Taxonomic filtering

Taxonomic complexity can confound the process of searching, filtering, and downloading records using galah, but there are a few ways to ensure records are not missed.

library(galah)
library(dplyr)

galah_config(email = "your_email_here", verbose = FALSE)

search_taxa()

search_taxa() enables users to look up taxonomic names before downloading data, which allows for disambiguating homonyms and checking that the search term matches the taxon name in the ALA . search_taxa() returns the scientific name, authorship, rank, and full classification for the taxon matched to the provided search term.

search_taxa("Petroica boodang") |> gt::gt()

search_term	scientific_name	scientific_name_authorship	taxon_concept_id	rank	match_type	kingdom	phylum	class	order	family	genus	species	vernacular_name	issues
Petroica boodang	Petroica (Petroica) boodang	(Lesson, 1838)	https://biodiversity.org.au/afd/taxa/a3e5376b-f9e6-4bdf-adae-1e7add9f5c29	species	exactMatch	Animalia	Chordata	Aves	Passeriformes	Petroicidae	Petroica	Petroica boodang	Scarlet Robin	noIssue

# Muscicapa chrysoptera is a synonym for the Flame Robin, Petroica phoenicea
# Guniibuu is the Yuwaalaraay Indigenous name for the Red-Capped Robin, Petroica goodenovii
search_taxa("Muscicapa chrysoptera", "Guniibuu") |> gt::gt()

search_term	scientific_name	scientific_name_authorship	taxon_concept_id	rank	match_type	kingdom	phylum	class	order	family	genus	species	vernacular_name	issues
Muscicapa chrysoptera	Petroica (Littlera) phoenicea	Gould, 1837	https://biodiversity.org.au/afd/taxa/fe74e658-4848-437a-a23d-f1001a198552	species	exactMatch	Animalia	Chordata	Aves	Passeriformes	Petroicidae	Petroica	Petroica phoenicea	Flame Robin	noIssue

Where homonyms exist, search_taxa() will prompt users to clarify the search term by providing one or more taxonomic ranks in a tibble. This example differentiates among the genus Morganella in three kingdoms:

search_taxa("Morganella") |> gt::gt()

## Warning: Search returned multiple taxa due to a homonym issue.
## ℹ Please provide another rank in your search to clarify taxa.
## ℹ Use a `tibble` to clarify taxa, see `?search_taxa`.
## ✖ Homonym issue with "Morganella".

search_term	issues
Morganella	homonym

search_taxa(tibble(kingdom = "Fungi", genus = "Morganella")) |> gt::gt()

search_term	scientific_name	scientific_name_authorship	taxon_concept_id	rank	match_type	kingdom	phylum	class	order	family	genus	issues
Fungi_Morganella	Morganella	Zeller	https://id.biodiversity.org.au/node/fungi/60091999	genus	exactMatch	Fungi	Basidiomycota	Agaricomycetes	Agaricales	Agaricaceae	Morganella	noIssue

identify()

identify() is similar to search_taxa(), except that it can be used within a piped workflow to retrieve counts, species, or records e.g.

galah_call() |>
  identify("Petroica boodang") |>
  count() |>
  collect()

## # A tibble: 1 × 1
##    count
##    <int>
## 1 119417

galah_call(type = "species") |>
  identify("Muscicapa chrysoptera", "Guniibuu") |>
  collect() |> 
  gt::gt()

taxon_concept_id	species_name	scientific_name_authorship	taxon_rank	kingdom	phylum	class	order	family	genus	vernacular_name
https://biodiversity.org.au/afd/taxa/10dbd908-00f3-4ec2-9a9c-a2fd4782eaf1	Petroica (Petroica) goodenovii	(Vigors & Horsfield, 1827)	species	Animalia	Chordata	Aves	Passeriformes	Petroicidae	Petroica	Red-capped Robin
https://biodiversity.org.au/afd/taxa/fe74e658-4848-437a-a23d-f1001a198552	Petroica (Littlera) phoenicea	Gould, 1837	species	Animalia	Chordata	Aves	Passeriformes	Petroicidae	Petroica	Flame Robin

galah_call() |>
  identify(tibble(kingdom = "Fungi", genus = "Morganella")) |>
  collect() |>
  head() |> 
  gt::gt()

