The atlas_ functions are used to return data from the
atlas chosen using galah_config(). They are:
atlas_counts()atlas_occurrences()atlas_species()atlas_media()atlas_taxonomy()The final atlas_
function—atlas_citation()—is unusual: It does not return
any new data, but instead provides a citation for an existing dataset
(downloaded using atlas_occurrences()) with an associated
DOI. The other functions are described below.
It is equally permissable to use the type argument of
galah_call() to specify the kind of data you want, and then
retrieve the data using collect(). Here we use the
atlas_ prefix for consistency with earlier versions of
galah, and because many atlas_ functions sometimes include
shortcuts to make life easier.
atlas_counts() provides summary counts of records in the
specified atlas without needing to download all the records first.
## # A tibble: 1 × 1
##       count
##       <int>
## 1 146185520Group and summarise record counts by specific fields using
galah_group_by().
## # A tibble: 12 × 2
##    kingdom           count
##    <chr>             <int>
##  1 Animalia      113408280
##  2 Plantae        27572183
##  3 Fungi           2448600
##  4 Chromista       1057157
##  5 Protista         316541
##  6 Bacteria         113480
##  7 Archaea            4120
##  8 Virus              2382
##  9 Bamfordvirae        210
## 10 Orthornavirae       138
## 11 Viroid              104
## 12 Shotokuvirae         41A common use case of atlas data is to identify which species occur in
a specified region, time period, or taxonomic group.
atlas_species() is similar to search_taxa(),
in that it returns taxonomic information and unique identifiers, but
differs by returning information only on species and is far more
flexible by supporting filtering.
species <- galah_call() |>
  galah_identify("Rodentia") |>
  galah_filter(stateProvince == "Northern Territory") |>
  atlas_species()
  
species |> head()## # A tibble: 6 × 11
##   taxon_concept_id species_name scientific_name_auth…¹ taxon_rank kingdom phylum class order family genus vernacular_name
##   <chr>            <chr>        <chr>                  <chr>      <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>          
## 1 https://biodive… Pseudomys d… (Gould, 1842)          species    Animal… Chord… Mamm… Rode… Murid… Pseu… Delicate Mouse 
## 2 https://biodive… Mesembriomy… (J.E. Gray, 1843)      species    Animal… Chord… Mamm… Rode… Murid… Mese… Black-footed T…
## 3 https://biodive… Zyzomys arg… (Thomas, 1889)         species    Animal… Chord… Mamm… Rode… Murid… Zyzo… Common Rock-rat
## 4 https://biodive… Pseudomys h… (Waite, 1896)          species    Animal… Chord… Mamm… Rode… Murid… Pseu… Sandy Inland M…
## 5 https://biodive… Melomys bur… (Ramsay, 1887)         species    Animal… Chord… Mamm… Rode… Murid… Melo… Grassland Melo…
## 6 https://biodive… Notomys ale… Thomas, 1922           species    Animal… Chord… Mamm… Rode… Murid… Noto… Spinifex Hoppi…
## # ℹ abbreviated name: ¹scientific_name_authorshipTo download occurrence data you will need to specify an email in
galah_config() that has been registered to an account with
your selected GBIF node. See more information in the config section.
Download occurrence records for Eolophus roseicapilla.
occ <- galah_call() |>
  galah_identify("Eolophus roseicapilla") |>
  galah_filter(
    stateProvince == "Australian Capital Territory",
    year >= 2010,
    profile = "ALA"
  ) |>
  galah_select(institutionID, group = "basic") |>
  atlas_occurrences()## Retrying in 1 seconds.
