traitRate {ips}

Trait-Dependent Shifts in Molecular Rate

Description

Detection of trait-dependent shifts in the rate of molecular evolution with traitRate (Mayrose & Otto, 2011).

Usage

traitRate(phy, seq, x, mainType = "Optimize_Model", 
   n, charModelParam1 = 0.5, charModelParam2 = 1, 
   gammaParam = 0.5, seqModelParam1 = 2,
   exec = "/Applications/traitRate-1.1/programs/traitRate")

Arguments

phy

a ultrametric phylogenetic tree of class phylo.

seq

a multiple sequence alignment of class DNAbin.

x

data frame containing a binary character in the first column.

mainType

character string giving the type of analysis; two choices are possible: "Optimize_Model" will produce MLE of parameters and "runTraitBootstrap" will perform a parametric bootstrap analysis.

n

numeric, the number of bootstrap replicates. Will be ignored if mainType = "Optimize_Model".

charModelParam1

numeric, giving an initial value for the rate of transitions of character state 0 to 1.

charModelParam2

numeric, giving an initial value for the rate of transitions of character state 1 to 0.

gammaParam

numeric, giving an initial value for the alpha parameter of the model of sequence evolution.

seqModelParam1

numeric, giving an initial value for the kappa parameter of the model of sequence evolution.

exec

character string giving the path to the program directory.

Value

Currently none, but look for the output files in the 'RESULTS' subdirectory in the current working directory.

Note

This function is under development!

Author(s)

Christoph Heibl

References

Mayrose, I. & S.P. Otto. 2011. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol. Biol. Evol. 28: 759-770

See Also

read.tree for reading phylogenetic trees, read.fas for reading multiple sequence alignments in FASTA format.