recordID	scientificName	taxonConceptID	decimalLatitude	decimalLongitude	eventDate	occurrenceStatus	dataResourceName
001ec30d-3376-4f63-ba32-b48bc3dd137d	Morganella purpurascens	https://id.biodiversity.org.au/node/fungi/60092001	-33.66218	150.2708	2021-04-10	PRESENT	NSW BioNet Atlas
02ba39cd-8077-4868-a0ff-e50765089788	Morganella compacta	NZOR-6-128055	-41.28082	174.7943	NA	PRESENT	New Zealand Virtual Herbarium
0422009d-c1f0-4e2e-8d29-e88df6de2049	Morganella compacta	NZOR-6-128055	-36.44838	174.6714	NA	PRESENT	New Zealand Virtual Herbarium
04aeeb8d-0538-477c-aff1-29574eafa349	Morganella compacta	NZOR-6-128055	-36.84225	174.4695	1993-06-19	PRESENT	New Zealand Virtual Herbarium
092b6f3e-ef27-4cbf-bb28-b172c1b200c5	Morganella purpurascens	https://id.biodiversity.org.au/node/fungi/60092001	-26.77940	152.8803	2009-02-19	PRESENT	National Herbarium of Victoria (MEL) AVH data
0be95d59-29a4-4475-8586-a497cac607f7	Morganella compacta	NZOR-6-128055	-43.15002	171.7305	NA	PRESENT	New Zealand Virtual Herbarium

filter()

filter() subsets records by searching for exact matches to an expression, and may also be used for taxonomic filtering e.g.

galah_call() |>
  filter(species == "Petroica boodang") |>
  count() |>
  collect()

## # A tibble: 1 × 1
##    count
##    <int>
## 1 119417

Alternatively, we could use filter() after first checking taxonomy with search_taxa(), in place of identify():

robins <- search_taxa("Muscicapa chrysoptera", "Guniibuu") 

galah_call() |>
  filter(taxonConceptID == robins$taxon_concept_id) |>
  count() |>
  collect()

## # A tibble: 1 × 1
##   count
##   <int>
## 1 81570

It is also possible to specify several species at once using filter():

aus_petroica <- c("Petroica boodang", "Petroica goodenovii", 
                  "Petroica phoenicea", "Petroica rosea",
                  "Petroica rodinogaster", "Petroica multicolor")

galah_call() |>
  filter(species %in% aus_petroica) |>
  group_by(species, vernacularName) |>
  count() |> 
  collect() |>
  gt::gt()

species	vernacularName	count
Petroica boodang	Scarlet Robin	115735
Petroica boodang	Eastern Scarlet Robin	3496
Petroica boodang	South-western Scarlet Robin	160
Petroica boodang	Tasmanian Scarlet Robin	26
Petroica goodenovii	Red-capped Robin	110284
Petroica phoenicea	Flame Robin	81570
Petroica rosea	Rose Robin	52414
Petroica rodinogaster	Pink Robin	13417
Petroica rodinogaster	Mainland Pink Robin	60
Petroica rodinogaster	Tasmanian Pink Robin	14
Petroica multicolor	Pacific Robin	6699

This can be useful in searching for paraphyletic or polyphyletic groups, which cannot be done using identify(). For example, to get counts of non-chordates:

galah_call() |>
  filter(kingdom == "Animalia", phylum != "Chordata") |>
  group_by(phylum) |>
  count() |>
  collect() |>
  head() |> 
  gt::gt()

phylum	count
Arthropoda	8567585
Mollusca	1378754
Annelida	316619
Cnidaria	273227
Echinodermata	196016
Porifera	130249

filter(), identify(), and taxonomic ranks

Deciding between using filter() and identify() in a query comes down to how a record has been classified, and whether or not you have the correct unique name and classification of the taxa of interest.

The ALA has fields for the primary taxonomic ranks (kingdom, phylum, class, order, family, genus, species) and some secondary ranks (e.g. subfamily, subgenus), all of which may be used with galah_filter() and galah_identify(). Additionally, there is a field named scientificName, which refers to the lowest taxonomic rank to which a record has been identified e.g.

galah_call() |>
  identify(tibble(genus = "Pitta")) |>
  group_by(scientificName, taxonRank) |>
  count() |>
  collect() |>
  filter(!is.na(scientificName)) |>
  gt::gt()

scientificName	taxonRank	count
Pitta (Pitta) versicolor	species	26085
Pitta (Pitta) iris	species	5722
Pitta (Erythropitta)	subgenus	728
Pitta (Pitta) versicolor versicolor	subspecies	310
Pitta (Erythropitta) erythrogaster	species	190
Pitta (Pitta) iris iris	subspecies	76
Pitta	genus	74
Pitta (Pitta) versicolor intermedia	subspecies	42
Pitta (Pitta) versicolor simillima	subspecies	38
Pitta (Pitta) iris johnstoneiana	subspecies	27
Pitta (Erythropitta) erythrogaster digglesi	subspecies	21

If, for instance, you have the correct species or subspecies name, then searching for matches against the species and subspecies fields, respectively, will provide more precise results. This is because the field scientificName may include subgenera. If you’ve used search_taxa() to get the ALA-matched name of a taxon and only want records identified to a particular level of classification, searching for matches against scientificName is recommended.

