BIEN R package

Brian Maitner

2023-01-05

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.

##Data Usage Agreement Please read the data usage agreement, available at: https://bien.nceas.ucsb.edu/bien/biendata/data-use-policy/

##Data Usage: Warnings and Caveats

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”.

##Database connection issues 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 Function names in the BIEN package follow a naming convention which was designed to make locating the desired function easier:

• All function names begin with the prefix “BIEN_”
• Functions to download occurrence records begin with the prefix “BIEN_occurrence_”
• Functions to download range maps begin with the prefix “BIEN_ranges_”
• Functions to download trait data begin with the prefix “BIEN_trait_”
• Functions to download species lists (or other lists) begin with the prefix “BIEN_list_”
• Functions to download plot data begin with the prefix “BIEN_plot_”
• Functions to download stem data begin with the prefix “BIEN_stem_”
• Functions to download taxonomic information begin with the prefix “BIEN_taxonomy_”
• Functions to download phylogenies begin with the prefix “BIEN_phylogeny_”
• Functions to access metadata begin with the prefix “BIEN_metadata_”

##Function Directory For full information on each function, see the associated help file.

###BIEN_metadata functions * BIEN_metadata_database_version Returns the BIEN database version number and release date * BIEN_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 functions * BIEN_list_all Lists all species present in the BIEN database * BIEN_list_country Produces species lists by country * BIEN_list_county Produces species lists by county * BIEN_list_state Produces species lists by state/province * BIEN_list_sf Produces species lists using an sf object

###BIEN_occurrence functions * BIEN_occurrence_box Returns all occurrence records within a GIS bounding box * BIEN_occurrence_country Returns all occurrence records within a given country * BIEN_occurrence_family Returns all occurrence records for a specified family * BIEN_occurrence_genus Returns all occurrence records for a specified genus * BIEN_occurrence_species Returns all occurrence records for a specified species * BIEN_occurrence_state Returns all occurrences records within a given state/province * BIEN_occurrence_occurrences_per_species Returns data on the number of occurrence records for species in the BIEN database * BIEN_occurrence_sf Returns occurrence records falling within the boundaries of an sf object.

###BIEN_ranges functions * BIEN_ranges_genus Downloads range maps for all the species within a given genus/genera * BIEN_ranges_species Downloads range maps for given species * BIEN_ranges_box Downloads range maps intersecting a given GIS bounding box * BIEN_ranges_list Lists available range maps * BIEN_ranges_sf Downloads range maps intersecting a user-supplied sf object.

###BIEN_trait functions * BIEN_trait_family Returns all available trait data for given families * BIEN_trait_genus Returns all available trait data for given genera * BIEN_trait_list Lists all available types of trait * BIEN_trait_mean Estimates species mean trait values using Genus or Family level data where needed * BIEN_trait_species Returns all available trait data for given species * BIEN_trait_trait Returns all available trait data for given trait(s) * BIEN_trait_traitbyfamily Returns specific trait data for given family * BIEN_trait_traitbygenus Returns specific trait data for given genus * BIEN_trait_traitbyspecies Returns specific trait data for given species * BIEN_trait_traits_per_species Returns data on the number of trait observations for each trait for each species in the BIEN database

###BIEN_plot functions * BIEN_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 functions * 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 functions * 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 functions * 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.