binomen (version 0.1.2)

make_taxon: Make taxon from class

Description

Make taxon from class

Usage

make_taxon(genus = "none", epithet = "none", authority = "none", ...)

Arguments

genus

Genus name, e.g., Homo (in Homo sapiens)

epithet

Specific epithet, e.g., sapiens (in Homo sapiens)

authority

Taxonomic authority

...

Further args.

Examples

(out <- make_taxon(genus="Poa"))
(out <- make_taxon(genus="Poa", epithet="annua", authority="L."))
(out <- make_taxon(genus="Poa", epithet="annua", authority="L.",
                   family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua'))
out$binomial
out$binomial$canonical
out$binomial$species
out$binomial$authority
out$grouping
out$grouping$family
out %>% pick(family) # get a single rank
out %>% span(kingdom, family) # get a range of ranks
gethier(out) # get hierarchy as data.frame

# Using dplyr
df <- data.frame(class=c('Magnoliopsida','Magnoliopsida','Magnoliopsida',
   'Magnoliopsida','Magnoliopsida','Magnoliopsida'),
 order=c('Asterales','Asterales','Fagales','Poales','Poales','Poales'),
 family=c('Asteraceae','Asteraceae','Fagaceae','Poaceae','Poaceae','Poaceae'),
 genus=c('Helianthus','Helianthus','Quercus','Poa','Festuca','Holodiscus'),
 species=c('annuus','petrus','kellog','annua','arundinaceae','fava'),
 stringsAsFactors = FALSE)

library(dplyr)
xx <- df %>% rowwise()
xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < family)) %>% .[[1]]
xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < genus)) %>% .[[1]]
xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < species)) %>% .[[1]]