## Retrying in 2 seconds.
## Retrying in 4 seconds.## # A tibble: 6 × 9
##   recordID            scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus
##   <chr>               <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>           
## 1 0000a928-d756-42eb… Eolophus rose… https://biodi…           -35.6             149. 2017-04-19 09:11:00 PRESENT         
## 2 0001bc78-d2e9-48aa… Eolophus rose… https://biodi…           -35.2             149. 2019-08-13 15:13:00 PRESENT         
## 3 0002064f-08ea-425b… Eolophus rose… https://biodi…           -35.3             149. 2014-03-16 06:48:00 PRESENT         
## 4 00022dd2-9f85-4802… Eolophus rose… https://biodi…           -35.3             149. 2022-05-08 08:20:00 PRESENT         
## 5 0002cc35-8d5a-4d20… Eolophus rose… https://biodi…           -35.3             149. 2015-11-01 08:00:00 PRESENT         
## 6 00030a8c-082f-44f0… Eolophus rose… https://biodi…           -35.3             149. 2022-01-06 11:47:00 PRESENT         
## # ℹ 2 more variables: dataResourceName <chr>, institutionID <lgl>In addition to text data describing individual occurrences and their
attributes, ALA stores images, sounds and videos associated with a given
record. Metadata on these records can be downloaded using
atlas_media().
media_data <- galah_call() |>
  galah_identify("Eolophus roseicapilla") |>
  galah_filter(
    year == 2020,
    cl22 == "Australian Capital Territory") |>
  atlas_media()
  
media_data |> head()## # A tibble: 6 × 19
##   media_id   recordID scientificName taxonConceptID decimalLatitude decimalLongitude eventDate           occurrenceStatus
##   <chr>      <chr>    <chr>          <chr>                    <dbl>            <dbl> <dttm>              <chr>           
## 1 ff8322d0-… 003a192… Eolophus rose… https://biodi…           -35.3             149. 2020-09-12 16:11:00 PRESENT         
## 2 c66fc819-… 015ee7c… Eolophus rose… https://biodi…           -35.4             149. 2020-08-09 15:11:00 PRESENT         
## 3 fe6d7b94-… 05e86b7… Eolophus rose… https://biodi…           -35.4             149. 2020-11-13 22:29:00 PRESENT         
## 4 2f4d32c0-… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 11:50:00 PRESENT         
## 5 73407414-… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 11:50:00 PRESENT         
## 6 89171c49-… 063bb0f… Eolophus rose… https://biodi…           -35.6             149. 2020-08-04 11:50:00 PRESENT         
## # ℹ 11 more variables: dataResourceName <chr>, multimedia <chr>, images <chr>, sounds <lgl>, videos <lgl>,
## #   creator <chr>, license <chr>, mimetype <chr>, width <int>, height <int>, image_url <chr>To actually download the media files to your computer, use [collect_media()].
atlas_taxonomy() provides a way to build taxonomic trees
from one clade down to another using each GBIF node’s internal taxonomy.
Specify which taxonomic level your tree will go down to with
galah_filter() using the rank argument.
## # A tibble: 19 × 4
##    name            rank      parent_taxon_concept_id                                                   taxon_concept_id  
##    <chr>           <chr>     <chr>                                                                     <chr>             
##  1 Chordata        phylum    <NA>                                                                      https://biodivers…
##  2 Cephalochordata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodivers…
##  3 Tunicata        subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodivers…
##  4 Appendicularia  class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodivers…
##  5 Ascidiacea      class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodivers…
##  6 Thaliacea       class     https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodivers…
##  7 Vertebrata      subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodivers…
##  8 Agnatha         informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodivers…
##  9 Myxini          informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodivers…
## 10 Petromyzontida  informal  https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodivers…
## 11 Gnathostomata   informal  https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodivers…
## 12 Amphibia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodivers…
## 13 Aves            class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodivers…
## 14 Mammalia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodivers…
## 15 Reptilia        class     https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodivers…
## 16 Pisces          informal  https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodivers…
## 17 Actinopterygii  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodivers…
## 18 Chondrichthyes  class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodivers…
## 19 Sarcopterygii   class     https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodivers…Various aspects of the galah package can be customized.
To download occurrence records, species lists or media, you will need to provide an email address registered with the service that you want to use (e.g. for the ALA you can create an account here).
Once an email is registered, it should be stored in the config:
By default, galah stores downloads in a temporary folder, meaning that the local files are automatically deleted when the R session is ended. This behaviour can be altered so that downloaded files are preserved by setting the directory to a non-temporary location.
ALA requires that you provide a reason when downloading occurrence
data (via the galah atlas_occurrences() function).
reason is set as “scientific research” by default, but you
can change this using galah_config(). See
show_all(reasons) for valid download reasons.