BIEN: Tools for accessing the BIEN database.

Description

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.

Getting started

Type vignette("BIEN") to view the vignette, which contains useful information on the BIEN package.

Author(s)

Maintainer: Brian Maitner bmaitner@gmail.com

References

Maitner BS, Boyle B, Casler N, et al. The BIEN R package: A tool to access the Botanical Information and Ecology Network (BIEN) Database. Methods Ecol Evol. 2018;9:373-379. https://doi.org/10.1111/2041-210X.12861

Run an SQL query on the BIEN database.

Description

.BIEN_sql is an internal function used to submit SQL queries.

Usage

.BIEN_sql(
  query,
  view_full_occurrence_individual = NULL,
  agg_traits = NULL,
  species_by_political_division = NULL,
  bien_species_all = NULL,
  ranges = NULL,
  bien_taxonomy = NULL,
  phylogeny = NULL,
  bien_metadata = NULL,
  plot_metadata = NULL,
  analytical_stem = NULL,
  datasource = NULL,
  centroid = NULL,
  limit = NULL,
  return.query = FALSE,
  schema = NULL,
  print.query = FALSE,
  fetch.query = TRUE,
  record_limit = 10000
)

Arguments

Value

A dataframe returned by the query.

Note

Using fetch.query = TRUE provides better error handling, but fetch.query = FALSE results in a more useful (but uncatchable) error.

Examples

## Not run: 
.BIEN_sql("SELECT DISTINCT country, scrubbed_species_binomial FROM view_full_occurrence_individual 
WHERE country in ( 'United States' );")
## End(Not run)

Set query details

Description

Helper function to set query components.

Usage

.collection_check(collection.info)

Set query details

Description

Helper function to set query components.

Usage

.collection_check_plot(collection.info)

Set query details

Description

Helper function to set query components.

Usage

.collection_check_stem(collection.info)

Set query details

Description

Helper function to set query components.

Usage

.cultivated_check(cultivated)

Set query details

Description

Helper function to set query components.

Usage

.cultivated_check_plot(cultivated)

Set query details

Description

Helper function to set query components.

Usage

.cultivated_check_stem(cultivated)

Set query details

Description

Helper function to set query components.

Usage

.genus_check(genus)

Arguments

Set query details

Description

Helper function to set query components.

Usage

.geovalid_check(only.geovalid)

Check that value is character

Description

Helper function to check data format.

Usage

.is_char(x)

Examples

## Not run: 
is_char(species)
## End(Not run)

Check that value is logical

Description

Helper function to check data format.

Usage

.is_log(x)

Examples

## Not run: 
is_log(TRUE)
## End(Not run)

Check that value is logical or null

Description

Helper function to check data format.

Usage

.is_log_or_null(x)

Examples

## Not run: 
is_log_or_null(new.world)
## End(Not run)

Check that value is numeric

Description

Helper function to check data format.

Usage

.is_num(x)

Examples

## Not run: 
is_num(min.lat)
## End(Not run)

Set query details

Description

Helper function to set query components.

Usage

.md_check_plot(all.metadata)

Set query details

Description

Helper function to set query components.

Usage

.md_check_stem(all.metadata)

Set query details

Description

Helper function to set query components.

Usage

.native_check(native.status)

Set query details

Description

Helper function to set query components.

Usage

.native_check_plot(native.status)

Set query details

Description

Helper function to set query components.

Usage

.native_check_stem(native.status)

Set query details

Description

Helper function to set query components.

Usage

.natives_check(natives.only)

Set query details

Description

Helper function to set query components.

Usage

.natives_check_plot(natives.only)

Set query details

Description

Helper function to set query components.

Usage

.natives_check_stem(natives.only)

Set query details

Description

Helper function to set query components.

Usage

.newworld_check(new.world)

Set query details

Description

Helper function to set query components.

Usage

.newworld_check_plot(new.world)

Set query details

Description

Helper function to set query components.

Usage

.newworld_check_stem(new.world)

Set query details

Description

Helper function to set query components.

Usage

.observation_check(observation.type)

Set query details

Description

Helper function to set query components.

Usage

.political_check(political.boundaries)

Set query details

Description

Helper function to set query components.

Usage

.political_check_plot(political.boundaries)

Set query details

Description

Helper function to set query components.

Usage

.political_check_stem(political.boundaries)

Set query details

Description

Helper function to set query components.

Usage

.political_check_traits(political.boundaries)

Set query details

Description

Helper function to set query components.

Usage

.source_check_traits(source.citation)

Set query details

Description

Helper function to set query components.

Usage

.species_check(species)

Arguments

Set query details

Description

Helper function to set query components.

Usage

.taxonomy_check(all.taxonomy)

Set query details

Description

Helper function to set query components.

Usage

.taxonomy_check_plot(all.taxonomy)

Set query details

Description

Helper function to set query components.

Usage

.taxonomy_check_stem(all.taxonomy)

Set query details

Description

Helper function to set query components.

Usage

.taxonomy_check_traits(all.taxonomy)

Set query details

Description

Helper function to set query components.

Usage

.vfoi_check_stem(native.status, cultivated, natives.only, collection.info)

Extract a list of all species in the BIEN database.

Description

BIEN_list_all produces a list of all species in the BIEN database.

Usage

BIEN_list_all(...)

Arguments

Value

Dataframe containing a list of all species in the BIEN database.

See Also

Other list functions: BIEN_list_country(), BIEN_list_county(), BIEN_list_sf(), BIEN_list_state()

Examples

## Not run: 
species_list<-BIEN_list_all()
## End(Not run)

Extract species list by country

Description

BIEN_list_country downloads a list of all species within a country or countries from the BIEN database.

Usage

BIEN_list_country(
  country = NULL,
  country.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  ...
)

Arguments

Value

Dataframe containing species list(s) for the specified country or countries.

