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RBIEN

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

News:

BIEN is currently not available on CRAN at the moment (but will be back soon). In the meantime, the development version of the package can be installed directly from Github using devtools.

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

1.2.6

License

MIT + file LICENSE

Maintainer

Brian Maitner

Last Published

January 6th, 2023

Functions in BIEN (1.2.6)

Extract a list of all species in the BIEN database.

BIEN_metadata_database_version

Download the current BIEN database version and release date

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_occurrence_box

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

BIEN_occurrence_sf

Extract occurrence data for specified sf polygon

BIEN_occurrence_species

Extract occurrence data for specified species from BIEN

BIEN_occurrence_family

Extract species occurrences by family.

BIEN_occurrence_county

Extract species occurrence records by county.

BIEN_occurrence_country

Extract species occurrence records by country.

BIEN_phylogeny_complete

Download the complete BIEN phylogenies

BIEN_occurrence_state

Extract species occurrence records by state.

BIEN_plot_datasource

Download plot data from a given datasource.

BIEN_phylogeny_conservative

Download the conservative BIEN phylogeny

BIEN_phylogeny_label_nodes

Label nodes on a phylogeny

BIEN_plot_list_sampling_protocols

List available sampling protocols.

BIEN_plot_metadata

Download plot metadata

BIEN_plot_list_datasource

List available datasources.

BIEN_ranges_shapefile_to_skinny

Extract range data and convert to smaller "skinny" format

Download plot data from specified sf object.

BIEN_plot_state

Download plot data from specified states/provinces.

BIEN_ranges_intersect_species

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

Download plot data by plot name.

BIEN_plot_country

Download plot data from specified countries.

BIEN_plot_sampling_protocol

Download plot data using a specified sampling protocol.

BIEN_plot_dataset

Download plot data by dataset.

BIEN_ranges_box

Download range maps that intersect a specified bounding box.

BIEN_ranges_skinny_ranges_to_richness_raster

Build a richness raster from a skinny range file

BIEN_stem_genus

Extract stem data for specified genera from BIEN

BIEN_stem_family

Extract stem data for specified families from BIEN

BIEN_stem_datasource

Extract stem data for a given datasource from BIEN

BIEN_ranges_genus

Download range maps for given genus.

BIEN_ranges_list

List available range maps

BIEN_stem_sampling_protocol

Download stem data using a specified sampling protocol.

BIEN_trait_mean

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

BIEN_taxonomy_genus

Extract taxonomic information for genera

BIEN_stem_species

Extract stem data for specified species from BIEN

BIEN_ranges_load_species

Load range maps for specified species.

BIEN_trait_genus

Download trait data for given genera.

BIEN_trait_species

Download trait data for given species.

.collection_check

Set query details

BIEN_ranges_species

Download range maps for given species.

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

BIEN_ranges_species_bulk

Extract range data for large numbers of species

BIEN_trait_traitbygenus

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

BIEN_trait_trait

Download all measurements of a specific trait(s).

BIEN_taxonomy_family

Extract taxonomic information for families

BIEN_trait_list

List all available types of trait data

Check that value is character

Set query details

BIEN_trait_traitbyfamily

Download trait data for given families and traits.

.geovalid_check

Set query details

BIEN_trait_traits_per_species

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

Run an SQL query on the BIEN database.

.collection_check_plot

Set query details

.native_check_plot

Set query details

Set query details

Set query details

.newworld_check_stem

Set query details

Set query details

BIEN_trait_traitbyspecies

Download trait data for given species and trait.

.native_check_stem

Set query details

BIEN_trait_country

Download trait data for given country.

BIEN_taxonomy_species

Extract taxonomic information for species

BIEN_trait_family

Download trait data for given families.

Set query details

.political_check_stem

Set query details

Check that value is logical

.source_check_traits

Set query details

.cultivated_check

Set query details

.collection_check_stem

Set query details

.political_check_traits

Set query details

.cultivated_check_plot

Set query details

.taxonomy_check

Set query details

.newworld_check_plot

Set query details

.cultivated_check_stem

Set query details

.taxonomy_check_plot

Set query details

.is_log_or_null

Check that value is logical or null

.newworld_check

Set query details

.natives_check_plot

Set query details

Set query details

.observation_check

Set query details

Check that value is numeric

.political_check_plot

Set query details

.political_check

Set query details

.vfoi_check_stem

Set query details

.natives_check_stem

Set query details

.taxonomy_check_stem

Set query details

.taxonomy_check_traits

Set query details

BIEN_metadata_list_political_names

List political divisions and associated geonames codes.

BIEN: Tools for accessing the BIEN database.

BIEN_list_country

Extract species list by country

BIEN_list_state

Extract a species list by state/province

Extract a list of species within a given sf polygon.

BIEN_metadata_match_data

Check for differing records between old and new dataframes.

BIEN_metadata_citation

Generate citations for data extracted from BIEN.

BIEN_list_county

Extract a species list by county.