show_all() & search_all()As of galah 1.5.0, there are two simplified functions to look up
information: show_all() and search_all().
These are individual functions that are able to return all types of information in one place, rather than using specific sub-functions to look up information.
For example, to show all available Living Atlases supported:
show_all(atlases)## # A tibble: 10 × 4
## atlas institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Australia Atlas of Living Australia ALA https://www.ala.org.au
## 2 Austria Biodiversitäts-Atlas Österreich BAO https://biodiversityatlas.at
## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr https://sibbr.gov.br
## 4 Estonia eElurikkus <NA> https://elurikkus.ee
## 5 France Inventaire National du Patrimoine Naturel INPN https://inpn.mnhn.fr
## 6 Guatemala Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt https://snib.conap.gob.gt
## 7 Portugal GBIF Portugal GBIF.pt https://www.gbif.pt
## 8 Spain GBIF Spain GBIF.es https://www.gbif.es
## 9 Sweden Swedish Biodiversity Data Infrastructure SBDI https://biodiversitydata.se
## 10 United Kingdom National Biodiversity Network NBN https://nbn.org.ukTo search for a specific available Living Atlas:
search_all(atlases, "Spain")## # A tibble: 1 × 4
## atlas institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Spain GBIF Spain GBIF.es https://www.gbif.esTo show all fields:
show_all(fields)## # A tibble: 813 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 abcdTypeStatus ABCD field in use by herbaria fiel… <NA>
## 2 acceptedNameUsage http://rs.tdwg.org/dwc/terms/acceptedNameUsage fiel… <NA>
## 3 acceptedNameUsageID http://rs.tdwg.org/dwc/terms/acceptedNameUsageID fiel… <NA>
## 4 accessRights <NA> fiel… <NA>
## 5 assertionUserId User ID of the person who has made an assertion about this record fiel… <NA>
## 6 assertions A list of all assertions (user and system supplied) for a record resulting from data quality te… fiel… <NA>
## 7 associatedMedia http://rs.tdwg.org/dwc/terms/associatedMedia fiel… <NA>
## 8 associatedOccurrences http://rs.tdwg.org/dwc/terms/associatedOccurrences fiel… <NA>
## 9 associatedOrganisms http://rs.tdwg.org/dwc/terms/associatedOrganisms fiel… <NA>
## 10 associatedReferences http://rs.tdwg.org/dwc/terms/associatedReferences fiel… <NA>
## # … with 803 more rowsAnd to search for a specific field:
search_all(fields, "australian states")## # A tibble: 2 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 cl2013 ASGS Australian States and Territories Australian Statistical Geography Standard Australian States and Territo… laye… http…
## 2 cl22 Australian States and Territories Australian States and Territories laye… http…Here is a list of information types that can be used with
show_all() and search_all():
| Information type | Description | Sub-functions |
|---|---|---|
| Configuration | ||
| atlases | Show what living atlases are available | show_all_atlases(), search_atlases() |
| apis | Show what APIs & functions are available for each atlas | show_all_apis(), search_apis() |
| reasons | Show what values are acceptable as ‘download reasons’ for a specified atlas | show_all_reasons(), search_reasons() |
| Taxonomy | ||
| taxa | Search for one or more taxonomic names | search_taxa() |
| identifiers | Take a universal identifier and return taxonomic information | search_identifiers() |
| ranks | Show valid taxonomic ranks (e.g. Kingdom, Class, Order, etc.) | show_all_ranks(), search_ranks()) |
| Filters | ||
| fields | Show fields that are stored in an atlas | show_all_fields(), search_fields() |
| assertions | Show results of data quality checks run by each atlas | show_all_assertions(), search_assertions() |
| Group filters | ||
| profiles | Show what data quality profiles are available | show_all_profiles(), search_profiles() |
| lists | Show what species lists are available | show_lists(), search_lists() |
| Data providers | ||
| providers | Show which institutions have provided data | show_all_providers(), search_providers() |
| collections | Show the specific collections within those institutions | show_all_collections(), search_collections() |
| datasets | Shows all the data groupings within those collections | show_all_datasets(), search_datasets() |