Note

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

See Also

Other list functions: BIEN_list_all(), BIEN_list_county(), BIEN_list_sf(), BIEN_list_state()

Examples

## Not run: 
BIEN_list_country("Canada")
country_vector<-c("Canada","United States")
BIEN_list_country(country_vector)
## End(Not run)

Extract a species list by county.

Description

BIEN_list_county produces a list of all species with geovalidated occurrences falling within specified county or counties.

Usage

BIEN_list_county(
  country = NULL,
  state = NULL,
  county = NULL,
  country.code = NULL,
  state.code = NULL,
  county.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  ...
)

Arguments

Value

Dataframe containing species list(s) for the specified states/provinces.

Note

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

We recommend using country, state, and county rather than codes, since county names have not been fully standardized.

This function requires you supply either 1) a single state and country with one or more counties, or 2) vectors of equal length for each political level.

See Also

Other list functions: BIEN_list_all(), BIEN_list_country(), BIEN_list_sf(), BIEN_list_state()

Examples

## Not run: 
BIEN_list_county("United States", "Michigan", "Kent")
BIEN_list_county(country = "United States", state = "Michigan", county = "Kent")
county_vector<-c("Kent","Kalamazoo")
BIEN_list_county(country = "United States", state = "Michigan", county = county_vector)
## End(Not run)

Extract a list of species within a given sf polygon.

Description

BIEN_list_sf produces a list of all species with occurrence records falling within a user-supplied sf object.

Usage

BIEN_list_sf(sf, cultivated = FALSE, new.world = NULL, ...)

Arguments

Value

Dataframe containing a list of all species with occurrences in the supplied sf object.

See Also

Other list functions: BIEN_list_all(), BIEN_list_country(), BIEN_list_county(), BIEN_list_state()

Examples

## Not run: 
library(sf)

BIEN_ranges_species("Carnegiea gigantea") # saves ranges to the current working directory

sf <- st_read(dsn = ".",
              layer = "Carnegiea_gigantea")

species_list <- BIEN_list_sf(sf = sf)

## End(Not run)

Extract a species list by state/province

Description

BIEN_list_state produces a list of all species with geovalidated occurrences falling within specified state(s) or province(s).

Usage

BIEN_list_state(
  country = NULL,
  country.code = NULL,
  state = NULL,
  state.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  ...
)

Arguments

Value

Dataframe containing species list(s) for the specified states/provinces.

Note

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

See Also

Other list functions: BIEN_list_all(), BIEN_list_country(), BIEN_list_county(), BIEN_list_sf()

Examples

## Not run: 
BIEN_list_state("United States","Michigan")
state_vector<-c("Michigan","Arizona")
BIEN_list_state(country="United States", state= state_vector)
## End(Not run)

Generate citations for data extracted from BIEN.

Description

BIEN_metadata_citation guides a user through the proper documentation for data downloaded from the BIEN database.

Usage

BIEN_metadata_citation(
  dataframe = NULL,
  trait.dataframe = NULL,
  trait.mean.dataframe = NULL,
  bibtex_file = NULL,
  acknowledgement_file = NULL,
  ...
)

Arguments

Value

A list object containing information needed for data attribution. Full information for herbaria is available at http://sweetgum.nybg.org/science/ih/

See Also

Other metadata functions: BIEN_metadata_data_dictionaries(), BIEN_metadata_database_version(), BIEN_metadata_list_political_names(), BIEN_metadata_match_data(), BIEN_plot_metadata(), BIEN_ranges_list()

Examples

## Not run: 
BIEN_metadata_citation()#If you are referencing the phylogeny or range maps.
Xanthium_data<-BIEN_occurrence_species("Xanthium strumarium")
citations<-BIEN_metadata_citation(dataframe=Xanthium_data)#If you are referencing occurrence data
## End(Not run)

Download data dictionaries

Description

BIEN_metadata_data_dictionaries downloads the data dictionaries for the BIEN database.

Usage

BIEN_metadata_data_dictionaries(...)

Arguments

Value

A list containing data.frames containing different data dictionaries. "Tables" contains information on the contents of tables. "Columns" contains information on the contents of columns within tables. "Values" contains information on some of the values that are used to populated columns, particularly where these may be unclear. "rbien" contains information on some of the values returned by the BIEN R package.

See Also

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_database_version(), BIEN_metadata_list_political_names(), BIEN_metadata_match_data(), BIEN_plot_metadata(), BIEN_ranges_list()

Examples

## Not run: 
BIEN_metadata_data_dictionaries()
## End(Not run)

Download the current BIEN database version and release date

Description

BIEN_metadata_database_version downloads the current version number and release date for the BIEN database.

Usage

BIEN_metadata_database_version(...)

Arguments

Value

A data frame containing the current version number and release date for the BIEN database.

See Also

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_data_dictionaries(), BIEN_metadata_list_political_names(), BIEN_metadata_match_data(), BIEN_plot_metadata(), BIEN_ranges_list()

Examples

## Not run: 
BIEN_metadata_database_version()
## End(Not run)

List political divisions and associated geonames codes.

Description

BIEN_metadata_list_political_names downloads country, state, and county names and associated codes used by BIEN.

Usage

BIEN_metadata_list_political_names(...)

Arguments

Value

A dataframe containing political division names and their associated codes.

Note

Political names and codes follow http://www.geonames.org/

See Also

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_data_dictionaries(), BIEN_metadata_database_version(), BIEN_metadata_match_data(), BIEN_plot_metadata(), BIEN_ranges_list()

Examples

## Not run: 
BIEN_metadata_list_political_names()
## End(Not run)

Check for differing records between old and new dataframes.

Description

BIEN_metadata_match_data compares old and new dataframes, and can check whether they are identical or be used to select rows that are unique to the old or new versions.

