downstream: Retrieve all taxa descending from a vector of taxa

In ropensci/taxizedb: Tools for Working with 'Taxonomic' Databases

Retrieve all taxa descending from a vector of taxa

Description

This function is nearly equivalent to the taxize::downstream() function

Usage

downstream(x, db = "ncbi", verbose = TRUE, ...)

Arguments

x	(character) Vector of taxon keys for the given database
db	(character) The database to search, one of ncbi, itis, gbif, col, or wfo
verbose	(logical) Print verbose messages
...	Additional arguments passed to database specific downstream functions

Value

list of data.frames with the columns: childtaxa_id, childtaxa_name, and rank. This is exactly equivalent to the output of taxize::downstream()

Examples

## Not run: 
# get descendents from all ranks
# downstream(c(3700, 9605)) # takes a while

# limit results to species
downstream(c(3700, 9605), downto='species')

# allow ambiguous nodes but no ambiguous species
downstream(
  c(3700, 9605),
  downto='species',
  ambiguous_nodes=FALSE,
  ambiguous_species=TRUE
)

# ITIS
id <- name2taxid('Aves', db = "itis")
downstream(id, db = "itis", downto = "family")
downstream(id, db = "itis", downto = "genus")
id <- name2taxid('Bombus', db = "itis")
downstream(id, db = "itis", downto = "species")

# COL
id <- name2taxid('Chordata', db = "col")
downstream(id, db = "col", downto = "family")

# GBIF
id <- name2taxid('Pinaceae', db = "gbif")
downstream(id, db = "gbif", downto = "genus")

# World Flora Online
id <- name2taxid('Pinaceae', db = "wfo")
downstream(id, db = "wfo", downto = "species")

## End(Not run)

ropensci/taxizedb documentation built on April 28, 2023, 2:05 a.m.