Extract all data for specific taxa — extract

Function to subset of all data associated with a particular taxon from a traits.build relational database.

Usage

extract_taxa(
  database,
  family = NULL,
  genus = NULL,
  taxon_name = NULL,
  partial_matches_allowed = TRUE
)

Arguments

database: traits.build database (list object)
family: character string of family or families
genus: character string of genus or genera
taxon_name: character string of taxon name(s)
partial_matches_allowed: logical. If TRUE (the default), each value is matched as a case-insensitive regular expression, so "Acacia" also matches "Acacia celsa"; a value that is itself in the column, such as a taxon name with brackets, is matched as plain text instead, so it finds itself and the values containing it; a value that is not a valid regular expression is also matched as plain text. If FALSE, only exact matches are kept.

Value

List of tibbles containing all traits.build data and metadata for the specified taxa.

Details

extract_taxa has been developed to extract data for specific taxa from databases built using the traits.build workflow. Learn more at: https://github.com/traitecoevo/traits.build & https://github.com/traitecoevo/traits.build-book

Note to AusTraits users:

This function works with AusTraits version >= 5.0.0 (from Nov 2023 release)
For AusTraits versions <= 4.2.0 (up to Sept 2023 release) see https://github.com/traitecoevo/austraits for how to install old versions of the package or download a newer version of the database.

Author

Fonti Kar - f.kar@unsw.edu.au

Examples

extract_taxa(database = austraits_lite, family = "Proteaceae")
#> 
#> ── 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 9069 records, for 1487 taxa and 111 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
extract_taxa(database = austraits_lite, genus = "Acacia")
#> 
#> ── 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 5571 records, for 267 taxa and 102 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