revise_taxa: Revise taxonomic data

In EDIorg/taxonomyCleanr: A workflow and set of functions to clean taxonomy data using R

Revise taxonomic data

Description

Update the taxonomic information in your data table based on the mapping containted in taxa_map.csv. function.

Usage

revise_taxa(path, x, col, sep)

Arguments

path	A path of the directory containing taxa_map.csv and the raw data table.
x	A data frame containing the vector of taxa names to be updated.
col	A character string specifying the column in x containing taxa names to be updated.
sep	The column delimiter to use when writting the table to file. Can be comma or tab.

Value

A copy of your data table (taxonomyCleanr_output) containing appended columns containing:

• taxa_clean Both resolved and unresolved taxa.

• taxa_rank Taxonomic rank of resolved taxa, otherwise NA.

• taxa_authority Authority system of resolved taxa, otherwise NA.

• taxa_authority_id Resolved taxa identifiers from corresponding authority system.

Unresolvable taxa will have NA values for the appended columns.

EDIorg/taxonomyCleanr documentation built on April 9, 2023, 2:43 a.m.