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RBIEN

Tools for accessing the Botanical Information and Ecology Network (BIEN) database

News:

BIEN is back up on CRAN.

Installing

To install the development version of BIEN from Github:

devtools::install_github("bmaitner/RBIEN")

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Version

Install

install.packages('BIEN')

Monthly Downloads

3,909

Version

1.2.7

License

MIT + file LICENSE

Maintainer

Brian Maitner

Last Published

January 31st, 2025

Functions in BIEN (1.2.7)

BIEN_occurrence_family

Extract species occurrences by family.

BIEN_occurrence_box

Extract species occurrence records by a latitude/longitude bounding box.

BIEN_metadata_match_data

Check for differing records between old and new dataframes.

BIEN_occurrence_genus

Extract occurrence data from BIEN for specified genera

BIEN_occurrence_records_per_species

Count the number of (geoValid) occurrence records for each species in BIEN

BIEN_phylogeny_conservative

Download the conservative BIEN phylogeny

BIEN_plot_list_datasource

List available datasources.

BIEN_occurrence_county

Extract species occurrence records by county.

BIEN_plot_list_sampling_protocols

List available sampling protocols.

Download plot data by plot name.

BIEN_occurrence_country

Extract species occurrence records by country.

BIEN_plot_metadata

Download plot metadata

BIEN_phylogeny_complete

Download the complete BIEN phylogenies

BIEN_occurrence_sf

Extract occurrence data for specified sf polygon

BIEN_plot_dataset

Download plot data by dataset.

BIEN_plot_datasource

Download plot data from a given datasource.

BIEN_phylogeny_label_nodes

Label nodes on a phylogeny

BIEN_plot_country

Download plot data from specified countries.

BIEN_ranges_intersect_species

Download range maps that intersect the range of a given species.

BIEN_ranges_genus

Download range maps for given genus.

BIEN_ranges_list

List available range maps

BIEN_plot_state

Download plot data from specified states/provinces.

BIEN_ranges_load_species

Load range maps for specified species.

BIEN_ranges_box

Download range maps that intersect a specified bounding box.

BIEN_plot_sampling_protocol

Download plot data using a specified sampling protocol.

Download plot data from specified sf object.

Download range maps that intersect a user-supplied sf object.

BIEN_ranges_skinny_ranges_to_richness_raster

Build a richness raster from a skinny range file

BIEN_stem_datasource

Extract stem data for a given datasource from BIEN

BIEN_ranges_species_bulk

Extract range data for large numbers of species

BIEN_taxonomy_family

Extract taxonomic information for families

BIEN_taxonomy_genus

Extract taxonomic information for genera

BIEN_ranges_shapefile_to_skinny

Extract range data and convert to smaller "skinny" format

BIEN_stem_family

Extract stem data for specified families from BIEN

BIEN_stem_genus

Extract stem data for specified genera from BIEN

BIEN_stem_sampling_protocol

Download stem data using a specified sampling protocol.

BIEN_trait_country

Download trait data for given country.

BIEN_stem_species

Extract stem data for specified species from BIEN

BIEN_taxonomy_species

Extract taxonomic information for species

BIEN_trait_traitbyspecies

Download trait data for given species and trait.

BIEN_trait_traitbyfamily

Download trait data for given families and traits.

Check that value is logical

Check that value is numeric

BIEN_trait_traits_per_species

Count the number of trait observations for each species in the BIEN database

BIEN_trait_traitbygenus

Download trait data for given genus/genera and trait(s).

.is_log_or_null

Check that value is logical or null

BIEN_trait_trait

Download all measurements of a specific trait(s).

BIEN_trait_species

Download trait data for given species.

BIEN_trait_family

Download trait data for given families.

BIEN_trait_genus

Download trait data for given genera.

Set query details

.cultivated_check_stem

Set query details

.geovalid_check

Set query details

Set query details

Run an SQL query on the BIEN database.

BIEN_ranges_species

Download range maps for given species.

BIEN_trait_list

List all available types of trait data

Set query details

BIEN_trait_mean

Calculates species mean values for a given trait, using Genus or Family level data where Species level data is lacking.

Set query details

.collection_check_plot

Set query details

.natives_check_plot

Set query details

.native_check_plot

Set query details

.native_check_stem

Set query details

.observation_check

Set query details

.collection_check_stem

Set query details

Check that value is character

Set query details

.collection_check

Set query details

Set query details

.newworld_check_plot

Set query details

.taxonomy_check_traits

Set query details

.vfoi_check_stem

Set query details

.political_check

Set query details

.political_check_stem

Set query details

.political_check_plot

Set query details

.taxonomy_check_stem

Set query details

.source_check_traits

Set query details

.taxonomy_check_plot

Set query details

.political_check_traits

Set query details

.newworld_check_stem

Set query details

.newworld_check

Set query details

.cultivated_check_plot

Set query details

.cultivated_check

Set query details

.natives_check_stem

Set query details

.taxonomy_check

Set query details

BIEN: Tools for accessing the BIEN database.

BIEN_list_country

Extract species list by country

BIEN_metadata_list_political_names

List political divisions and associated geonames codes.

BIEN_list_county

Extract a species list by county.

Extract a list of all species in the BIEN database.

BIEN_list_state

Extract a species list by state/province

BIEN_metadata_data_dictionaries

Download data dictionaries

BIEN_metadata_database_version

Download the current BIEN database version and release date

BIEN_metadata_citation

Generate citations for data extracted from BIEN.

Extract a list of species within a given sf polygon.

BIEN_occurrence_species

Extract occurrence data for specified species from BIEN

BIEN_occurrence_state

Extract species occurrence records by state.