Make it clearer how lists are used in `galah_filter()`
daxkellie opened this issue · 1 comments
daxkellie commented
At the moment, it is opaque how to use lists in a galah query. Despite the lists IDs being held in the field dataResourceUid, you need to supply the list id to galah_filter() with the field species_list_uid.
library(galah)
# Search returns IDs under field `dataResourceUid`
search_all(lists, "New South Wales")
#> # A tibble: 2 × 19
#> dataResourceUid listName listType dateCreated lastUpdated lastUploaded
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 dr650 New South Wales… CONSERV… 2015-04-04… 2023-06-07… 2023-06-07T…
#> 2 dr487 New South Wales… SENSITI… 2013-06-20… 2023-08-30… 2023-08-30T…
#> # ℹ 13 more variables: lastMatched <chr>, username <chr>, itemCount <int>,
#> # isAuthoritative <lgl>, isInvasive <lgl>, isThreatened <lgl>, wkt <chr>,
#> # region <chr>, category <chr>, generalisation <chr>, authority <chr>,
#> # sdsType <chr>, looseSearch <lgl>
# To filter by list in a query, supply list id to field `species_list_uid`
galah_config(email = "your-email-here")
galah_call() |>
filter(cl10923 == "YASS VALLEY COUNCIL",
year == 2023,
species_list_uid == dr650) |>
atlas_species()
#> # A tibble: 17 × 10
#> kingdom phylum class order family genus species author species_guid
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Animalia Chordata Aves Psit… Cacat… Call… Calloc… (Gran… https://bio…
#> 2 Animalia Chordata Aves Pass… Petro… Petr… Petroi… (Less… https://bio…
#> 3 Animalia Chordata Aves Pass… Estri… Stag… Stagon… (Shaw… https://bio…
#> 4 Animalia Chordata Aves Pass… Petro… Petr… Petroi… Gould… https://bio…
#> 5 Animalia Chordata Aves Pass… Neosi… Daph… Daphoe… (Lath… https://bio…
#> 6 Animalia Chordata Aves Acci… Accip… Hier… Hieraa… (Goul… https://bio…
#> 7 Animalia Chordata Aves Stri… Strig… Ninox Ninox … (Goul… https://bio…
#> 8 Plantae Charophyta Equisetop… Aste… Aster… Ammo… Ammobi… Benth. https://id.…
#> 9 Animalia Chordata Aves Psit… Psitt… Poly… Polyte… (Desm… https://bio…
#> 10 Animalia Chordata Aves Pass… Pachy… Pach… Pachyc… Vigor… https://bio…
#> 11 Animalia Chordata Aves Pass… Melip… Epth… Epthia… (Jard… https://bio…
#> 12 Animalia Chordata Amphibia Anura Hylid… Lito… Litori… (Dumé… https://bio…
#> 13 Animalia Arthropoda Insecta Lepi… Castn… Syne… Synemo… Walke… https://bio…
#> 14 Animalia Chordata Aves Acci… Accip… Hali… Haliae… (Gmel… https://bio…
#> 15 Animalia Chordata Mammalia Dipr… Phasc… Phas… Phasco… (Gold… https://bio…
#> 16 Plantae Charophyta Equisetop… Aste… Aster… Leuc… Leucoc… (A.Cu… https://id.…
#> 17 Plantae Charophyta Equisetop… Myrt… Myrta… Euca… Eucaly… Siebe… https://id.…
#> # ℹ 1 more variable: vernacular_name <chr>Created on 2023-11-27 with reprex v2.0.2
Is it possible to either supply a message when using search_all(lists) and show_all(lists) of how to supply this information to galah_filter()? For example:
Supply a list to `galah_filter()` by using field `species_list_uid`
e.g., `galah_filter(species_list_uid == dr650)`
Alternatively, would it be bad to replace the column name dataResourceUid to species_list_uid in search_all(lists)/show_all(lists) output?
daxkellie commented
Fixed as of v2.0.1 & commit d0f1931, search_all(lists) now outputs species_list_uid as the list ID column name
library(galah)
# list IDs are now under `species_list_uid` column
search_all(lists, "New South Wales") |> select(1:3)
#> # A tibble: 2 × 3
#> species_list_uid listName listType
#> <chr> <chr> <chr>
#> 1 dr650 New South Wales : Conservation Status CONSERVATION_LIST
#> 2 dr487 New South Wales Sensitive Species List SENSITIVE_LIST
# This matches the field name used by `filter()`
galah_config(email = "your-email-here")
galah_call() |>
filter(cl10923 == "YASS VALLEY COUNCIL",
year == 2023,
species_list_uid == dr650) |> # `filter()` also uses `species_list_uid`
atlas_species()
#> # A tibble: 21 × 10
#> species_guid species author kingdom phylum class order family genus
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 https://biodiversity.… Calloc… (Gran… Animal… Chord… Aves Psit… Cacat… Call…
#> 2 https://biodiversity.… Petroi… (Less… Animal… Chord… Aves Pass… Petro… Petr…
#> 3 https://biodiversity.… Stagon… (Shaw… Animal… Chord… Aves Pass… Estri… Stag…
#> 4 https://biodiversity.… Petroi… Gould… Animal… Chord… Aves Pass… Petro… Petr…
#> 5 https://biodiversity.… Daphoe… (Lath… Animal… Chord… Aves Pass… Neosi… Daph…
#> 6 https://biodiversity.… Hieraa… (Goul… Animal… Chord… Aves Acci… Accip… Hier…
#> 7 https://id.biodiversi… Ammobi… Benth. Plantae Charo… Equi… Aste… Aster… Ammo…
#> 8 https://biodiversity.… Ninox … (Goul… Animal… Chord… Aves Stri… Strig… Ninox
#> 9 https://id.biodiversi… Eucaly… Siebe… Plantae Charo… Equi… Myrt… Myrta… Euca…
#> 10 https://biodiversity.… Polyte… (Desm… Animal… Chord… Aves Psit… Psitt… Poly…
#> # ℹ 11 more rows
#> # ℹ 1 more variable: vernacular_name <chr>Created on 2024-02-16 with reprex v2.0.2