Skip to contents

Load any traits.build database into R console

Source: R/load_database.R
load_database.Rd

Loads a traits.build formatted database, given its doi. The doi is resolved to its repository, the relational database .rds file (or with flattened = TRUE, the flattened one) is downloaded (if there is no copy already, or if the copy does not match the record's md5 checksum) and then loaded. Zenodo and Figshare records are supported, as are dois that resolve directly to an .rds file.

By default the download is kept in a folder shared by all your projects (see database_cache_dir()), so each release is downloaded once per computer. Use list_cached_databases() and clear_database_cache() to see and delete what is there.

Usage

load_database(doi = NULL, path = NULL, update = TRUE, flattened = FALSE)

Arguments

doi

character string - doi of the database, e.g. "10.5281/zenodo.11188867". A Zenodo concept doi will load the latest version of that record.

path

folder the database is downloaded to and cached in. If NULL (the default), the folder shared by all your projects, given by database_cache_dir(). Give a folder such as "data/austraits" to keep a copy with a project instead, or tempdir() for one session.

update

if TRUE, the record's metadata .json will be re-downloaded; if that fails (e.g. offline), the saved copy is used. With FALSE, a concept doi loads the version last fetched into path, which for the cache folder may have been by another project.

flattened

if TRUE, load the flattened version of the database instead: one table with the other tables joined to the traits table, made with flatten_database() when the release was built. Releases of AusTraits from 7.0.0 include it. Its reference columns follow the flatten_database() of that time, so may differ from what flatten_database() makes now (e.g. AusTraits 7.0.0 has source_primary_citation, not dataset_id_citation). It is several times larger than the relational database (AusTraits 7.0.0: a 77 MB download, about 1 GB once loaded).

Value

a large list containing traits.build data tables, or with flattened = TRUE, a single table (tibble)

See also

database_cache_dir(); austraits::load_austraits(), which loads a release of AusTraits by version number

Examples

if (FALSE) { # interactive()
# Downloads AusTraits (about 20 MB, several hundred MB once loaded) the
# first time, then loads it from the cache. To try the package without
# downloading anything, see ?austraits_lite.
austraits <- load_database(doi = "10.5281/zenodo.11188867")

# Keeping a copy in a folder of your choice instead, here a temporary one
austraits <- load_database(doi = "10.5281/zenodo.11188867",
  path = file.path(tempdir(), "austraits"))
}