plant_lookup: Plant taxonomy lookup table

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

Description

Lookup table relating plant genera, families and orders along with number of species in each genus. Data persists across package installations.

Usage

plant_lookup(version = NULL, include_counts = FALSE, family.tax = "apweb",
  path = NULL)

plant_lookup_versions(local = TRUE, path = NULL)

plant_lookup_version_current_local(path = NULL)

plant_lookup_version_current_github(path = NULL)

get_most_recent_plant_lookup(path = NULL)

plant_lookup_del(version, path = NULL)

Arguments

version	Version number. The default will load the most recent version on your computer or the most recent version known to the package if you have never downloaded the data before. With plant_lookup_del, specifying version=NULL will delete all data sets.
include_counts	Logical: Include a column of number of "accepted" species within each genus counts as number.of.species.
family.tax	the value "ap.web" will return the family names from apweb otherwise the lookup will include the family names from the plant list. Currently there are 8 family names that differ between the two sources (e.g., Compositae in the plant list versus Asteraceae in ap.web)
path	Path to store the data at. If not given, datastorr will use rappdirs to find the best place to put persistent application data on your system. You can delete the persistent data at any time by running mydata_del(NULL) (or mydata_del(NULL, path) if you use a different path).
local	Logical indicating if local or github versions should be pulled. With any luck, local=FALSE is a superset of local=TRUE. For mydata_version_current, if TRUE, but there are no local versions, then we do check for the most recent github version.

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.

These data are then currated–we correct some spelling errors, special character issues, genera listed in multiple families, family-level synonomy, and other issues that arise in assembling a resources like this. Details of the curation are at https://github.com/traitecoevo/taxonlookup

Examples

#
# see the format of the resource
#
head(plant_lookup())
#
# or with number of species in each genus.
#
head(plant_lookup(include_counts = TRUE))
#
# load the data.frame into memory
#
pl<-plant_lookup(include_counts = TRUE)
#
# return family, order, and number of species for the genus Eucalyptus
#
pl$family[pl$genus=="Eucalyptus"]
pl$order[pl$genus=="Eucalyptus"]
pl$number.of.species[pl$genus=="Eucalyptus"]
#
# find the number of accepted species within the Myrtaceae
#
sum(pl$number.of.species[pl$family=="Myrtaceae"])

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