Usage

BIEN_metadata_match_data(old, new, return = "identical")

Arguments

Value

Logical of varying length (depending on choice of "return" parameter)

Note

Since comparisons are done by row (except when using return="identical"), this function may fail to flag additions or deletions if they are exact duplicates of existing rows.

See Also

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_data_dictionaries(), BIEN_metadata_database_version(), BIEN_metadata_list_political_names(), BIEN_plot_metadata(), BIEN_ranges_list()

Examples

## Not run: 
new<-BIEN_occurrence_species("Acer nigrum")
old<-new[-1:-4,]#simulate having an older dataset by removing four rows
BIEN_metadata_match_data(old,new,return="identical")
BIEN_metadata_match_data(old,new,return="additions")
## End(Not run)

Extract species occurrence records by a latitude/longitude bounding box.

Description

BIEN_occurrence_box extracts occurrences records falling within the specific area.

Usage

BIEN_occurrence_box(
  min.lat,
  max.lat,
  min.long,
  max.long,
  species = NULL,
  genus = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = TRUE,
  collection.info = FALSE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified area.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Specifying species and/or genera will limit records returned to that set of taxa.

See Also

Other occurrence functions: BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
output_test<-
BIEN_occurrence_box(min.lat = 32,max.lat = 33,min.long = -114,max.long = -113,
cultivated = TRUE, new.world = FALSE)
## End(Not run)

Extract species occurrence records by country.

Description

BIEN_occurrence_country extracts occurrences records for the specified country/countries.

Usage

BIEN_occurrence_country(
  country = NULL,
  country.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  only.geovalid = TRUE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified country.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
BIEN_occurrence_country("Cuba")
country_vector<-c("Cuba","Bahamas")
BIEN_occurrence_country(country_vector)
## End(Not run)

Extract species occurrence records by county.

Description

BIEN_occurrence_county extracts occurrences records for the specified county or counties.

Usage

BIEN_occurrence_county(
  country = NULL,
  state = NULL,
  county = NULL,
  country.code = NULL,
  state.code = NULL,
  county.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified states/provinces.

Note

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

This function requires you supply either 1) a single country with one or more states, or 2) vectors of equal length for each political level.

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
BIEN_occurrence_county("United States","Arizona","Pima")
country_vector<-c("United States","United States")
state_vector<-c("Arizona","Michigan")
county_vector<-c("Pima","Kent")
BIEN_occurrence_county(country=country_vector, state = state_vector, county = county_vector)
## End(Not run)

Extract species occurrences by family.

Description

BIEN_occurrence_family extracts all occurrences for a given family (or families) from the BIEN database.

Usage

BIEN_occurrence_family(
  family,
  cultivated = FALSE,
  new.world = NULL,
  observation.type = FALSE,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  only.geovalid = TRUE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified family/families.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
BIEN_occurrence_family("Theaceae")
family_vector<-c("Theaceae","Ericaceae")
BIEN_occurrence_family(family_vector)
## End(Not run)

Extract occurrence data from BIEN for specified genera

Description

BIEN_occurrence_genus downloads occurrence records for specific genus/genera from the BIEN database.

Usage

BIEN_occurrence_genus(
  genus,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified genera.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
BIEN_occurrence_genus("Abutilon")
genus_vector<-c("Abutilon","Abronia")
BIEN_occurrence_genus(genus_vector)
BIEN_occurrence_genus(genus = "Abutilon",cultivated = TRUE,new.world = FALSE)
## End(Not run)

Count the number of (geoValid) occurrence records for each species in BIEN

Description

BIEN_occurrence_records_per_species downloads a count of the number of geovalidated occurrence records for each species in the BIEN database.

Usage

BIEN_occurrence_records_per_species(species = NULL, ...)

Arguments

Value

A dataframe listing the number of geovalidated occurrence records for each species in the BIEN database.

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_sf(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
occurrence_counts<-BIEN_occurrence_records_per_species()
## End(Not run)

Extract occurrence data for specified sf polygon

Description

BIEN_occurrence_sf downloads occurrence records falling within a user-specified sf polygon

Usage

BIEN_occurrence_sf(
  sf,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  ...
)

Arguments

Value

Dataframe containing occurrence records falling within the polygon.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_species(), BIEN_occurrence_state()

Examples

## Not run: 
library(sf)  

# first, we download an example shapefile to use (a species range)

BIEN_ranges_species("Carnegiea gigantea")#saves range to the current working directory

# load the range map as an sf object

sf <- st_read(dsn = ".",layer = "Carnegiea_gigantea")

# get the occurrences that occur within the polygon.

species_occurrences <- BIEN_occurrence_sf(sf = sf)

## End(Not run)

Extract occurrence data for specified species from BIEN

Description

BIEN_occurrence_species downloads occurrence records for specific species from the BIEN database.

Usage

BIEN_occurrence_species(
  species,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  only.geovalid = TRUE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified species.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_state()

Examples

## Not run: 
BIEN_occurrence_species("Abies amabilis")
species_vector<-c("Abies amabilis", "Acer nigrum")
BIEN_occurrence_species(species_vector)
BIEN_occurrence_species(species_vector,all.taxonomy = TRUE)
## End(Not run)

Extract species occurrence records by state.

Description

BIEN_occurrence_state extracts occurrences records for the specified state(s).

Usage

BIEN_occurrence_state(
  country = NULL,
  state = NULL,
  country.code = NULL,
  state.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  observation.type = FALSE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  ...
)

Arguments

Value

Dataframe containing occurrence records for the specified states/provinces.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

This function requires you supply either 1) a single country with one or more states, or 2) vectors of equal length for each political level.

