Nothing
Look up information
In galah: Biodiversity Data from the GBIF Node Network
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: 11 × 4
## region institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Australia Atlas of Living Australia ALA http…
## 2 Austria Biodiversitäts-Atlas Österreich BAO http…
## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr http…
## 4 Estonia eElurikkus <NA> http…
## 5 France Portail français d'accès aux données d'observation sur les … OpenObs http…
## 6 Global Global Biodiversity Information Facility GBIF http…
## 7 Guatemala Sistema Nacional de Información sobre Diversidad Biológica … SNIBgt http…
## 8 Portugal GBIF Portugal GBIF.pt http…
## 9 Spain GBIF Spain GBIF.es http…
## 10 Sweden Swedish Biodiversity Data Infrastructure SBDI http…
## 11 United Kingdom National Biodiversity Network NBN http…
To search for a specific available Living Atlas:
search_all(atlases, "Spain")
## # A tibble: 1 × 4
## region institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Spain GBIF Spain GBIF.es https://www.gbif.es
To show all fields:
show_all(fields)
## # A tibble: 646 × 3
## id description type
## <chr> <chr> <chr>
## 1 _nest_parent_ <NA> fields
## 2 _nest_path_ <NA> fields
## 3 _root_ <NA> fields
## 4 abcdTypeStatus <NA> fields
## 5 acceptedNameUsage Accepted name fields
## 6 acceptedNameUsageID Accepted name fields
## 7 accessRights Access rights fields
## 8 annotationsDoi <NA> fields
## 9 annotationsUid Referenced by publication fields
## 10 assertionUserId Assertions by user fields
## # ℹ 636 more rows
And to search for a specific field:
search_all(fields, "australian states")
## # A tibble: 2 × 3
## id description type
## <chr> <chr> <chr>
## 1 cl2013 ASGS Australian States and Territories fields
## 2 cl22 Australian States and Territories fields
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_ subfunctions
While 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_reasons
show_all_ functions require no arguments. Simply call the function and it will
return all accepted values as a tibble:
show_all_atlases()
## # A tibble: 11 × 4
## region institution acronym url
## <chr> <chr> <chr> <chr>
## 1 Australia Atlas of Living Australia ALA http…
## 2 Austria Biodiversitäts-Atlas Österreich BAO http…
## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr http…
## 4 Estonia eElurikkus <NA> http…
## 5 France Portail français d'accès aux données d'observation sur les … OpenObs http…
## 6 Global Global Biodiversity Information Facility GBIF http…
## 7 Guatemala Sistema Nacional de Información sobre Diversidad Biológica … SNIBgt http…
## 8 Portugal GBIF Portugal GBIF.pt http…
## 9 Spain GBIF Spain GBIF.es http…
## 10 Sweden Swedish Biodiversity Data Infrastructure SBDI http…
## 11 United Kingdom National Biodiversity Network NBN http…
show_all_reasons()
## # A tibble: 13 × 2
## id name
## <int> <chr>
## 1 1 biosecurity management/planning
## 2 11 citizen science
## 3 5 collection management
## 4 0 conservation management/planning
## 5 7 ecological research
## 6 3 education
## 7 2 environmental assessment
## 8 12 restoration/remediation
## 9 4 scientific research
## 10 8 systematic research/taxonomy
## 11 13 species modelling
## 12 6 other
## 13 10 testing
search_ subfunctions
The 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_fieldsshow_values
Search 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_type kingdom phylum class issues
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 reptilia REPTILIA https://biodiver… class exactMatch Animal… Chord… Rept… noIss…
search_taxa("reptilia", "aves", "mammalia", "pisces")
## # A tibble: 1 × 9
## search_term scientific_name taxon_concept_id rank match_type kingdom phylum class issues
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 reptilia REPTILIA https://biodiver… class exactMatch Animal… Chord… Rept… noIss…
Alternatively, 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 × 15
## search_term success scientific_name taxon_concept_id rank rank_id lft rgt match_type
## <chr> <lgl> <chr> <chr> <chr> <int> <int> <int> <chr>
## 1 urn:lsid:bi… TRUE REPTILIA https://biodive… class 3000 46718 49924 taxonIdMa…
## # ℹ 6 more variables: kingdom <chr>, kingdom_id <chr>, phylum <chr>, phylum_id <chr>,
## # class <chr>, class_id <chr>
Sifting 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 × 3
## id description type
## <chr> <chr> <chr>
## 1 eventDate Event Date fields
## 2 lastLoadDate lastLoadDate fields
## 3 datePrecision Date precision fields
## 4 eventDateEnd <NA> fields
## 5 dateIdentified Date Identified fields
## 6 raw_eventDate <NA> fields
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 × 1
## basisOfRecord
## <chr>
## 1 Human observation
## 2 Preserved specimen
## 3 Observation
## 4 Occurrence
## 5 Machine observation
## 6 Material Sample
## 7 Living specimen
## 8 Material Citation
## 9 Fossil specimen
This 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 126135
This works for other types of query, such as data profiles:
search_all(profiles, "ALA") |>
show_values() |>
head()
