Choosing an atlas
Martin Westgate, Dax Kellie
2023-03-10
Source:vignettes/choosing_an_atlas.Rmd
choosing_an_atlas.RmdThe GBIF network consists of a series of a series of ‘node’
organisations who collate biodiversity data from their own countries,
with GBIF acting as an umbrella organisation to store data from all
nodes. Several nodes have their own APIs, often built from the ‘living
atlas’ codebase developed by the ALA. At present, galah
supports the following functions and atlases:
Set Organisation
Set which atlas you want to use by changing the atlas
argument in galah_config(). The atlas argument
can accept a full name, an acronym, or a region to select a given atlas,
all of which are available via show_all(atlases). Once a
value is provided, it will automatically update galah’s
server configuration to your selected atlas. The default
atlas is Australia.
If you intend to download records, you may need to register a user profile with the relevant atlas first.
galah_config(atlas = "GBIF.es", email = "your_email_here")Look up Information
You can use the same look-up functions to find useful information about the Atlas you have set. Available information may vary for each Living Atlas.
galah_config(atlas = "Guatemala")## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala]
show_all(datasets)## # A tibble: 100 × 3
## name uri uid
## <chr> <chr> <chr>
## 1 A Distribution and Taxonomic Reference Dataset of Geranium (Geraniaceae) in the New World http… dr321
## 2 A global database for the distributions of crop wild relatives http… dr12
## 3 A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera Tenebrionidae) http… dr467
## 4 A new Mexican species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae), with nomenclatural changes, new records, and a key to th… http… dr554
## 5 A new species of Setostylus Matile and new records of Setostylus bellulus (Williston) (Diptera: Keroplatidae) http… dr538
## 6 A revision of the genus Bromeloecia Spuler (Diptera: Sphaeroceridae: Limosininae) http… dr481
## 7 A synopsis of American Caraphia Gahan, 1906 (Coleoptera: Cerambycidae: Lepturinae) with description of two new species http… dr539
## 8 A synopsis of the Neotropical genus Protoneura (Odonata: Coenagrionidae) http… dr448
## 9 A systematic revision of the genus Archocentrus (Perciformes: Cichlidae), with the description of two new genera and six new species. http… dr362
## 10 A taxonomic monograph of the genus Tylodinus Champion (Coleoptera: Curculionidae: Cryptorhynchinae: Tylodina) of Chiapas, Mexico http… dr564
## # … with 90 more rows
show_all(fields)## # A tibble: 129 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 all_image_url Image URLs for this record fiel… <NA>
## 2 assertion_user_id User ID of the person who has made an assertion about this record fiel… <NA>
## 3 assertions A list of all assertions (user and system supplied) for a record resulting from data quality tests fiel… <NA>
## 4 assertions_missing Assertion indicating missing field values for a record. E.g. missing basis of record fiel… <NA>
## 5 assertions_passed Assertion indicating a data quality test has been passed by this record fiel… <NA>
## 6 assertions_unchecked Assertion indicating a data quality test was not performed for this record typically due to the absence of fields … fiel… <NA>
## 7 basis_of_record The basis of record e.g. Specimen, Observation http://rs.tdwg.org/dwc/terms/basisOfRecord fiel… <NA>
## 8 catalogue_number http://rs.tdwg.org/dwc/terms/catalogNumber fiel… <NA>
## 9 class The class the Atlas has matched this record to in the NSL http://rs.tdwg.org/dwc/terms/class fiel… <NA>
## 10 collection_code The collection code for this record. This will be populated if the data has come from a museum or herbaria http://… fiel… <NA>
## # … with 119 more rows
search_all(fields, "year")## # A tibble: 3 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 year http://rs.tdwg.org/dwc/terms/year fields <NA>
## 2 occurrence_year Year ranges for a search. Calculated based on the unique values for a query. fields <NA>
## 3 date_precision The precision of the date information for the record. Values include 'Day', 'Month', 'Year', 'Year range', 'Month range' fields <NA>
search_taxa("lagomorpha")## # A tibble: 1 × 12
## search_term taxon_concept_id scientific_name scientific_name_authorship rank kingdom phylum class order family genus species
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 lagomorpha 785 Lagomorpha <NA> order Animalia Chordata Mammalia Lagomorpha <NA> <NA> <NA>Download data
You can build queries as you normally would in galah.
For taxonomic queries, use search_taxa() to make sure your
searches are returning the correct taxonomic data.
galah_config(atlas = "United Kingdom")## Atlas selected: National Biodiversity Network (NBN) [United Kingdom]
search_taxa("vlps") # Returns no data due to misspelling## # A tibble: 1 × 1
## search_term
## <chr>
## 1 vlps
search_taxa("vulpes") # Returns data## # A tibble: 1 × 13
## search_term taxon_concept_id scientific_name scientific_name_authorship rank kingdom superclass order class genus phylum family species
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 vulpes NBNSYS0000138878 Vulpes Frisch, 1775 genus Animalia Tetrapoda Carnivora Mammalia Vulpes Chordata Canidae <NA>
galah_call() |>
galah_identify("vulpes") |>
galah_filter(year > 2010) |>
atlas_counts()## # A tibble: 1 × 1
## count
## <int>
## 1 98760Download species occurrence records from other atlases with
atlas_occurrences()
galah_config(atlas = "Guatemala")## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala]
galah_call() |>
galah_identify("Lagomorpha") |>
galah_filter(year <= 1980) |>
galah_select(taxon_name, year) |>
atlas_occurrences()## # A tibble: 39 × 2
## scientificName year
## <chr> <dbl>
## 1 Sylvilagus floridanus (J. A. Allen, 1890) 1960
## 2 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890) 1960
## 3 Sylvilagus floridanus (J. A. Allen, 1890) 1952
## 4 Sylvilagus floridanus (J. A. Allen, 1890) 1955
## 5 Sylvilagus floridanus (J. A. Allen, 1890) 1955
## 6 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 7 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890) 1947
## 8 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 9 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 10 Sylvilagus floridanus subsp. aztecus (J. Allen, 1890) 1895
## # … with 29 more rowsComplex queries with multiple Atlases
It is also possible to create more complex queries that return data
from multiple Living Atlases. As an example, setting atlases within a
loop with galah_config() and purrr::map()
allows us to return the total number of species records in each Living
Atlas in one table.
library(purrr)
library(tibble)
library(dplyr)
library(gt)
atlases <- show_all(atlases)
counts <- map(atlases$region,
function(x){
galah_config(atlas = x)
atlas_counts()
})
tibble(
atlas = atlases$region,
n = unlist(counts)) |>
filter(n > 0) |>
arrange(desc(n)) |>
gt() |>
fmt_number(column = n)| atlas | n |
|---|---|
| Global | 1,814,565,214.00 |
| United Kingdom | 208,111,761.00 |
| France | 128,490,040.00 |
| Australia | 114,091,351.00 |
| Sweden | 103,417,222.00 |
| Spain | 38,330,113.00 |
| Brazil | 24,139,042.00 |
| Portugal | 16,043,865.00 |
| Austria | 8,075,385.00 |
| Estonia | 7,163,505.00 |
| Guatemala | 3,586,634.00 |