check_poss_synyms: Checks if scientific name for sample is likely a species, or...

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

Description

check_poss_synyms

Usage

check_poss_synyms(data, file_path = getwd())

Arguments

data	data frame with '$sci_nam' column (expected to be 'GB_with_SeqDat', the data frame result of the pipeline so far).
file_path	path to newly created .csv file, defaults to working directory

Details

Function takes data frame with column $sci_nam and returns a list of scientific names that are longer than 2 words. Also writes out a .csv file of these names.

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 takes any instances of names longer than 2 words, outputs the result as an object and a .csv which can then be edited by the user.

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