See Also

Other occurrence functions: BIEN_occurrence_box(), BIEN_occurrence_country(), BIEN_occurrence_county(), BIEN_occurrence_family(), BIEN_occurrence_genus(), BIEN_occurrence_records_per_species(), BIEN_occurrence_sf(), BIEN_occurrence_species()

Examples

## Not run: 
BIEN_occurrence_state("United States","Rhode Island")
state_vector<-c("Rhode Island","Maryland")
BIEN_occurrence_state(country="United States",state=state_vector)
## End(Not run)

Download the complete BIEN phylogenies

Description

BIEN_phylogeny_complete downloads a specified number of the BIEN phylogeny replicates.

Usage

BIEN_phylogeny_complete(n_phylogenies = 1, seed = NULL, replicates = NULL, ...)

Arguments

Value

A phylo or multiphylo object containing the specified phylogenies

Note

Information on the construction of the BIEN phylogenies is available online at https://bien.nceas.ucsb.edu/bien/biendata/bien-2/phylogeny/

See Also

Other phylogeny functions: BIEN_phylogeny_conservative(), BIEN_phylogeny_label_nodes()

Examples

## Not run: 
phylos<-BIEN_phylogeny_complete(n_phylogenies = 10,seed = 1)
phylos<-BIEN_phylogeny_complete(replicates = c(1,2,99,100))
## End(Not run)

Download the conservative BIEN phylogeny

Description

BIEN_phylogeny_conservative downloads the conservative BIEN phylogeny, which only includes species with molecular data available.

Usage

BIEN_phylogeny_conservative(...)

Arguments

Value

A phylo object containing the BIEN conservative phylogeny

Note

Information on the construction of the BIEN phylogenies is available online at https://bien.nceas.ucsb.edu/bien/biendata/bien-2/phylogeny/

See Also

Other phylogeny functions: BIEN_phylogeny_complete(), BIEN_phylogeny_label_nodes()

Examples

## Not run: 
BIEN_phylo<-BIEN_phylogeny_conservative()
## End(Not run)

Label nodes on a phylogeny

Description

BIEN_phylogeny_label_nodes will label the nodes on a phylogeny based on either the BIEN taxonomy or user-supplied taxa.

Usage

BIEN_phylogeny_label_nodes(
  phylogeny,
  family = TRUE,
  genus = FALSE,
  other_taxa = NULL,
  ...
)

Arguments

Value

Input phylogeny with labeled nodes.

Note

Information on the construction of the BIEN phylogenies is available online at https://bien.nceas.ucsb.edu/bien/biendata/bien-2/phylogeny/

See Also

Other phylogeny functions: BIEN_phylogeny_complete(), BIEN_phylogeny_conservative()

Examples

## Not run: 
phylogeny<-BIEN_phylogeny_conservative()

phylogeny<-drop.tip(phy = phylogeny,tip = 101:length(phylogeny$tip.label))
plot.phylo(x = phylogeny,show.tip.label = FALSE)

fam_nodes<-BIEN_phylogeny_label_nodes(phylogeny = phylogeny,family = TRUE)
plot.phylo(x = fam_nodes,show.tip.label = FALSE, show.node.label = TRUE)

gen_nodes<-BIEN_phylogeny_label_nodes(phylogeny = phylogeny, family = FALSE, genus = TRUE)
plot.phylo(x = gen_nodes, show.tip.label = FALSE, show.node.label = TRUE)

other_taxa <- as.data.frame(matrix(nrow = 10,ncol = 2))
colnames(other_taxa)<-c("taxon","species")
other_taxa$taxon[1:5]<-"A" #Randomly assign a few species to taxon A
other_taxa$taxon[6:10]<-"B" #Randomly assign a few species to taxon B
tax_nodes <- 
 BIEN_phylogeny_label_nodes(phylogeny = phylogeny,
                            family = FALSE, genus = FALSE, other_taxa = other_taxa)
plot.phylo(x = tax_nodes,show.tip.label = FALSE,show.node.label = TRUE)
## End(Not run)

Download plot data from specified countries.

Description

BIEN_plot_country downloads all plot data from specified countries.

Usage

BIEN_plot_country(
  country = NULL,
  country.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified countries.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

See Also

Other plot functions: BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_country("Costa Rica")
BIEN_plot_country(c("Costa Rica","Panama"))
## End(Not run)

Download plot data by dataset.

Description

BIEN_plot_dataset downloads all plot data for a given dataset or datasets.

Usage

BIEN_plot_dataset(
  dataset,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified dataset.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Datasets and related information can be looked up with BIEN_plot_metadata

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_dataset("Gentry Transect Dataset")
## End(Not run)

Download plot data from a given datasource.

Description

BIEN_plot_datasource downloads all plot data from a given datasource.

Usage

BIEN_plot_datasource(
  datasource,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified datasource.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_datasource("SALVIAS")
## End(Not run)

List available datasources.

Description

BIEN_plot_list_datasource list all plot datasources in the BIEN database.

Usage

BIEN_plot_list_datasource(...)

Arguments

Value

A vector of available datasources.

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_list_datasource()
## End(Not run)

List available sampling protocols.

Description

BIEN_plot_list_sampling_protocols list all available sampling protocols.

Usage

BIEN_plot_list_sampling_protocols(...)

Arguments

Value

A vector of available sampling protocols.

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_list_sampling_protocols()
## End(Not run)

Download plot metadata

Description

BIEN_plot_metadata downloads the plot metadata table.

Usage

BIEN_plot_metadata(...)

Arguments

Value

A dataframe containing plot metadata.

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_data_dictionaries(), BIEN_metadata_database_version(), BIEN_metadata_list_political_names(), BIEN_metadata_match_data(), BIEN_ranges_list()

Examples

## Not run: 
BIEN_plot_metadata()
## End(Not run)

Download plot data by plot name.

