tv_prep: Prepare taxonomic data

In ropensci/taxview: Tools for Vizualizing Data Taxonomically

Prepare taxonomic data

Description

Prepare taxonomic data

Usage

tv_prep_names(x, col = NULL, names = NULL, db = NULL)

tv_prep_ids(x, col = NULL, ids = NULL, db = NULL)

Arguments

x	(data.frame) input data.frame or file path
col	(character) column name holding taxonomic names or taxonomic ids to use
names	(character) column name holding taxonomic names to use. if given, db is required
db	(character) database IDs from. see below for options
ids	(character) column name holding taxonomic IDs to use. if given, db is required

Value

an object of class data.frame

db options

• bold: Barcode of Life

• col: Catalogue of Life

• eol: Encyclopedia of Life

• gbif: Global Biodiversity Information Facility

• iucn: International Union for Conservation of Nature Red List

• natserv: Nature Serve

• nbn: National Biodiversity Network (UK)

• tol: Tree of Life

• tropicos: Tropicos

• itis: Integrated Taxonomic Information Service

• ncbi: National Center for Biotechnology Information

• worms: World Register of Marine Species

Examples

## Not run: 
x <- system.file("examples/plant_spp.csv", package = "taxview")

# assuming you only have taxonomic names
# tv_prep_names(x, names = "name")

# if you have taxonomic IDs (from set of allowed databases, see above)
## if a column name
# tv_prep_ids(x, ids = "id", db = "eol")
## if a vector of IDs
dat <- tibble::as_tibble(
 data.table::fread(x, stringsAsFactors = FALSE, 
   data.table = FALSE))
out <- tv_prep_ids(x, ids = dat$id, db = "ncbi")
head(out)

## End(Not run)

ropensci/taxview documentation built on Sept. 13, 2022, 8:41 p.m.