Tools for Accessing the Botanical Information and Ecology Network Database


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Documentation for package ‘BIEN’ version 1.2.4

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BIEN-package BIEN: Tools for accessing the BIEN database.
BIEN BIEN: Tools for accessing the BIEN database.
BIEN_list_all Extract a list of all species in the BIEN database.
BIEN_list_country Extract species list by country
BIEN_list_county Extract a species list by county.
BIEN_list_spatialpolygons Extract a list of species within a given spatialpolygons.
BIEN_list_state Extract a species list by state/province
BIEN_metadata_citation Generate citations for data extracted from BIEN.
BIEN_metadata_database_version Download the current BIEN database version and release date
BIEN_metadata_list_political_names List political divisions and associated geonames codes.
BIEN_metadata_match_data Check for differing records between old and new dataframes.
BIEN_occurrence_box Extract species occurrence records by a latitude/longitude bounding box.
BIEN_occurrence_country Extract species occurrence records by country.
BIEN_occurrence_county Extract species occurrence records by county.
BIEN_occurrence_family Extract species occurrences by family.
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_spatialpolygons Extract occurrence data for specified SpatialPolygons or SpatialPolygonsDataFrame
BIEN_occurrence_species Extract occurrence data for specified species from BIEN
BIEN_occurrence_state Extract species occurrence records by state.
BIEN_phylogeny_complete Download the complete BIEN phylogenies
BIEN_phylogeny_conservative Download the conservative BIEN phylogeny
BIEN_phylogeny_label_nodes Label nodes on a phylogeny
BIEN_plot_country Download plot data from specified countries.
BIEN_plot_dataset Download plot data by dataset.
BIEN_plot_datasource Download plot data from a given datasource.
BIEN_plot_list_datasource List available datasources.
BIEN_plot_list_sampling_protocols List available sampling protocols.
BIEN_plot_metadata Download plot metadata
BIEN_plot_name Download plot data by plot name.
BIEN_plot_sampling_protocol Download plot data using a specified sampling protocol.
BIEN_plot_spatialpolygons Download plot data from specified spatialPolygons object.
BIEN_plot_state Download plot data from specified states/provinces.
BIEN_ranges_box Download range maps that intersect a specified bounding box.
BIEN_ranges_genus Download range maps for given genus.
BIEN_ranges_intersect_species Download range maps that intersect the range of a given species.
BIEN_ranges_list List available range maps
BIEN_ranges_load_species Load range maps for specified species.
BIEN_ranges_shapefile_to_skinny Extract range data and convert to smaller "skinny" format
BIEN_ranges_skinny_ranges_to_richness_raster Build a richness raster from a skinny range file
BIEN_ranges_spatialpolygons Download range maps that intersect a user-supplied SpatialPolygons object.
BIEN_ranges_species Download range maps for given species.
BIEN_ranges_species_bulk Extract range data for large numbers of species
BIEN_stem_datasource Extract stem data for a given datasource from BIEN
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_stem_species Extract stem data for specified species from BIEN
BIEN_taxonomy_family Extract taxonomic information for families
BIEN_taxonomy_genus Extract taxonomic information for genera
BIEN_taxonomy_species Extract taxonomic information for species
BIEN_trait_country Download trait data for given country.
BIEN_trait_family Download trait data for given families.
BIEN_trait_genus Download trait data for given genera.
BIEN_trait_list List all available types of trait data
BIEN_trait_mean Calculates species mean values for a given trait, using Genus or Family level data where Species level data is lacking.
BIEN_trait_species Download trait data for given species.
BIEN_trait_trait Download all measurements of a specific trait(s).
BIEN_trait_traitbyfamily Download trait data for given families and traits.
BIEN_trait_traitbygenus Download trait data for given genus/genera and trait(s).
BIEN_trait_traitbyspecies Download trait data for given species and trait.
BIEN_trait_traits_per_species Count the number of trait observations for each species in the BIEN database