show_all_ subfunctionsWhile show_all is useful for a variety of cases, you can
still call the underlying subfunctions if you prefer. These functions -
with the prefix show_all_ - return a tibble
doing exactly that; showing all the possible values of the category
specified. These functions include:
show_all_fieldsshow_all_atlasesshow_all_ranksshow_all_profilesshow_all_reasonsshow_all_cached_filesshow_all_ functions require no arguments. Simply call
the function and it will return all accepted values as a tibble:
show_all_atlases()## # A tibble: 10 × 4
## atlas institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Australia Atlas of Living Australia ALA https://www.ala.org.au
## 2 Austria Biodiversitäts-Atlas Österreich BAO https://biodiversityatlas.at
## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr https://sibbr.gov.br
## 4 Estonia eElurikkus <NA> https://elurikkus.ee
## 5 France Inventaire National du Patrimoine Naturel INPN https://inpn.mnhn.fr
## 6 Guatemala Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt https://snib.conap.gob.gt
## 7 Portugal GBIF Portugal GBIF.pt https://www.gbif.pt
## 8 Spain GBIF Spain GBIF.es https://www.gbif.es
## 9 Sweden Swedish Biodiversity Data Infrastructure SBDI https://biodiversitydata.se
## 10 United Kingdom National Biodiversity Network NBN https://nbn.org.ukshow_all_reasons()## # A tibble: 13 × 2
## id name
## <int> <chr>
## 1 0 conservation management/planning
## 2 1 biosecurity management/planning
## 3 2 environmental assessment
## 4 3 education
## 5 4 scientific research
## 6 5 collection management
## 7 6 other
## 8 7 ecological research
## 9 8 systematic research/taxonomy
## 10 10 testing
## 11 11 citizen science
## 12 12 restoration/remediation
## 13 13 species modellingsearch_ subfunctionsThe second subset of lookup subfunctions use the search_
prefix, and differ from show_all_ in that they require a
query to work. They are used to search for detailed information that
can’t be summarised across the whole atlas, and include:
search_taxasearch_identifierssearch_fieldssearch_field_valuessearch_profile attributesSearch for a single taxon or multiple taxa by name with
search_taxa.
search_taxa("reptilia")## # A tibble: 1 × 9
## search_term scientific_name taxon_concept_id rank match…¹ kingdom phylum class issues
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 reptilia REPTILIA https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b… class exactM… Animal… Chord… Rept… noIss…
## # … with abbreviated variable name ¹match_typesearch_taxa("reptilia", "aves", "mammalia", "pisces")## # A tibble: 4 × 10
## search_term scientific_name taxon_concept_id rank match…¹ kingdom phylum class issues verna…²
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 reptilia REPTILIA https://biodiversity.org.au/afd/taxa/682e1228-5b3c-4… class exactM… Animal… Chord… Rept… noIss… <NA>
## 2 aves AVES https://biodiversity.org.au/afd/taxa/65625205-db74-4… class exactM… Animal… Chord… Aves noIss… Birds
## 3 mammalia MAMMALIA https://biodiversity.org.au/afd/taxa/e9e7db31-04df-4… class exactM… Animal… Chord… Mamm… noIss… Mammals
## 4 pisces PISCES https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4… <NA> exactM… Animal… Chord… <NA> noIss… Fishes
## # … with abbreviated variable names ¹match_type, ²vernacular_nameAlternatively, search_identifiers is the partner
function to search_taxa. If we already know a taxonomic
identifier, we can search for which taxa the identifier belongs to with
search_identifiers:
search_identifiers("urn:lsid:biodiversity.org.au:afd.taxon:682e1228-5b3c-45ff-833b-550efd40c399")## # A tibble: 1 × 8
## scientific_name taxon_concept_id rank match…¹ kingdom phylum class issues
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 REPTILIA https://biodiversity.org.au/afd/taxa/682e1228-5b3c-45ff-833b-550efd40c399 class taxonI… Animal… Chord… Rept… noIss…
## # … with abbreviated variable name ¹match_typeSifting through the output of show_all_fields to find a
specific field can be inefficient. Instead, we might wish to use
search_fields to look for specific fields that match a
search. As with search_taxa, search_fields
requires a query to work.
