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hisse (version 1.3)

TransMatMaker: Transition Rate matrix generator

Description

Generates and manipulates the index of the rate parameters to be optimized

Usage

TransMatMaker(hidden.states=FALSE)
ParDrop(rate.mat.index=NULL, drop.par=NULL)
ParEqual(rate.mat.index=NULL, eq.par=NULL)

Arguments

hidden.states
a logical indicating whether the underlying model includes hidden states. The default is FALSE.
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.

Value

  • Returns a rate matrix index

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.