The Botanical Information and Ecology Network(BIEN) R package provides access to the BIEN database as well as useful tools for working with the BIEN data.
Please read the data usage agreement, available at: https://bien.nceas.ucsb.edu/bien/biendata/data-use-policy/
Please be aware of quality and appropriateness of BIEN data for the analyses that you may wish to perform or information that you would like to obtain
Versioning - data available via BIENdata.org and the the BIEN R package (BIEN) are being updated and improved. This is an active collaborative group who is aiming to continue to improve the quality of botanical information and data. As a result, users should take note of the version number (using the function BIEN_metadata_database_version() ) and be sure to check back periodically for updates. Checking for new results to a query can be done using the function BIEN_metadata_match_data().
Data quality - All data are presented ‘as is’. Default BIEN downloads return all data associated with a given taxonomic name string. There may be additional issues associated with a given name string. Please be aware that data returned may also include data whose geographic coordinates and cultivated status are uncertain or unverifiable.
Hybrids - Hybrid species are assigned the specific epithet "x" by the TNRS. To view the full name information for these occurrences, set "all.taxonomy = TRUE".
Some institution and computer programs (e.g. some antivirus programs) block the SQL connections that this package relies on. While we are exploring ways around this issue, at present the simplest method is to use the package on a computer/network that doesn't block SQL connections.
Function names in the BIEN package follow a naming convention which was designed to make locating the desired function easier:
For full information on each function, see the associated help file.
BIEN_metadata_database_version
Returns the BIEN database version number and release dateBIEN_metadata_match_data
Compares the stored results of two (old vs new) queries to check for additions or deletions.BIEN_metadata_citation
Generates information needed to cite data downloaded from BIEN.BIEN_metadata_list_political_names
Provides a list of political division names used by BIEN.BIEN_list_all
Lists all species present in the BIEN databaseBIEN_list_country
Produces species lists by countryBIEN_list_county
Produces species lists by countyBIEN_list_state
Produces species lists by state/provinceBIEN_list_sf
Produces species lists using an sf objectBIEN_occurrence_box
Returns all occurrence records within a GIS bounding box BIEN_occurrence_country
Returns all occurrence records within a given countryBIEN_occurrence_family
Returns all occurrence records for a specified familyBIEN_occurrence_genus
Returns all occurrence records for a specified genusBIEN_occurrence_species
Returns all occurrence records for a specified speciesBIEN_occurrence_state
Returns all occurrences records within a given state/provinceBIEN_occurrence_occurrences_per_species
Returns data on the number of occurrence records for species in the BIEN databaseBIEN_occurrence_sf
Returns occurrence records falling within the boundaries of an sf object.BIEN_ranges_genus
Downloads range maps for all the species within a given genus/generaBIEN_ranges_species
Downloads range maps for given speciesBIEN_ranges_box
Downloads range maps intersecting a given GIS bounding boxBIEN_ranges_list
Lists available range mapsBIEN_ranges_sf
Downloads range maps intersecting a user-supplied sf object.BIEN_trait_family
Returns all available trait data for given familiesBIEN_trait_genus
Returns all available trait data for given generaBIEN_trait_list
Lists all available types of traitBIEN_trait_mean
Estimates species mean trait values using Genus or Family level data where neededBIEN_trait_species
Returns all available trait data for given speciesBIEN_trait_trait
Returns all available trait data for given trait(s)BIEN_trait_traitbyfamily
Returns specific trait data for given familyBIEN_trait_traitbygenus
Returns specific trait data for given genusBIEN_trait_traitbyspecies
Returns specific trait data for given speciesBIEN_trait_traits_per_species
Returns data on the number of trait observations for each trait for each species in the BIEN databaseBIEN_plot_datasource
Downloads all plot data from a given datasource.BIEN_plot_list_datasource
List all datasources in the BIEN database.BIEN_plot_country
Downloads all plot data from specified countries.BIEN_plot_state
Downloads all plot data from specified states/provinces.BIEN_plot_list_sampling_protocols
List all available sampling protocols.BIEN_plot_sampling_protocol
Downloads all plot data using a specified sampling protocol.BIEN_stem_species
Downloads all stem data for given species.BIEN_stem_genus
Downloads all stem data for given genera.BIEN_stem_family
Downloads all stem data for given families.BIEN_taxonomy_species
Downloads all taxonomic information for given species.BIEN_taxonomy_genus
Downloads all taxonomic information for given genera.BIEN_taxonomy_family
Downloads all taxonomic information for given families.BIEN_phylogeny_complete
Downloads a specified number of the BIEN phylogeny replicates.BIEN_phylogeny_conservative
Downloads the conservative BIEN phylogeny, which only includes species with molecular data available.Any scripts or data that you put into this service are public.
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