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

In mmodely: Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology

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')

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

Value

None

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')

mmodely documentation built on May 31, 2023, 6:47 p.m.