mmodely (version 0.2.5)

gs.names.mismatch.check: Check "Genus species" name formatting

Description

This convienience function checks to make sure that all of the elements the provided character vector adhere to the "Genus species" naming convention format. Default delimiters between genus and species names in the string are " ", "_", or "."

Usage

gs.names.mismatch.check(df, alias.table.path, gs.clmn='gn_sp')

Value

None

Arguments

df

a data frame with genus species information as row names and optionally in a column named "gn_sp"

alias.table.path

a file system path (e.g. 'inst/extdata/primate.taxa.aliases.tab') to a lookup table with 'old.name' and 'new.name' as columns

gs.clmn

the name of the column containing the 'Genus_species' vector

Examples

path <- system.file("extdata","primate-example.data.csv", package="mmodely")
gs.tab <- read.csv(path, row.names=1)
gs.tab$gn_sp <- rownames(gs.tab)

path.look <- system.file("extdata","primate.taxa.aliases.tab", package="mmodely")

gs.names.mismatch.check(gs.tab, alias.table.path=path.look, gs.clmn='gn_sp')