Package: BIEN 1.2.6

BIEN: Tools for Accessing the Botanical Information and Ecology Network Database

Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.

Authors:Brian Maitner [aut, cre]

BIEN_1.2.6.tar.gz
BIEN_1.2.6.zip(r-4.5)BIEN_1.2.6.zip(r-4.4)BIEN_1.2.6.zip(r-4.3)
BIEN_1.2.6.tgz(r-4.4-any)BIEN_1.2.6.tgz(r-4.3-any)
BIEN_1.2.6.tar.gz(r-4.5-noble)BIEN_1.2.6.tar.gz(r-4.4-noble)
BIEN_1.2.6.tgz(r-4.4-emscripten)BIEN_1.2.6.tgz(r-4.3-emscripten)
BIEN.pdf |BIEN.html✨
BIEN/json (API)
NEWS

# Install 'BIEN' in R:
install.packages('BIEN', repos = c('https://bmaitner.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

60 exports 1.64 score 27 dependencies 6 dependents 193 scripts 1.9k downloads

Last updated 2 years agofrom:257147fe39. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 24 2024
R-4.5-winOKAug 24 2024
R-4.5-linuxOKAug 24 2024
R-4.4-winOKAug 24 2024
R-4.4-macOKAug 24 2024
R-4.3-winOKAug 24 2024
R-4.3-macOKAug 24 2024

Exports:BIEN_list_allBIEN_list_countryBIEN_list_countyBIEN_list_sfBIEN_list_stateBIEN_metadata_citationBIEN_metadata_database_versionBIEN_metadata_list_political_namesBIEN_metadata_match_dataBIEN_occurrence_boxBIEN_occurrence_countryBIEN_occurrence_countyBIEN_occurrence_familyBIEN_occurrence_genusBIEN_occurrence_records_per_speciesBIEN_occurrence_sfBIEN_occurrence_speciesBIEN_occurrence_stateBIEN_phylogeny_completeBIEN_phylogeny_conservativeBIEN_phylogeny_label_nodesBIEN_plot_countryBIEN_plot_datasetBIEN_plot_datasourceBIEN_plot_list_datasourceBIEN_plot_list_sampling_protocolsBIEN_plot_metadataBIEN_plot_nameBIEN_plot_sampling_protocolBIEN_plot_sfBIEN_plot_stateBIEN_ranges_boxBIEN_ranges_genusBIEN_ranges_intersect_speciesBIEN_ranges_listBIEN_ranges_load_speciesBIEN_ranges_sfBIEN_ranges_shapefile_to_skinnyBIEN_ranges_skinny_ranges_to_richness_rasterBIEN_ranges_speciesBIEN_ranges_species_bulkBIEN_stem_datasourceBIEN_stem_familyBIEN_stem_genusBIEN_stem_sampling_protocolBIEN_stem_speciesBIEN_taxonomy_familyBIEN_taxonomy_genusBIEN_taxonomy_speciesBIEN_trait_countryBIEN_trait_familyBIEN_trait_genusBIEN_trait_listBIEN_trait_meanBIEN_trait_speciesBIEN_trait_traitBIEN_trait_traitbyfamilyBIEN_trait_traitbygenusBIEN_trait_traitbyspeciesBIEN_trait_traits_per_species

Dependencies:apeclassclassIntcodetoolsDBIdigestdoParallele1071fasterizeforeachiteratorsKernSmoothlatticemagrittrMASSnlmeproxyrasterRcppRcppArmadilloRPostgreSQLs2sfspterraunitswk

BIEN R package

Brian Maitner

Rendered fromBIEN.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2023-01-06
Started: 2017-01-12

BIEN tutorial

Rendered fromBIEN_tutorial.Rmdusingknitr::knitron Aug 24 2024.

