add_higher_order: Add higher order taxonomy

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

Description

Augment the genus-family-order lookup table with plant higher taxa data, from http://datadryad.org/resource/doi:10.5061/dryad.63q27

Usage

add_higher_order(lookup = plant_lookup(include_counts = TRUE),
  order_column = "order")

Arguments

lookup	A lookup table (by default plant_lookup())
order_column	The column within lookup that corresponds to taxonomic order.

Details

Data for the higher-level taxonomy lookup (http://datadryad.org/resource/doi:10.5061/dryad.63q27.2/1.1) compiled by Dave Tank and colleagues

Because of the currently non-nested structure of higher clade information for plants, the format of the lookup is also not nested. In the lookup the higher nodes are columns within the data.frame. If a genus is a descendent of a particular node, the row for that genus repeats the node name (which is also the column name). If a genus is not a descendent of that particular node, the cell is left blank.

Examples

##' # see the format of the resource
head(add_higher_order())
#
# load the data.frame into memory
ho<-add_higher_order()
#
# return Rosid orders
unique(ho$order[ho$Rosidae=="Rosidae"])
#
# find the number of Conifer species in the world
sum(ho$number.of.accepted.species[ho$Coniferae=="Coniferae"])

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