In ropensci/binomen: 'Taxonomic' Specification and Parsing Methods

binomen

knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>"
)

to https://github.com/ropensci/taxa

MOST FUNCTIONALITY OF THIS PACKAGE HAS MOVED TO THE taxa PACKAGE. THIS PACKAGE IS NOW ARCHIVED ON CRAN

binomen provides various taxonomic classes for defining a single taxon, multiple taxa, and a taxonomic data.frame

It is designed as a companion to taxize, where you can get taxonomic data on taxonomic names from the web.

classes (S3)

• taxon
• taxonref
• taxonrefs
• binomial
• grouping (i.e., classification - used different term to avoid conflict with classification in taxize)

verbs

• gethier() - get hierarchy from a taxon class
• scatter() - make each row in taxonomic data.frame (taxondf) a separate taxon object within a single taxa object
• assemble() - make a taxa object into a taxondf data.frame
• pick() - pick out one or more taxonomic groups
• pop() - pop out (drop) one or more taxonomic groups
• span() - pick a range between two taxonomic groups (inclusive)
• strain() - filter by taxonomic groups, like dplyr's filter
• name() - get the taxon name for each taxonref object
• uri() - get the reference uri for each taxonref object
• rank() - get the taxonomic rank for each taxonref object
• id() - get the reference uri for each taxonref object

Installation

Stable CRAN version

install.packages("binomen")

Development GitHub version

install.packages("devtools")
devtools::install_github("ropensci/binomen")

library('binomen')

Make a taxon

Make a taxon object

(obj <- make_taxon(genus="Poa", epithet="annua", authority="L.",
  family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua'))

Index to various parts of the object

The binomial

obj$binomial

The authority

obj$binomial$authority

The classification

obj$grouping

The family

obj$grouping$family

Subset taxon objects

Get one or more ranks via pick()

obj %>% pick(family)
obj %>% pick(family, genus)

Drop one or more ranks via pop()

obj %>% pop(family)
obj %>% pop(family, genus)

Get a range of ranks via span()

obj %>% span(kingdom, family)

Extract classification as a data.frame

gethier(obj)

Taxonomic data.frame's

Make one

df <- data.frame(order = c('Asterales','Asterales','Fagales','Poales','Poales','Poales'),
  family = c('Asteraceae','Asteraceae','Fagaceae','Poaceae','Poaceae','Poaceae'),
  genus = c('Helianthus','Helianthus','Quercus','Poa','Festuca','Holodiscus'),
  stringsAsFactors = FALSE)
(df2 <- taxon_df(df))

Parse - get rank order via pick()

df2 %>% pick(order)

get ranks order, family, and genus via pick()

df2 %>% pick(order, family, genus)

get range of names via span(), from rank X to rank Y

df2 %>% span(family, genus)

Separate each row into a taxon class (many taxon objects are a taxa class)

scatter(df2)

And you can re-assemble a data.frame from the output of scatter() with assemble()

out <- scatter(df2)
assemble(out)

ToDo

See our issue tracker to see what we have planned

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for binomen in R doing citation(package = 'binomen')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

ropensci/binomen documentation built on May 18, 2022, 9:47 a.m.