calcPresSpec: Calculate percentage of present species in each super taxon

Description Usage Arguments Value Author(s) See Also Examples

View source: R/parsePhyloProfile.R

Description

Calculate percentage of present species in each super taxon

Usage

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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 tran@bio.uni-frankfurt.de

See Also

profileWithTaxonomy for a demo input data

Examples

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# 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)

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.