Generates and manipulates the index of the rate parameters to be optimized
TransMatMaker.old(hidden.states=FALSE)
ParDrop(rate.mat.index=NULL, drop.par=NULL)
ParEqual(rate.mat.index=NULL, eq.par=NULL)Returns a rate matrix index
a logical indicating whether the underlying model includes hidden states. The default is FALSE.
A user-supplied rate matrix index to be manipulated.
a vector of transitions to be dropped from the model.
a vector of transitions pairs to be set equal.
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.