| calcPresSpec {PhyloProfile} | R Documentation |
Calculate percentage of present species in each super taxon
calcPresSpec(profileWithTax, taxaCount)
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) |
A data frame with
Vinh Tran tran@bio.uni-frankfurt.de
profileWithTaxonomy for a demo input data
# 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)