calc_pres_spec: Calculate percentage of present species in each ortholog...

In trvinh/test: PhyloProfile

Description

Calculate percentage of present species in each ortholog group

Usage

calc_pres_spec(profile_with_tax, taxa_count)

Arguments

profile_with_tax	long data frame of main phyloprofile input together with their taxonomy info
taxa_count	number of species occur in each supertaxon

Value

A data frame with each supertaxon

Author(s)

Vinh Tran [e-mail]

See Also

profile_with_taxonomy for a demo input data

Examples

# NOTE: for internal testing only - not recommended for outside using
data("profile_with_taxonomy", package="phyloprofile")
taxa_count <- plyr::count(profile_with_taxonomy, "supertaxon")
taxa_count$freq <- 1
calc_pres_spec(profile_with_taxonomy, taxa_count)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.