standardise_spp_names: Updates any species names user wants to alter

In EvolEcolGroup/mtDNAcombine: R package to download, combine, and curate sequences from public databases

Description

standardise_spp_names

Usage

standardise_spp_names(data, new_names_file = NULL)

Arguments

data	data frame with '$sci_nam' column (expected to be 'GB_with_SeqDat', the data frame result of the pipeline so far).
new_names_file	A csv file name. csv file with two columns. First column is existing scientific name, second column is name to replace existing character string with. Structure built on exported "poss_synonyms.csv" file.

Details

Function takes data frame with column $sci_nam and uses a .csv file containing existing names and desired replacement names to standise species nomenclature across all accessions.

Sequence data can be uploaded to GenBank with scientific names that may be non-standard/of different taxonomic rank, filtering based on species name will therefore not work unless names are standardised. This function reads in a .csv file of old and user-defined replacement species names, these are then used to update the data$sci_nam column.

EvolEcolGroup/mtDNAcombine documentation built on July 8, 2021, 10:30 p.m.