Show valid record information

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 showing all the available options or categories for the type of information they are interested in. Functions prefixed with show_all_ do this, displaying all valid options for the information specified by the suffix.

show_all() is a helper function that can display multiple types of information from show_all_ sub-functions. See Details (below) for accepted values.

Usage

show_all(type, limit = NULL)

show_all_assertions(limit = NULL)

show_all_atlases(limit = NULL)

show_all_cached_files(limit = NULL)

show_all_apis(limit = NULL)

show_all_collections(limit = NULL)

show_all_datasets(limit = NULL)

show_all_providers(limit = NULL)

show_all_fields(limit = NULL)

show_all_licences(limit = NULL)

show_all_reasons(limit = NULL)

show_all_ranks(limit = NULL)

show_all_profiles(limit = NULL)

show_all_lists(limit = NULL)

Arguments

type: A string to specify what type of parameters should be shown.
limit: Optional number of values to return. Defaults to NULL, i.e. all records

Value

An object of class tbl_df and data.frame (aka a tibble) containing all data of interest.

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 show_all_ are:

Category	Type	Description	Sub-functions
configuration	`atlases`	Show what atlases are available	`show_all_atlases()`
	`apis`	Show what APIs & functions are available for each atlas	`show_all_apis()`
	`reasons`	Show what values are acceptable as 'download reasons' for a specified atlas	`show_all_reasons()`
taxonomy	`ranks`	Show valid taxonomic ranks (e.g. Kingdom, Class, Order, etc.)	`show_all_ranks()`
filters	`fields`	Show fields that are stored in an atlas	`show_all_fields()`
	`assertions`	Show results of data quality checks run by each atlas	`show_all_assertions()`
	`licenses`	Show what copyright licenses are applied to media	`show_all_licenses()`
group filters	`profiles`	Show what data profiles are available	`show_all_profiles()`
	`lists`	Show what species lists are available	`show_all_lists()`
data providers	`providers`	Show which institutions have provided data	`show_all_providers()`
	`collections`	Show the specific collections within those institutions	`show_all_collections()`
	`datasets`	Shows all the data groupings within those collections	`show_all_datasets()`

References

Darwin Core terms https://dwc.tdwg.org/terms/

Examples

# See all supported atlases
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 … SiBBr   http…
#>  4 Estonia        eElurikkus                                       NA      http…
#>  5 France         Portail français d'accès aux données d'observat… OpenObs http…
#>  6 Global         Global Biodiversity Information Facility         GBIF    http…
#>  7 Guatemala      Sistema Nacional de Información sobre Diversida… 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 a list of all available data quality profiles
show_all(profiles)
#> # A tibble: 7 × 4
#>      id name                                                  shortName  descr…¹
#>   <int> <chr>                                                 <chr>      <chr>  
#> 1     2 ALA General (pre-pipelines 3)                         ALA-legacy "The d…
#> 2    35 Species Distribution Modelling (CSDM) (pre-pipelines) CSDM-lega… "Base …
#> 3    44 Data licensed for all uses (pre-pipelines)            re-usable… "Data …
#> 4    92 ALA General                                           ALA        "The d…
#> 5   124 Species Distribution Modelling (CSDM)                 CSDM       "Base …
#> 6   133 Data licensed for all uses                            re-usable  "Data …
#> 7   224 AVH                                                   AVH        "AVH d…
#> # … with abbreviated variable name ¹description

# Show a listing of all accepted reasons for downloading occurrence data
show_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 modelling               

# Show a listing of all taxonomic ranks
show_all(ranks)
#> # A tibble: 69 × 2
#>       id name        
#>    <int> <chr>       
#>  1     1 root        
#>  2     2 superkingdom
#>  3     3 kingdom     
#>  4     4 subkingdom  
#>  5     5 superphylum 
#>  6     6 phylum      
#>  7     7 subphylum   
#>  8     8 superclass  
#>  9     9 class       
#> 10    10 subclass    
#> # … with 59 more rows