A traits.build database with 24 of the datasets in AusTraits
7.0.0, the Australian plant trait database. It is in the same form as the
databases load_database() downloads, so every function in the package
works on it, and the examples use it. For analysis, load a full release
with load_database() instead.
Format
A list of class traits.build, with the tables of a traits.build
database: traits (90,568 values of 151 traits for 7,259 taxa),
locations, contexts, methods, excluded_data, taxonomic_updates,
taxa, identifiers, contributors, sources, definitions, schema,
metadata and build_info. AusTraits 7.0.0 fills in source_id for
only a few datasets, and predates the reference columns of the methods
table that traits.build 2.3 introduced (it has source_primary_key and
others; see join_sources()).
Source
AusTraits 7.0.0, doi:10.5281/zenodo.15718081
, licensed under
CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/), cut down to
24 datasets with extract_dataset() (the script is data-raw/create_data.R
in the package's GitHub repository). Please cite AusTraits as described
in Falster et al. (2021) doi:10.1038/s41597-021-01006-6
, and the
original studies, listed in sources (as in the full release, a few keys
in source_id and the methods table, such as unpublished data, have no
entry). The taxa table, compiled from curated taxon lists such as the
Australian Plant Census, is released under CC BY 3.0, as its description
in schema says. See the file COPYRIGHTS installed with the package.
Examples
austraits_lite
#>
#> ── This is 7.0.0 of AusTraits: a curated plant trait database for the Australian
#> ℹ This database is built using traits.build version 2.1.0
#> ℹ This database contains a total of 90568 records, for 7259 taxa and 151
#> traits.
#>
#> ── This object is a 'list' with the following components: ──
#>
#> • traits: A table containing measurements of traits.
#> • locations: A table containing observations of location/site characteristics
#> associated with information in `traits`. Cross referencing between the two
#> dataframes is possible using combinations of the variables `dataset_id`,
#> `location_name`.
#> • contexts: A table containing observations of contextual characteristics
#> associated with information in `traits`. Cross referencing between the two
#> dataframes is possible using combinations of the variables `dataset_id`,
#> `link_id`, and `link_vals`.
#> • methods: A table containing details on methods with which data were
#> collected, including time frame and source. Cross referencing with the `traits`
#> table is possible using combinations of the variables `dataset_id`,
#> `trait_name`.
#> • excluded_data: A table of data that did not pass quality test and so were
#> excluded from the master dataset.
#> • taxonomic_updates: A table of all taxonomic changes implemented in the
#> construction of AusTraits. Changes are determined by comparing against the APC
#> (Australian Plant Census) and APNI (Australian Plant Names Index).
#> • taxa: A table containing details on taxa associated with information in
#> `traits`. This information has been sourced from the APC (Australian Plant
#> Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3
#> license.
#> • contributors: A table of people contributing to each study.
#> • identifiers: A table of identifiers that cross-references observations
#> between datasets or with other data resources such as museum or herbarium
#> specimens.
#> • sources: Bibtex entries for all primary and secondary sources in the
#> compilation.
#> • definitions: A copy of the definitions for all tables and terms. Information
#> included here was used to process data and generate any documentation for the
#> study.
#> • schema: A copy of the schema for all tables and terms. Information included
#> here was used to process data and generate any documentation for the study.
#> • metadata: Metadata associated with the dataset, including title, creators,
#> license, subject, funding sources.
#> • build_info: A description of the computing environment used to create this
#> version of the dataset, including version number, git commit and R
#> session_info.
#> ℹ To access a component, try using the $ e.g. database$traits
summarise_database(austraits_lite, "trait_name")
#> # A tibble: 151 × 5
#> trait_name n_records n_dataset n_taxa percent_total
#> <chr> <int> <int> <int> <dbl>
#> 1 atmospheric_CO2_concentration 217 1 17 0.0024
#> 2 bark_C_per_dry_mass 159 1 17 0.00176
#> 3 bark_N_per_dry_mass 159 1 17 0.00176
#> 4 bark_delta13C 159 1 17 0.00176
#> 5 bark_delta15N 159 1 17 0.00176
#> 6 bark_thickness 198 2 17 0.00219
#> 7 branch_mass_fraction 45 1 45 0.000497
#> 8 bud_bank_location 218 2 204 0.00241
#> 9 clonal_spread_mechanism 7 1 7 0.0000773
#> 10 dispersal_appendage 13 1 13 0.000144
#> # ℹ 141 more rows