## • Showing values for 'ALA'.
## # A tibble: 6 × 5
## id enabled description filter displayOrder
## <int> <lgl> <chr> <chr> <int>
## 1 94 TRUE "Exclude all records where spatial validity is \"false\… "-spa… 1
## 2 96 TRUE "Exclude all records with an assertion that the scienti… "-ass… 1
## 3 97 TRUE "Exclude all records with an assertion that the scienti… "-ass… 2
## 4 98 TRUE "Exclude all records with an assertion that the name an… "-ass… 3
## 5 99 TRUE "Exclude all records with an assertion that kingdom pro… "-ass… 4
## 6 100 TRUE "Exclude all records with an assertion that the scienti… "-ass… 5
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galah documentation built on Nov. 20, 2023, 9:07 a.m.
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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: 11 × 4 ## region institution acronym url ## <chr> <chr> <chr> <chr> ## 1 Australia Atlas of Living Australia ALA http… ## 2 Austria Biodiversitäts-Atlas Österreich BAO http… ## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr http… ## 4 Estonia eElurikkus <NA> http… ## 5 France Portail français d'accès aux données d'observation sur les … OpenObs http… ## 6 Global Global Biodiversity Information Facility GBIF http… ## 7 Guatemala Sistema Nacional de Información sobre Diversidad Biológica … SNIBgt http… ## 8 Portugal GBIF Portugal GBIF.pt http… ## 9 Spain GBIF Spain GBIF.es http… ## 10 Sweden Swedish Biodiversity Data Infrastructure SBDI http… ## 11 United Kingdom National Biodiversity Network NBN http…
To search for a specific available Living Atlas:
search_all(atlases, "Spain")
## # A tibble: 1 × 4 ## region institution acronym url ## <chr> <chr> <chr> <chr> ## 1 Spain GBIF Spain GBIF.es https://www.gbif.es
To show all fields:
show_all(fields)
## # A tibble: 646 × 3 ## id description type ## <chr> <chr> <chr> ## 1 _nest_parent_ <NA> fields ## 2 _nest_path_ <NA> fields ## 3 _root_ <NA> fields ## 4 abcdTypeStatus <NA> fields ## 5 acceptedNameUsage Accepted name fields ## 6 acceptedNameUsageID Accepted name fields ## 7 accessRights Access rights fields ## 8 annotationsDoi <NA> fields ## 9 annotationsUid Referenced by publication fields ## 10 assertionUserId Assertions by user fields ## # ℹ 636 more rows
And to search for a specific field:
search_all(fields, "australian states")
## # A tibble: 2 × 3 ## id description type ## <chr> <chr> <chr> ## 1 cl2013 ASGS Australian States and Territories fields ## 2 cl22 Australian States and Territories fields
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_ subfunctions
While 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_reasons
show_all_ functions require no arguments. Simply call the function and it will
return all accepted values as a tibble:
show_all_atlases()
## # A tibble: 11 × 4 ## region institution acronym url ## <chr> <chr> <chr> <chr> ## 1 Australia Atlas of Living Australia ALA http… ## 2 Austria Biodiversitäts-Atlas Österreich BAO http… ## 3 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr http… ## 4 Estonia eElurikkus <NA> http… ## 5 France Portail français d'accès aux données d'observation sur les … OpenObs http… ## 6 Global Global Biodiversity Information Facility GBIF http… ## 7 Guatemala Sistema Nacional de Información sobre Diversidad Biológica … SNIBgt http… ## 8 Portugal GBIF Portugal GBIF.pt http… ## 9 Spain GBIF Spain GBIF.es http… ## 10 Sweden Swedish Biodiversity Data Infrastructure SBDI http… ## 11 United Kingdom National Biodiversity Network NBN http…
show_all_reasons()