Description

BIEN_plot_name downloads all plot data for a set of plot names.

Usage

BIEN_plot_name(
  plot.name,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified plot(s).

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Plot names can be looked up with BIEN_plot_metadata.

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_sampling_protocol(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_name("SR-1")
## End(Not run)

Download plot data using a specified sampling protocol.

Description

BIEN_plot_sampling_protocol downloads all plot data using a specified sampling protocol.

Usage

BIEN_plot_sampling_protocol(
  sampling_protocol,
  cultivated = FALSE,
  new.world = FALSE,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified datasource.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sf(), BIEN_plot_state()

Examples

## Not run: 
BIEN_plot_sampling_protocol("Point-intercept")
## End(Not run)

Download plot data from specified sf object.

Description

BIEN_plot_sf downloads all plot data falling within a supplied sf polygon.

Usage

BIEN_plot_sf(
  sf,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = TRUE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all plot data from within the specified sf polygon.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_state()

Examples

## Not run: 
library(sf)

BIEN_ranges_species("Carnegiea gigantea") #saves ranges to the current working directory

sf <- st_read(dsn = ".",
              layer = "Carnegiea_gigantea")

saguaro_plot_data <- BIEN_plot_sf(sf = sf)

## End(Not run)

Download plot data from specified states/provinces.

Description

BIEN_plot_state downloads all plot data from specified states/provinces.

Usage

BIEN_plot_state(
  country = NULL,
  state = NULL,
  country.code = NULL,
  state.code = NULL,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = TRUE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified states.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Political division (or political division code) spelling needs to be exact and case-sensitive, see BIEN_metadata_list_political_names for a list of political divisions and associated codes.

This function requires you supply either 1) a single country with one or states, or 2) vectors of equal length for each political level.

See Also

Other plot functions: BIEN_plot_country(), BIEN_plot_dataset(), BIEN_plot_datasource(), BIEN_plot_list_datasource(), BIEN_plot_list_sampling_protocols(), BIEN_plot_metadata(), BIEN_plot_name(), BIEN_plot_sampling_protocol(), BIEN_plot_sf()

Examples

## Not run: 
BIEN_plot_state(country="United States", state="Colorado")
BIEN_plot_state(country="United States",state= c("Colorado","California"))
## End(Not run)

Download range maps that intersect a specified bounding box.

Description

BIEN_ranges_box extracts range maps for a specified bounding box.

Usage

BIEN_ranges_box(
  min.lat,
  max.lat,
  min.long,
  max.long,
  directory = NULL,
  species.names.only = FALSE,
  return.species.list = TRUE,
  crop.ranges = FALSE,
  include.gid = FALSE,
  ...
)

Arguments

Value

Range maps for all available species within the specified bounding box.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 
temp_dir <- file.path(tempdir(), "BIEN_temp") #Set a working directory
BIEN_ranges_box(42,43,-85,-84,species.names.only = TRUE)
BIEN_ranges_box(42,43,-85,-84,directory = temp_dir)
## End(Not run)

Download range maps for given genus.

Description

BIEN_ranges_genus extracts range maps for the specified genera.

Usage

BIEN_ranges_genus(
  genus,
  directory = NULL,
  matched = TRUE,
  match_names_only = FALSE,
  include.gid = FALSE,
  ...
)

Arguments

Value

Range maps for all available species within the specified genera.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 
library(maps)
library(sf)

genus_vector <- c("Abies","Acer")

temp_dir <- file.path(tempdir(), "BIEN_temp")#Set a working directory

BIEN_ranges_genus(genus_vector)

BIEN_ranges_genus(genus = genus_vector,
                  match_names_only = TRUE)

BIEN_ranges_genus(genus = genus_vector,
                  directory = temp_dir) #saves ranges to a specified working directory

BIEN_ranges_genus("Abies")

BIEN_ranges_genus(genus = "Abies",
                  directory = temp_dir)

#Reading files

Abies_poly <- read_sf(dsn = temp_dir,layer = "Abies_lasiocarpa")

#Plotting files

plot(Abies_poly[1]) #plots the range, but doesn't mean much without any reference

map('world', fill = TRUE, col = "grey") #plots a world map (WGS84 projection), in grey

plot(Abies_poly[1],
     col="forest green",
     add = TRUE) #adds the range of Abies lasiocarpa to the map

# Getting data from the files (currently only species names)

Abies_poly$species#gives the species name associated with "Abies_poly"

## End(Not run)

Download range maps that intersect the range of a given species.

Description

BIEN_ranges_intersect_species extracts range maps for a specified bounding box.

Usage

BIEN_ranges_intersect_species(
  species,
  directory = NULL,
  species.names.only = FALSE,
  include.focal = TRUE,
  return.species.list = TRUE,
  include.gid = FALSE,
  ...
)

Arguments

Value

Range maps for all available species that intersect the range of the focal species.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 
temp_dir <- file.path(tempdir(), "BIEN_temp") #Set a working directory
BIEN_ranges_intersect_species(species = "Carnegiea_gigantea",
directory = temp_dir,include.focal = TRUE)
species_vector<-c("Carnegiea_gigantea","Echinocereus coccineus")
BIEN_ranges_intersect_species(species = species_vector,species.names.only = TRUE)

## End(Not run)

List available range maps

Description

BIEN_ranges_list a data.frame containing listing all range maps currently available.

Usage

BIEN_ranges_list(...)

Arguments

Value

A data.frame containing the available species and their associated GIDs.

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Other metadata functions: BIEN_metadata_citation(), BIEN_metadata_data_dictionaries(), BIEN_metadata_database_version(), BIEN_metadata_list_political_names(), BIEN_metadata_match_data(), BIEN_plot_metadata()

Examples

## Not run: 
available_maps<-BIEN_ranges_list()
## End(Not run)

Load range maps for specified species.