Paraphyletic or polyphyletic groups may contain taxa identified to different taxonomic levels. In this case, it is simpler to use search_taxa() and identify() rather than filter(). In the example below, search_taxa() matches terms to one genus, three species, and two subspecies. This can then be used in a piped workflow with identify().

tas_endemic <- c("Sarcophilus", # Tasmanian Devil
                 "Bettongia gaimardi", # Tasmanian Bettong
                 "Melanodryas vittata", # Dusky Robin
                 "Platycercus caledonicus",# Green Rosella
                 "Aquila audax fleayi", # Tasmanian Wedge-Tailed Eagle
                 "Tyto novaehollandiae castanops") # Tasmanian Masked Owl

search_taxa(tas_endemic) |> gt::gt()

search_term	scientific_name	scientific_name_authorship	taxon_concept_id	rank	match_type	kingdom	phylum	class	order	family	genus	species	vernacular_name	issues
Sarcophilus	Sarcophilus	Cuvier, 1837	https://biodiversity.org.au/afd/taxa/06455b77-7d50-4ec7-9122-8ab48cfb0c1c	genus	exactMatch	Animalia	Chordata	Mammalia	Dasyuromorphia	Dasyuridae	Sarcophilus	NA	NA	noIssue
Bettongia gaimardi	Bettongia gaimardi	(Desmarest, 1822)	https://biodiversity.org.au/afd/taxa/8f7da937-6338-4c39-8b11-4f83807afe11	species	exactMatch	Animalia	Chordata	Mammalia	Diprotodontia	Potoroidae	Bettongia	Bettongia gaimardi	Tasmanian Bettong	noIssue
Melanodryas vittata	Melanodryas (Amaurodryas) vittata	(Quoy & Gaimard, 1830)	https://biodiversity.org.au/afd/taxa/0f04889f-5489-4369-a545-8a041fba9f6d	species	exactMatch	Animalia	Chordata	Aves	Passeriformes	Petroicidae	Melanodryas	Melanodryas vittata	Dusky Robin	noIssue
Platycercus caledonicus	Platycercus (Platycercus) caledonicus	(Gmelin, 1788)	https://biodiversity.org.au/afd/taxa/c6e478fe-f199-463f-8576-a77108fd73e2	species	exactMatch	Animalia	Chordata	Aves	Psittaciformes	Psittacidae	Platycercus	Platycercus caledonicus	Green Rosella	noIssue
Aquila audax fleayi	Aquila (Uroaetus) audax fleayi	Condon & Amadon, 1954	https://biodiversity.org.au/afd/taxa/ac93f7f0-0686-4589-801a-5832378cb7c1	subspecies	exactMatch	Animalia	Chordata	Aves	Accipitriformes	Accipitridae	Aquila	Aquila audax	Tasmanian Wedge-tailed Eagle	noIssue
Tyto novaehollandiae castanops	Tyto novaehollandiae castanops	(Gould, 1837)	https://biodiversity.org.au/afd/taxa/2c30d58b-572b-4dab-8644-b222c28eb0ec	subspecies	exactMatch	Animalia	Chordata	Aves	Strigiformes	Tytonidae	Tyto	Tyto novaehollandiae	Tasmanian Masked Owl	noIssue

galah_call() |>
  identify(tas_endemic) |>
  group_by(scientificName) |>
  count() |>
  collect() |>
  arrange(scientificName) |>
  gt::gt()

scientificName	count
Aquila (Uroaetus) audax fleayi	4935
Bettongia gaimardi	1941
Bettongia gaimardi cuniculus	41
Bettongia gaimardi gaimardi	9
Melanodryas (Amaurodryas) vittata	14131
Melanodryas (Amaurodryas) vittata kingi	15
Melanodryas (Amaurodryas) vittata vittata	39
Platycercus (Platycercus) caledonicus	43463
Platycercus (Platycercus) caledonicus brownii	24
Platycercus (Platycercus) caledonicus caledonicus	33
Sarcophilus	3
Sarcophilus harrisii	36302
Tyto novaehollandiae castanops	63

Callum Waite & Shandiya Balasubramaniam

2023-10-13

search_taxa()

identify()

filter()

filter(), identify(), and taxonomic ranks