In DesiQuintans/taxizehelper: Convenience Functions For ROpenSci's 'taxize' Package

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

library(dplyr)
library(magrittr)
library(taxize)
library(stringr)
library(knitr)
library(taxizehelper)

taxizehelper: Convenience functions for the taxize package.

What is taxizehelper?

taxizehelper is a personal package that helps me use rOpenSci's taxize package more succinctly. taxize helps you retrieve up-to-date taxonomic information, so you can easily do things like:

1. Ensure that you're referring to species by their current names.
2. Error-check and repair a list of misspelled names.
3. Retrieve taxonomic ranks (order, class, family etc.) for names.
4. Discover the authorities who named your species.

Project participants

• Desi Quintans (https://twitter.com/eco_desi)

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.

Installation

install.packages("devtools")
devtools::install_github("DesiQuintans/taxizehelper")
library(taxizehelper)

taxizehelper currently has only one function:

1. search_gnr(species_list) --- Get taxonomic info for a list of taxa in a tidy dataframe.

Ex. 1: Use search_gnr() to get a dataframe of taxonomic ranks

# A list of insect species recorded within 1 km of my university.
data("wsu_hwk_insects")
print(wsu_hwk_insects)

output <- search_gnr(wsu_hwk_insects) 

class(output) 

glimpse(output, width = 85)

The ICN ranks are ordered so that you can access them with kingdom:genus.

DesiQuintans/taxizehelper documentation built on May 14, 2019, 3:04 a.m.