Description

BIEN_ranges_load_species returns spatial data for the specified species.

Usage

BIEN_ranges_load_species(species, ...)

Arguments

Value

A sf containing range maps for the specified species.

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 
library(maps)
species_vector<-c("Abies_lasiocarpa","Abies_amabilis")
abies_maps <- BIEN_ranges_load_species(species = species_vector)
xanthium_strumarium <- BIEN_ranges_load_species(species = "Xanthium strumarium")

#Plotting files
plot(abies_maps) # plots the sf, but doesn't mean much without any reference
map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey
plot(xanthium_strumarium,col="forest green",add = TRUE) #adds the range of X. strumarium
plot(abies_maps[1,], add = TRUE, col ="light green")

## End(Not run)

Download range maps that intersect a user-supplied sf object.

Description

BIEN_ranges_sf extracts range maps that intersect a specified simple features (sf) object.

Usage

BIEN_ranges_sf(
  sf,
  directory = NULL,
  species.names.only = FALSE,
  return.species.list = TRUE,
  crop.ranges = FALSE,
  include.gid = FALSE,
  ...
)

Arguments

Value

All range maps that intersect the user-supplied sf object.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 

# Here we use a range map as our example polygon

BIEN_ranges_species("Carnegiea gigantea") #saves ranges to the current working directory

# Read in the polygon  with sf   
sf <- sf::st_read(dsn = ".",
                  layer = "Carnegiea_gigantea")

BIEN_ranges_sf(sf = sf,
               limit = 10) 
               # We use the limit argument to return only 10 range maps.
               # Omit the limit argument to get all ranges

#Note that this will save many shapefiles to the working directory.

## End(Not run)

Extract range data and convert to smaller "skinny" format

Description

BIEN_ranges_shapefile_to_skinny converts ranges to a "skinny" format to save space.

Usage

BIEN_ranges_shapefile_to_skinny(directory, raster, skinny_ranges_file = NULL)

Arguments

Value

Matrix containing 2 columns: 1) Species name; and 2) the raster cell number it occurs within.

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 
BIEN_ranges_shapefile_to_skinny(directory = BIEN_ranges_species_bulk(species = c("Acer rubrum")),
raster = terra::rast(crs = "+proj=laea +lat_0=15 +lon_0=-80 +x_0=0 +y_0=0 +datum=WGS84 
+units=m +no_defs +ellps=WGS84 +towgs84=0,0,0",
           extent = terra::ext(c(-5261554,5038446,-7434988,7165012 )),
           resolution =c(100000,100000)
           )
)

## End(Not run)

Build a richness raster from a skinny range file

Description

BIEN_ranges_skinny_ranges_to_richness_raster takes in "skinny" range data and converts it to a richness raster.

Usage

BIEN_ranges_skinny_ranges_to_richness_raster(skinny_ranges, raster)

Arguments

Value

Raster

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_species(), BIEN_ranges_species_bulk()

Examples

## Not run: 


template_raster <- terra::rast(
  crs = "+proj=laea +lat_0=15 +lon_0=-80 +x_0=0 +y_0=0 +datum=WGS84 
  +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0",
  ext = ext(c(-5261554, 5038446, -7434988, 7165012 )),
  resolution =  c(100000, 100000))

#Download ranges and convert to a "skinny" format
skinny_ranges <- BIEN_ranges_shapefile_to_skinny(
directory = BIEN_ranges_species_bulk(species = c("Acer rubrum"), 
raster = template_raster)

#Convert from skinny format to richness raster                                                 
richness_raster<- BIEN_ranges_skinny_ranges_to_richness_raster(
 skinny_ranges = skinny_ranges,raster = template_raster)
 
 plot(richness_raster)

## End(Not run)

Download range maps for given species.

Description

BIEN_ranges_species extracts range maps for the specified species.

Usage

BIEN_ranges_species(
  species,
  directory = NULL,
  matched = TRUE,
  match_names_only = FALSE,
  include.gid = FALSE,
  ...
)

Arguments

Value

Range maps for specified species.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species_bulk()

Examples

## Not run: 
library(sf)
library(maps) #a convenient source of maps
species_vector <- c("Abies_lasiocarpa","Abies_amabilis")
BIEN_ranges_species(species_vector)
BIEN_ranges_species(species_vector, match_names_only = TRUE)
temp_dir <- file.path(tempdir(), "BIEN_temp")#Set a working directory
BIEN_ranges_species(species = species_vector,
                    directory = temp_dir)#saves ranges to a temporary directory
BIEN_ranges_species("Abies_lasiocarpa")
BIEN_ranges_species("Abies_lasiocarpa",
                    directory = temp_dir)

#Reading files

Abies_poly <- st_read(dsn = temp_dir,
                      layer = "Abies_lasiocarpa")

#Plotting files
plot(Abies_poly[1])#plots the range, but doesn't mean much without any reference
map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey

plot(Abies_poly[1],
     col = "forest green",
     add = TRUE) #adds the range of Abies lasiocarpa to the map

# Getting data from the files (currently only species names and a BIEN ID field)
Abies_poly$species#gives the species name associated with "Abies_poly"
## End(Not run)#'

Extract range data for large numbers of species

Description

BIEN_ranges_species_bulk downloads ranges for a large number of species using parallel processing.

Usage

BIEN_ranges_species_bulk(
  species = NULL,
  directory = NULL,
  batch_size = 1000,
  return_directory = TRUE,
  use_parallel = FALSE
)

Arguments

Value

Optionally, the directory to which the files were saved.

Note

This function may take a long time (hours) to run depending on the number of cores, download speed, etc.

