TransMatMaker.old {hisse} | R Documentation |
Transition Rate matrix generator
Description
Generates and manipulates the index of the rate parameters to be optimized
Usage
TransMatMaker.old(hidden.states=FALSE)
ParDrop(rate.mat.index=NULL, drop.par=NULL)
ParEqual(rate.mat.index=NULL, eq.par=NULL)
Arguments
a logical indicating whether the underlying model includes hidden states. The default is | |
rate.mat.index |
A user-supplied rate matrix index to be manipulated. |
drop.par |
a vector of transitions to be dropped from the model. |
eq.par |
a vector of transitions pairs to be set equal. |
Details
Outputs the full index of the rate parameters that are to be optimized. The intention is that a user might want to see how the matrix is designed prior to an analysis and perhaps drop a few parameters beforehand due to some hypothesis that he or she might have. The resulting matrix is to be plugged directly into hisse.old
.
Value
Returns a rate matrix index
[Package hisse version 2.1.11 Index]