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 detectiong 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.