The living atlases store a huge amount of information, above and beyond the
occurrence records that are their main output. In galah, one way that
users can investigate this information is by searching for a specific option
or category for the type of information they are interested in.
Functions prefixed with search_ do this, displaying any matches to a
search term within the valid options for the information specified by the
suffix.
![[Experimental]](figures/lifecycle-experimental.svg)
search_all() is a helper function that can do searches within multiple
types of information from search_ sub-functions.
See Details (below) for accepted values.
Usage
search_all(type, query)
search_apis(query)
search_assertions(query)
search_atlases(query)
search_collections(query)
search_datasets(query)
search_providers(query)
search_fields(query)
search_licences(query)
search_reasons(query)
search_ranks(query)
search_profiles(query)
search_lists(query)Arguments
- type
A string to specify what type of parameters should be searched.
- query
A string specifying a search term. Searches are not case-sensitive.
Value
An object of class tbl_df and data.frame (aka a tibble)
containing all data that match the search query.
Details
There are five categories of information, each with their own
specific sub-functions to look-up each type of information.
The available types of information for search_all() are:
| Category | Type | Description | Sub-functions |
| configuration | atlases | Search for what atlases are available | search_atlases() |
apis | Search for what APIs & functions are available for each atlas | search_apis() | |
reasons | Search for what values are acceptable as 'download reasons' for a specified atlas | 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 | Search for valid taxonomic ranks (e.g. Kingdom, Class, Order, etc.) | search_ranks() | |
| filters | fields | Search for fields that are stored in an atlas | search_fields() |
assertions | Search for results of data quality checks run by each atlas | search_assertions() | |
licenses | Search for copyright licences applied to media | search_licenses() | |
| group filters | profiles | Search for what data profiles are available | search_profiles() |
lists | Search for what species lists are available | search_lists() | |
| data providers | providers | Search for which institutions have provided data | search_providers() |
collections | Search for the specific collections within those institutions | search_collections() | |
datasets | Search for the data groupings within those collections | search_datasets() |
References
Darwin Core terms https://dwc.tdwg.org/terms/
See also
See search_taxa() and search_identifiers() for more information
on taxonomic searches.
Use the show_all() function and show_all_() sub-functions to
show available options of information. These functions are used to pass valid
arguments to galah_select(), galah_filter(), and related functions.
Examples
# Search for fields that include the word "date"
search_all(fields, "date")
#> # A tibble: 22 × 4
#> id description type link
#> <chr> <chr> <chr> <chr>
#> 1 month "Month of observation, specimen collection date. … fiel… NA
#> 2 cl23 "Local Government Areas 2012 deprecated LGA Bound… laye… http…
#> 3 eventDate "The ISO formatted date of observation, specimen … fiel… NA
#> 4 cl10903 "Tenure of Australia's forests (2013) v2.0 Tenure… laye… http…
#> 5 cl10955 "National Indicative Aggregated Fire Extent Datas… laye… http…
#> 6 lastLoadDate NA fiel… NA
#> 7 datePrecision "The precision of the date information for the re… fiel… NA
#> 8 eventDateEnd NA fiel… NA
#> 9 dateIdentified "http://rs.tdwg.org/dwc/terms/dateIdentified" fiel… NA
#> 10 raw_eventDate NA fiel… NA
#> # … with 12 more rows
# Search for fields that include the word "marine"
search_all(fields, "marine")
#> # A tibble: 9 × 4
#> id description type link
#> <chr> <chr> <chr> <chr>
#> 1 biome "A field indicating if the record has been located in Ter… fiel… NA
#> 2 cl990 "Atlas of Life in the Coastal Wilderness The ALCW Bioregi… laye… http…
#> 3 cl21 "IMCRA 4 Regions Integrated Marine and Coastal Regionalis… laye… http…
#> 4 cl900 "Areas for Further Assessment within the East Marine Regi… laye… http…
#> 5 cl11033 "CAPAD 2020 Terrestrial The Collaborative Australian Prot… laye… http…
#> 6 cl11032 "CAPAD 2020 Marine The Collaborative Australian Protected… laye… http…
#> 7 cl10912 "Australia's network of Marine Parks Consistent with the … laye… http…
#> 8 cl10945 "CAPAD 2016 Marine The Collaborative Australian Protected… laye… http…
#> 9 cl10944 "CAPAD 2016 Terrestrial The Collaborative Australian Prot… laye… http…
# Search using a single taxonomic term
# (see `?search_taxa()` for more information)
search_all(taxa, "Reptilia") # equivalent
#> # A tibble: 1 × 9
#> search_term scientific_name taxon_…¹ rank match…² kingdom phylum class issues
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Reptilia REPTILIA https:/… class exactM… Animal… Chord… Rept… noIss…
#> # … with abbreviated variable names ¹taxon_concept_id, ²match_type
# Look up a unique taxon identifier
# (see `?search_identifiers()` for more information)
search_all(identifiers,
"https://id.biodiversity.org.au/node/apni/2914510")
#> # A tibble: 1 × 14
#> scient…¹ scien…² taxon…³ rank match…⁴ kingdom phylum class order family genus
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Eucalyp… Maiden https:… spec… taxonI… Plantae Charo… Equi… Myrt… Myrta… Euca…
#> # … with 3 more variables: species <chr>, vernacular_name <chr>, issues <chr>,
#> # and abbreviated variable names ¹scientific_name,
#> # ²scientific_name_authorship, ³taxon_concept_id, ⁴match_type
# Search for species lists that match "endangered"
search_all(lists, "endangered") # equivalent
#> # A tibble: 9 × 16
#> dataR…¹ listN…² listT…³ dateC…⁴ lastU…⁵ usern…⁶ fullN…⁷ itemC…⁸ region categ…⁹
#> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <int> <chr> <chr>
#> 1 dr19257 Endang… OTHER 2022-0… 2022-0… alanah… NA 17 NA NA
#> 2 dr20088 Top 30… CONSER… 2022-1… 2022-1… aprill… NA 30 NA NA
#> 3 dr4890 Endang… CONSER… 2016-0… 2016-0… kiashe… NA 340 NA NA
#> 4 dr17208 My spe… OTHER 2021-0… 2021-0… caterp… NA 1 NA NA
#> 5 dr17134 Endang… CONSER… 2021-0… 2022-1… 100588… NA 20 NA NA
#> 6 dr21057 threat… CONSER… 2023-0… 2023-0… amie.t… NA 9 NA NA
#> 7 dr16896 Rare a… CONSER… 2021-0… 2022-1… matthe… NA 1 NA NA
#> 8 dr16203 EPBC A… SPATIA… 2020-0… 2020-0… robina… NA 10 NA NA
#> 9 dr19750 Endang… OTHER 2022-0… 2022-1… anneke… NA 73 NA NA
#> # … with 6 more variables: generalisation <chr>, authority <chr>,
#> # sdsType <chr>, isAuthoritative <lgl>, isInvasive <lgl>, isThreatened <lgl>,
#> # and abbreviated variable names ¹dataResourceUid, ²listName, ³listType,
#> # ⁴dateCreated, ⁵lastUpdated, ⁶username, ⁷fullName, ⁸itemCount, ⁹category
# Search for a valid taxonomic rank, "subphylum"
search_all(ranks, "subphylum")
#> # A tibble: 1 × 2
#> id name
#> <int> <chr>
#> 1 7 subphylum