search_fields("date") |> head()## # A tibble: 6 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 month "Month of observation, specimen collection date. http://rs.tdwg.org/dwc/terms/month" fiel… <NA>
## 2 cl23 "Local Government Areas 2012 deprecated LGA Boundaries (superceeded by update Local Government Areas 2012… laye… http…
## 3 eventDate "The ISO formatted date of observation, specimen collection date. http://rs.tdwg.org/dwc/terms/eventDate" fiel… <NA>
## 4 cl10903 "Tenure of Australia's forests (2013) v2.0 Tenure of Australia's forests (2013) v2.0 is a continental dat… laye… http…
## 5 cl10955 "National Indicative Aggregated Fire Extent Dataset 2019-2020 - v20200324 The National Indicative Aggrega… laye… http…
## 6 lastLoadDate <NA> fiel… <NA>show_values() & search_values()Once a desired field is found, you can use show_values
to understand the information contained within that field, e.g.
search_all(fields, "basis") |> show_values()## ! Search returned 2 matched fields.
## • Showing values for 'basisOfRecord'.## # A tibble: 9 × 2
## field category
## <chr> <chr>
## 1 basisOfRecord HUMAN_OBSERVATION
## 2 basisOfRecord PRESERVED_SPECIMEN
## 3 basisOfRecord OBSERVATION
## 4 basisOfRecord OCCURRENCE
## 5 basisOfRecord MACHINE_OBSERVATION
## 6 basisOfRecord MATERIAL_SAMPLE
## 7 basisOfRecord LIVING_SPECIMEN
## 8 basisOfRecord MATERIAL_CITATION
## 9 basisOfRecord FOSSIL_SPECIMENThis provides the information you need to pass meaningful queries to
galah_filter.
galah_call() |>
galah_filter(basisOfRecord == "LIVING_SPECIMEN") |>
atlas_counts()## # A tibble: 1 × 1
## count
## <int>
## 1 213918This works for several other types of query, such as data profiles:
search_all(profiles, "ALA") |>
show_values() |>
head()## ! Search returned 2 matched profiles.
## • Showing values for 'ALA'.## # A tibble: 6 × 2
## description filter
## <chr> <chr>
## 1 "Exclude all records where spatial validity is \"false\"" "-spa…
## 2 "Exclude all records with an assertion that the scientific name provided does not match any of the names lists used by the … "-ass…
## 3 "Exclude all records with an assertion that the scientific name provided is not structured as a valid scientific name. Also… "-ass…
## 4 "Exclude all records with an assertion that the name and classification supplied can't be used to choose between 2 homonyms" "-ass…
## 5 "Exclude all records with an assertion that kingdom provided doesn't match a known kingdom e.g. Animalia, Plantae" "-ass…
## 6 "Exclude all records with an assertion that the scientific name provided in the record does not match the expected taxonomi… "-ass…Or collections:
search_all(collections, "herbarium") |>
show_values() |>
head()## ! Search returned 46 matched collections.
## • Showing values for 'co214'.## # A tibble: 1 × 17
## name acronym uid phone email pubDe…¹ latit…² longi…³ websi…⁴ alaPu…⁵ dateC…⁶ lastU…⁷ userL…⁸ active numRe…⁹ numRe…˟ geogr…˟
## <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <int> <int> <chr>
## 1 Allan Her… CHR co214 +64 … Herb… "The A… -43.6 172. http:/… https:… 2015-0… 2021-1… not av… Activ… 660000 236000 Worldw…
## # … with abbreviated variable names ¹pubDescription, ²latitude, ³longitude, ⁴websiteUrl, ⁵alaPublicUrl, ⁶dateCreated, ⁷lastUpdated,
## # ⁸userLastModified, ⁹numRecords, ˟numRecordsDigitised, ˟geographicDescription