getf: Get f

In dinaIssakova/rgenesconverged: A Package for Estimating Probability of Convergent Evolution from Genomic Data

Description

Obtain f - probability of any configuration satisfying the hypothesis of convergent evolution under the constraint of the given tree

Usage

getf(
  tree,
  phydat,
  spe1,
  spe2,
  p = (1/20),
  type = c("abs", "score"),
  threshold = NA
)

Arguments

tree	a phylogenetic tree
phydat	a phyDat object containing the relevant alignment
spe1	The name of species 1
spe2	The name of species 2
p	Probability of occurence for any AA (default 1/20)
type	type of analysis: absolute ("abs") or by score ("score")
threshold	minimum threshold for score option

Value

probability (f)

dinaIssakova/rgenesconverged documentation built on Jan. 7, 2020, 4:25 p.m.