,spiral,inferred_from_family,,mode
@@ -54404,7 +54404,7 @@ Flora_of_Australia,Opuntia microdasys,leaf_compoundness,,simple,inferred_from_fa
 Flora_of_Australia,Opuntia monacantha,leaf_compoundness,,simple,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha,leaf_compoundness,,simple,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha var. hystricina,leaf_compoundness,,simple,inferred_from_family,,mode
-Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_compoundness,,simple,inferred_from_family,,mode
+Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_compoundness,,simple,inferred_from_family,,mode
 Flora_of_Australia,Opuntia puberula,leaf_compoundness,,simple,inferred_from_family,,mode
 Flora_of_Australia,Opuntia robusta,leaf_compoundness,,simple,inferred_from_family,,mode
 Flora_of_Australia,Opuntia schickendantzii,leaf_compoundness,,simple,inferred_from_family,,mode
@@ -89520,7 +89520,7 @@ Flora_of_Australia,Opuntia microdasys,leaf_margin,,entire,inferred_from_family,,
 Flora_of_Australia,Opuntia monacantha,leaf_margin,,entire,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha,leaf_margin,,entire,inferred_from_family,,mode
 Flora_of_Australia,Opuntia polyacantha var. hystricina,leaf_margin,,entire,inferred_from_family,,mode
-Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_margin,,entire,inferred_from_family,,mode
+Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,leaf_margin,,entire,inferred_from_family,,mode
 Flora_of_Australia,Opuntia puberula,leaf_margin,,entire,inferred_from_family,,mode
 Flora_of_Australia,Opuntia robusta,leaf_margin,,entire,inferred_from_family,,mode
 Flora_of_Australia,Opuntia schickendantzii,leaf_margin,,entire,inferred_from_family,,mode
@@ -189437,7 +189437,7 @@ Flora_of_Australia,Opuntia microdasys,plant_photosynthetic_organ,,cladode,manual
 Flora_of_Australia,Opuntia monacantha,plant_photosynthetic_organ,,cladode,manual,,mode
 Flora_of_Australia,Opuntia polyacantha,plant_photosynthetic_organ,,cladode,manual,,mode
 Flora_of_Australia,Opuntia polyacantha var. hystricina,plant_photosynthetic_organ,,cladode,manual,,mode
-Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,plant_photosynthetic_organ,,cladode,manual,,mode
+Flora_of_Australia,Opuntia polyacantha var. erinacea (Engelm. & J.M.Bigelow) B.D.Parfitt,plant_photosynthetic_organ,,cladode,manual,,mode
 Flora_of_Australia,Opuntia puberula,plant_photosynthetic_organ,,cladode,manual,,mode
 Flora_of_Australia,Opuntia robusta,plant_photosynthetic_organ,,cladode,manual,,mode
 Flora_of_Australia,Opuntia schickendantzii,plant_photosynthetic_organ,,cladode,manual,,mode