fishbase_name_species_bold: Validates species names of BOLD specimen and returns synonyms...

In Grelot/geogendivr: Geographic Gene Diversity in R

Description

Add a column named "fishbase_species_names" to a curated BOLD specimen dataframe. This column gives the species name used to identify the specimen into fishbase. If the specimen BOLD species name is not found into fishbase, then a NA value is attributed.

Usage

prparedResBold.fishbaseValid <- fishbase_name_species_bold(prparedResBold)

Arguments

prparedResBold

A curated dataframe generated by prepare_bold_res with 80 columns including: species_name this column is a list of string object. The only one necessary to validate species name on fishbase

Value

A dataframe with a supplementary column "fishbase_name_species". This column is a list of strings. It gives synonyms of species names used by fishbase to describe a BOLD specimen. If the specimen BOLD species name is not found into fishbase, then a NA value is attributed.

Author(s)

Pierre-Edouard GUERIN, Stephanie MANEL

Examples

## load BOLD specimen and sequence data with matching taxa "Pomacanthidae"
data(requestPomacanthidaeBOLD)
## filter and mutate
prparedResBold <- prepare_bold_res(resBold,
                                   marker_code="COI-5P",
                                   species_names=TRUE, 
                                   coordinates=TRUE, 
                                   ambiguities=TRUE, 
                                   min_length=420,
                                   max_length=720
                                  )
## validate species names
prparedResBold.fishbaseValid <- fishbase_name_species_bold(prparedResBold)
## display BOLD specimen fishbase species names
print(prparedResBold.fishbaseValid$fishbase_species_name)

Grelot/geogendivr documentation built on Sept. 3, 2020, 6:25 p.m.