rphast (version 1.6.9)

setup.branch.site.tm: Set up a tree model for branch site selection analysis

Description

Set up a tree model for branch site selection analysis

Usage

setup.branch.site.tm(mod, foreground, bgc = FALSE, altModel = TRUE,
  init.sel.neg = 0, init.sel.pos = 0, init.bgc = 0, init.weights = NULL)

Arguments

mod

an object of type tm

foreground

a character string giving a tree branch name or label identifying foreground branches

bgc

If TRUE, then use 8 categories of sites; four with bgc in the foreground and four without.

altModel

If TRUE, then optimize the foreground positive selection parameter (constrained > 0). Otherwise hold constant at 0.

init.sel.neg

Initial value for negative selection parameter

init.sel.pos

Initial value for positive selection paramter

init.bgc

Initial value for bgc parameter (Ignored if bgc==FALSE)

init.weights

Numeric vector of length three giving the initial weight parameters. The first two values determine the relative frequencies of negatively, neutral, and positively selected sites. The last parameter determines the frequency of sites affected by bgc, and is ignored if bgc==FALSE. All values should be >= 0.

Value

An object of type tm which can be used as the init.mod argument to phyloFit to perform the branch-site test.