Closed mjwestgate closed 1 year ago
There was lists functionality was in ALA4R. Might be worth revisiting that.
The lists that are "authoritative" are indeed indexed in biocache. I would like to clean them up because there are a lot of historical and possibly nonsensical artefacts in there. https://lists.ala.org.au/public/speciesLists?sort=itemsCount&order=desc&isAuthoritative=eq%3Atrue&max=100&q=
Thanks for this Peggy, that's really helpful! Looking at the urls for this I note that each list is identified by an id, e.g. for the EPBC list:
https://lists.ala.org.au/speciesListItem/list/dr656
...from which point we can click on 'view occurrences' to go to:
https://biocache.ala.org.au/occurrences/search?q=species_list_uid%3Adr651#tab_mapView
...which suggests that the following should work:
galah_config(run_checks = FALSE) # needed as `species_list_uid` not valid according to `show_all_fields`
galah_call() |>
galah_filter(species_list_uid == dr656) |>
atlas_counts()
# A tibble: 1 × 1
count
<int>
1 1614661
This count matches that given by the biocache. Another cool option is to subset to particular taxa, e.g. to get a list of all EPBC-listed mammals:
galah_call() |>
galah_identify("Mammalia") |>
galah_filter(species_list_uid == dr656) |>
atlas_species()
I'm currently writing new search
functions that would allow users to lookup list identifiers (see #132), so the only point of ambiguity is how to tell users that the field name species_list_uid
works. This is similar to the problem we have with using taxonConceptId
for advanced taxonomic queries, so perhaps we just need a vignette or similar.
Addendum to the above; in the dev
branch you can now find the list identifier using:
search_datasets("Australia wide : Conservation Status : EPBC")
# A tibble: 1 × 3
name uri uid
<chr> <chr> <chr>
1 Australia wide : Conservation Status : EPBC https://collections.ala.org.au/ws/dataResource/dr656 dr656
Although this works, search_datasets
is quite messy as it incorporates species lists and occurrence datasets. A neater option might be to add show_all_lists
and search_lists
using the API here: https://lists.ala.org.au/ws/speciesList
lists are now able to be displayed and searched as of v1.5.0
A useful feature would be to filter counts or occurrences by species threatened status, or other some set of (potentially user-defined) species-level attributes or traits. One toolset that could support this functionality is the 'lists' tool (https://lists.ala.org.au/). Apparently some lists are designated as 'authoritative' and indexed in the biocache; but they don't appear in
show_all_fields()
to my knowledge. Working out how to pass something like:...would be really helpful.