See Also

Other range functions: BIEN_ranges_box(), BIEN_ranges_genus(), BIEN_ranges_intersect_species(), BIEN_ranges_list(), BIEN_ranges_load_species(), BIEN_ranges_sf(), BIEN_ranges_shapefile_to_skinny(), BIEN_ranges_skinny_ranges_to_richness_raster(), BIEN_ranges_species()

Examples

## Not run: 
#To download all BIEN ranges maps:
BIEN_ranges_species_bulk()

## End(Not run)

Extract stem data for a given datasource from BIEN

Description

BIEN_stem_datasource downloads occurrence records for specific datasources from the BIEN database.

Usage

BIEN_stem_datasource(
  datasource,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

Dataframe containing stem data for the specified datasource.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Setting either "cultivated" or "native.status" to TRUE will significantly slow the speed of a query.

#' @note For a list of available datasources, use BIEN_plot_list_datasource.

See Also

Other stem functions: BIEN_stem_family(), BIEN_stem_genus(), BIEN_stem_sampling_protocol(), BIEN_stem_species()

Examples

## Not run: 
BIEN_stem_datasource(datasource = "SALVIAS")
## End(Not run)

Extract stem data for specified families from BIEN

Description

BIEN_stem_family downloads occurrence records for specific families from the BIEN database.

Usage

BIEN_stem_family(
  family,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

Dataframe containing stem data for the specified families.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Setting either "cultivated" or "native.status" to TRUE will significantly slow the speed of a query.

See Also

Other stem functions: BIEN_stem_datasource(), BIEN_stem_genus(), BIEN_stem_sampling_protocol(), BIEN_stem_species()

Examples

## Not run: 
BIEN_stem_family(family = "Marantaceae")
family_vector<-c("Marantaceae", "Buxaceae")
BIEN_stem_family(family = family_vector)
BIEN_stem_family(family = family_vector, all.taxonomy = TRUE, native.status = TRUE)
## End(Not run)

Extract stem data for specified genera from BIEN

Description

BIEN_stem_genus downloads occurrence records for specific genera from the BIEN database.

Usage

BIEN_stem_genus(
  genus,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

Dataframe containing stem data for the specified genera.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Setting either "cultivated" or "native.status" to TRUE will significantly slow the speed of a query.

See Also

Other stem functions: BIEN_stem_datasource(), BIEN_stem_family(), BIEN_stem_sampling_protocol(), BIEN_stem_species()

Examples

## Not run: 
BIEN_stem_genus(genus = "Tovomita")
genus_vector<-c("Tovomita", "Myrcia")
BIEN_stem_genus(genus = genus_vector)
BIEN_stem_genus(genus = genus_vector, all.taxonomy = TRUE)
## End(Not run)

Download stem data using a specified sampling protocol.

Description

BIEN_stem_sampling_protocol downloads plot-based stem data using a specified sampling protocol.

Usage

BIEN_stem_sampling_protocol(
  sampling_protocol,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

A dataframe containing all data from the specified sampling protocol.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

See Also

Other stem functions: BIEN_stem_datasource(), BIEN_stem_family(), BIEN_stem_genus(), BIEN_stem_species()

Examples

## Not run: 
BIEN_stem_sampling_protocol("Point-intercept")
## End(Not run)

Extract stem data for specified species from BIEN

Description

BIEN_stem_species downloads occurrence records for specific species from the BIEN database.

Usage

BIEN_stem_species(
  species,
  cultivated = FALSE,
  new.world = NULL,
  all.taxonomy = FALSE,
  native.status = FALSE,
  natives.only = TRUE,
  political.boundaries = FALSE,
  collection.info = FALSE,
  all.metadata = FALSE,
  ...
)

Arguments

Value

Dataframe containing stem data for the specified species.

Note

US FIA coordinates have been fuzzed and swapped, for more details see: https://www.fia.fs.fed.us/tools-data/spatial/Policy/index.php

Setting either "cultivated" or "native.status" to TRUE will significantly slow the speed of a query.

See Also

Other stem functions: BIEN_stem_datasource(), BIEN_stem_family(), BIEN_stem_genus(), BIEN_stem_sampling_protocol()

Examples

## Not run: 
BIEN_stem_species("Abies amabilis")
species_vector<-c("Abies amabilis", "Acer nigrum")
BIEN_stem_species(species_vector)
BIEN_stem_species(species_vector,all.taxonomy = TRUE)
## End(Not run)

Extract taxonomic information for families

Description

BIEN_taxonomy_family downloads a dataframe of all taxonomic information for given families.

Usage

BIEN_taxonomy_family(family, ...)

Arguments

Value

Dataframe containing taxonomic information for the specified families.

See Also

Other taxonomy functions: BIEN_taxonomy_genus(), BIEN_taxonomy_species()

Examples

## Not run: 
BIEN_taxonomy_family("Orchidaceae")
family_vector<-c("Orchidaceae","Poaceae")
BIEN_taxonomy_family(family_vector)
## End(Not run)

Extract taxonomic information for genera

Description

BIEN_taxonomy_genus downloads a dataframe of all taxonomic information for given genera.

Usage

BIEN_taxonomy_genus(genus, ...)

Arguments

Value

Dataframe containing taxonomic information for the specified genera.

See Also

Other taxonomy functions: BIEN_taxonomy_family(), BIEN_taxonomy_species()

Examples

## Not run: 
BIEN_taxonomy_genus("Acer")
genus_vector<-c("Acer","Quercus")
BIEN_taxonomy_genus(genus_vector)
## End(Not run)

Extract taxonomic information for species

Description

BIEN_taxonomy_species downloads a dataframe of all taxonomic information for given species.

Usage

BIEN_taxonomy_species(species, ...)

Arguments

Value

Dataframe containing taxonomic information for the specified species.

