lookup_table: Build a family and order lookup table for a set of species

In traitecoevo/taxonlookup: A dynamically-updating versioned taxonomic resource for vascular plants

Description

Build a lookup table for a set of species, connecting the species names to plant genera, families and orders

Usage

lookup_table(species_list, lookup_table = NULL, genus_column = "genus",
  missing_action = c("drop", "NA", "error"), by_species = FALSE,
  family.tax = "apweb", include_counts = FALSE, ...)

Arguments

species_list	Character vector of species bionomials Genus and species may be seperated by " " or "_"
lookup_table	Any higher taxonomy lookup table, but by default plant_lookup
genus_column	The column within lookup_table that corresponds to genus. By default this is "genus", which is the correct name for plant_lookup.
missing_action	How to behave when there are genera in the species_list that are not found in the lookup table. "drop" (the default) generates a table without these genera, "NA" will leave the non-genus taxonomic levels as missing values and error will throw an error.
by_species	If TRUE, then return a larger data frame with one row per species and with species as row names.
family.tax	There are two available family taxonomies–"apweb" and "plantlist". the default is "apweb"
include_counts	This will include the number of species in the genus (data from the plant list) in the output
...	variables passed on to plant_lookup, including version number.

Details

The data within this lookup table comes from two sources:

1. The Plant List v1.1. (http://www.theplantlist.org/) for accepted genera to families and species richness within each genera. Note that we do not consider hybrids (e.g. Genus X species) as distinct species for this count while the plant list summary statistics do, so the the counts from this package will not line up exactly with the ones on the TPL website.

2. APWeb (http://www.mobot.org/MOBOT/research/APweb/) for family-level synonymies and family-to-order for all vascular plant families. Note that there is not currently order-level information available for Bryophytes.

Examples

lookup_table("Pinus_ponderosa")
#
# or with a space
#
lookup_table("Pinus ponderosa")
#
#
# control how you want the function to handle non-matches
#
lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies"))
#
lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies"),missing_action="NA")

traitecoevo/taxonlookup documentation built on May 31, 2019, 7:44 p.m.