## # A tibble: 13 × 2 ## id name ## <int> <chr> ## 1 1 biosecurity management/planning ## 2 11 citizen science ## 3 5 collection management ## 4 0 conservation management/planning ## 5 7 ecological research ## 6 3 education ## 7 2 environmental assessment ## 8 12 restoration/remediation ## 9 4 scientific research ## 10 8 systematic research/taxonomy ## 11 13 species modelling ## 12 6 other ## 13 10 testing
search_ subfunctions
The 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_fieldsshow_values
Search 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_type kingdom phylum class issues ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> ## 1 reptilia REPTILIA https://biodiver… class exactMatch Animal… Chord… Rept… noIss…
search_taxa("reptilia", "aves", "mammalia", "pisces")
## # A tibble: 1 × 9 ## search_term scientific_name taxon_concept_id rank match_type kingdom phylum class issues ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> ## 1 reptilia REPTILIA https://biodiver… class exactMatch Animal… Chord… Rept… noIss…
Alternatively, 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 × 15 ## search_term success scientific_name taxon_concept_id rank rank_id lft rgt match_type ## <chr> <lgl> <chr> <chr> <chr> <int> <int> <int> <chr> ## 1 urn:lsid:bi… TRUE REPTILIA https://biodive… class 3000 46718 49924 taxonIdMa… ## # ℹ 6 more variables: kingdom <chr>, kingdom_id <chr>, phylum <chr>, phylum_id <chr>, ## # class <chr>, class_id <chr>
Sifting 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 × 3 ## id description type ## <chr> <chr> <chr> ## 1 eventDate Event Date fields ## 2 lastLoadDate lastLoadDate fields ## 3 datePrecision Date precision fields ## 4 eventDateEnd <NA> fields ## 5 dateIdentified Date Identified fields ## 6 raw_eventDate <NA> fields
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 × 1 ## basisOfRecord ## <chr> ## 1 Human observation ## 2 Preserved specimen ## 3 Observation ## 4 Occurrence ## 5 Machine observation ## 6 Material Sample ## 7 Living specimen ## 8 Material Citation ## 9 Fossil specimen
This 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 126135
This works for other types of query, such as data profiles:
search_all(profiles, "ALA") |> show_values() |> head()
## • Showing values for 'ALA'.
## # A tibble: 6 × 5 ## id enabled description filter displayOrder ## <int> <lgl> <chr> <chr> <int> ## 1 94 TRUE "Exclude all records where spatial validity is \"false\… "-spa… 1 ## 2 96 TRUE "Exclude all records with an assertion that the scienti… "-ass… 1 ## 3 97 TRUE "Exclude all records with an assertion that the scienti… "-ass… 2 ## 4 98 TRUE "Exclude all records with an assertion that the name an… "-ass… 3 ## 5 99 TRUE "Exclude all records with an assertion that kingdom pro… "-ass… 4 ## 6 100 TRUE "Exclude all records with an assertion that the scienti… "-ass… 5
Try the galah package in your browser
Any scripts or data that you put into this service are public.
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