See Also

Other taxonomy functions: BIEN_taxonomy_family(), BIEN_taxonomy_genus()

Examples

## Not run: 
BIEN_taxonomy_species("Cannabis sativa")
species_vector<-c("Acer nigrum","Cannabis sativa")
BIEN_taxonomy_species(species_vector)
## End(Not run)

Download trait data for given country.

Description

BIEN_trait_species extracts trait data for the species country.

Usage

BIEN_trait_country(
  country,
  trait.name = NULL,
  all.taxonomy = FALSE,
  political.boundaries = TRUE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all available trait data for the given country.

See Also

Other trait functions: BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_country("South Africa")
BIEN_trait_country(country="South Africa",trait="whole plant growth form")
## End(Not run)

Download trait data for given families.

Description

BIEN_trait_family extracts all trait data for the specified families.

Usage

BIEN_trait_family(
  family,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all data matching the specified families.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_family("Poaceae")
family_vector<-c("Poaceae","Orchidaceae")
BIEN_trait_family(family_vector)
## End(Not run)

Download trait data for given genera.

Description

BIEN_trait_genus extracts entries that contain the specified genera.

Usage

BIEN_trait_genus(
  genus,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all data matching the specified genera.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_genus("Acer")
genus_vector <- c("Acer","Abies")
BIEN_trait_genus(genus_vector)
## End(Not run)

List all available types of trait data

Description

BIEN_trait_list produces a dataframe of all available types of trait data.

Usage

BIEN_trait_list(...)

Arguments

Value

A dataframe containing all currently available types of trait data and details on measurement.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_list()
## End(Not run)

Calculates species mean values for a given trait, using Genus or Family level data where Species level data is lacking.

Description

BIEN_trait_mean Estimates species mean values for a given trait, using Genus or Family level data where Species level data is absent.

Usage

BIEN_trait_mean(species, trait, ...)

Arguments

Value

A dataframe of estimated trait means and associated metadata for the given species.

Note

Trait spelling needs to be exact and case-sensitive, see BIEN_trait_list for a list of traits.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_mean(species=c("Poa annua","Juncus trifidus"),trait="leaf dry mass per leaf fresh mass") 
## End(Not run)

Download trait data for given species.

Description

BIEN_trait_species extracts trait data for the species specified.

Usage

BIEN_trait_species(
  species,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all available trait data for the given species.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_species("Poa annua")
species_vector<-c("Poa annua","Juncus trifidus")
BIEN_trait_species(species_vector)
## End(Not run)

Download all measurements of a specific trait(s).

Description

BIEN_trait_trait downloads all measurements of the trait(s) specified.

Usage

BIEN_trait_trait(
  trait,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all available trait data for the given trait(s).

Note

Trait spelling needs to be exact and case-sensitive, see BIEN_trait_list for a list of traits.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_trait("whole plant height")
trait_vector<-c("whole plant height", "leaf dry mass per leaf fresh mass")
BIEN_trait_trait(trait_vector)
## End(Not run)

Download trait data for given families and traits.

Description

BIEN_trait_traitbyfamily extracts entries that contain the specified families and trait(s).

Usage

BIEN_trait_traitbyfamily(
  family,
  trait,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all data matching the specified trait(s) and family/families.

Note

Trait spelling needs to be exact and case-sensitive, see BIEN_trait_list for a list of traits.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_traitbyfamily(trait = "whole plant height", family = "Poaceae")
trait_vector <- c("whole plant height", "leaf fresh mass")
family_vector < -c("Orchidaceae","Poaceae")
BIEN_trait_traitbyfamily(trait = trait_vector, family = family_vector)
## End(Not run)

Download trait data for given genus/genera and trait(s).

Description

BIEN_trait_traitbygenus extracts entries that contain the specified genus/genera and trait(s).

Usage

BIEN_trait_traitbygenus(
  genus,
  trait,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all data matching the specified trait(s) and genus/genera.

Note

Trait spelling needs to be exact and case-sensitive, see BIEN_trait_list for a list of traits.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbyspecies(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_traitbygenus(trait = "whole plant height", genus = "Carex")
trait_vector<-c("whole plant height", "leaf area")
genus_vector<-c("Carex","Betula")
BIEN_trait_traitbygenus(trait=trait_vector,genus=genus_vector)
## End(Not run)

Download trait data for given species and trait.

Description

BIEN_trait_traitbyspecies extracts entries that contain the specified species and trait(s).

Usage

BIEN_trait_traitbyspecies(
  species,
  trait,
  all.taxonomy = FALSE,
  political.boundaries = FALSE,
  source.citation = FALSE,
  ...
)

Arguments

Value

A dataframe of all data matching the specified trait(s) and species.

Note

Trait spelling needs to be exact and case-sensitive, see BIEN_trait_list for a list of traits.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traits_per_species()

Examples

## Not run: 
BIEN_trait_traitbyspecies(trait = "whole plant height", species = "Carex capitata")
trait_vector<-c("whole plant height", "leaf area")
species_vector<-c("Carex capitata","Betula nana")
BIEN_trait_traitbyspecies(trait=trait_vector,species=species_vector)
## End(Not run)

Count the number of trait observations for each species in the BIEN database

Description

BIEN_trait_traits_per_species downloads a count of the number of records for each trait for each species in the BIEN database.

Usage

BIEN_trait_traits_per_species(species = NULL, ...)

Arguments

Value

Returns a dataframe containing the number of trait records for each species in the BIEN database.

See Also

Other trait functions: BIEN_trait_country(), BIEN_trait_family(), BIEN_trait_genus(), BIEN_trait_list(), BIEN_trait_mean(), BIEN_trait_species(), BIEN_trait_trait(), BIEN_trait_traitbyfamily(), BIEN_trait_traitbygenus(), BIEN_trait_traitbyspecies()

Examples

## Not run: 
trait_observation_counts<-BIEN_trait_traits_per_species()
## End(Not run)