species: Extract the species name
In cstubben/genomes2: Genome sequencing project metadata

Description Usage Arguments Details Value Author(s) See Also Examples

Extracts the species name from a scientific name

1	species(x, abbrev=FALSE, epithet=FALSE)

`x`	A vector of scientific names
`abbrev`	Abbreviate the genus name
`epithet`	Return only the specific epithet (default is genus + specific epithat)

Returns the species name. For candidate species labeled Candidatus, the qualifier is not included

A vector of species names

Chris Stubben

genus

species("Bacillus anthracis Ames")
species("Bacillus anthracis Ames", abbrev=TRUE)
species("Bacillus anthracis Ames", epithet=TRUE)
data(proks)
x <- table2(species(proks$name))[1:10,]
dotchart(rev(x), xlab="Genomes", pch=16)
## abbreviate genus name
x <- subset(proks, name %like% 'Bacillus*')
x <- table2(species(x$name))[1:10, ]
names(x) <- species(names(x), TRUE)
dotchart(rev(x), xlab=expression(italic(Bacillus) ~ genomes), pch=16)