calcPresSpec: Calculate percentage of present species in each super taxon

In BIONF/PhyloProfile: PhyloProfile

Calculate percentage of present species in each super taxon

Description

Calculate percentage of present species in each super taxon

Usage

calcPresSpec(profileWithTax, taxaCount)

Arguments

profileWithTax	data frame of main PhyloProfile input together with their taxonomy info (see ?profileWithTaxonomy)
taxaCount	number of species occur in each supertaxon (e.g. phylum or kingdom)

Value

A data frame with

Author(s)

Vinh Tran [e-mail]

See Also

profileWithTaxonomy for a demo input data

Examples

# NOTE: for internal testing only - not recommended for outside using
data("profileWithTaxonomy", package="PhyloProfile")
taxaCount <- plyr::count(profileWithTaxonomy, "supertaxon")
taxaCount$freq <- 1
calcPresSpec(profileWithTaxonomy, taxaCount)

BIONF/PhyloProfile documentation built on April 14, 2024, 10:39 p.m.