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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 boxBIEN_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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.