Last update: 2023-01-06
Started: 2017-07-31

Readme and manuals

Help Manual

Help pageTopics
BIEN: Tools for accessing the BIEN database.BIEN-package BIEN
Extract a list of all species in the BIEN database.BIEN_list_all
Extract species list by countryBIEN_list_country
Extract a species list by county.BIEN_list_county
Extract a list of species within a given sf polygon.BIEN_list_sf
Extract a species list by state/provinceBIEN_list_state
Generate citations for data extracted from BIEN.BIEN_metadata_citation
Download the current BIEN database version and release dateBIEN_metadata_database_version
List political divisions and associated geonames codes.BIEN_metadata_list_political_names
Check for differing records between old and new dataframes.BIEN_metadata_match_data
Extract species occurrence records by a latitude/longitude bounding box.BIEN_occurrence_box
Extract species occurrence records by country.BIEN_occurrence_country
Extract species occurrence records by county.BIEN_occurrence_county
Extract species occurrences by family.BIEN_occurrence_family
Extract occurrence data from BIEN for specified generaBIEN_occurrence_genus
Count the number of (geoValid) occurrence records for each species in BIENBIEN_occurrence_records_per_species
Extract occurrence data for specified sf polygonBIEN_occurrence_sf
Extract occurrence data for specified species from BIENBIEN_occurrence_species
Extract species occurrence records by state.BIEN_occurrence_state
Download the complete BIEN phylogeniesBIEN_phylogeny_complete
Download the conservative BIEN phylogenyBIEN_phylogeny_conservative
Label nodes on a phylogenyBIEN_phylogeny_label_nodes
Download plot data from specified countries.BIEN_plot_country
Download plot data by dataset.BIEN_plot_dataset
Download plot data from a given datasource.BIEN_plot_datasource
List available datasources.BIEN_plot_list_datasource
List available sampling protocols.BIEN_plot_list_sampling_protocols
Download plot metadataBIEN_plot_metadata
Download plot data by plot name.BIEN_plot_name
Download plot data using a specified sampling protocol.BIEN_plot_sampling_protocol
Download plot data from specified sf object.BIEN_plot_sf
Download plot data from specified states/provinces.BIEN_plot_state
Download range maps that intersect a specified bounding box.BIEN_ranges_box
Download range maps for given genus.BIEN_ranges_genus
Download range maps that intersect the range of a given species.BIEN_ranges_intersect_species
List available range mapsBIEN_ranges_list
Load range maps for specified species.BIEN_ranges_load_species
Download range maps that intersect a user-supplied sf object.BIEN_ranges_sf
Extract range data and convert to smaller "skinny" formatBIEN_ranges_shapefile_to_skinny
Build a richness raster from a skinny range fileBIEN_ranges_skinny_ranges_to_richness_raster
Download range maps for given species.BIEN_ranges_species
Extract range data for large numbers of speciesBIEN_ranges_species_bulk
Extract stem data for a given datasource from BIENBIEN_stem_datasource
Extract stem data for specified families from BIENBIEN_stem_family
Extract stem data for specified genera from BIENBIEN_stem_genus
Download stem data using a specified sampling protocol.BIEN_stem_sampling_protocol
Extract stem data for specified species from BIENBIEN_stem_species
Extract taxonomic information for familiesBIEN_taxonomy_family
Extract taxonomic information for generaBIEN_taxonomy_genus
Extract taxonomic information for speciesBIEN_taxonomy_species
Download trait data for given country.BIEN_trait_country
Download trait data for given families.BIEN_trait_family
Download trait data for given genera.BIEN_trait_genus
List all available types of trait dataBIEN_trait_list
Calculates species mean values for a given trait, using Genus or Family level data where Species level data is lacking.BIEN_trait_mean
Download trait data for given species.BIEN_trait_species
Download all measurements of a specific trait(s).BIEN_trait_trait
Download trait data for given families and traits.BIEN_trait_traitbyfamily
Download trait data for given genus/genera and trait(s).BIEN_trait_traitbygenus
Download trait data for given species and trait.BIEN_trait_traitbyspecies
Count the number of trait observations for each species in the BIEN databaseBIEN_trait_traits_per_species