transMatMakerHiSSE: Transition Rate matrix generator for the HiSSE model

In hisse: Hidden State Speciation and Extinction

Transition Rate matrix generator for the HiSSE model

Description

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

Usage

TransMatMakerHiSSE(hidden.traits=0, make.null=FALSE, cat.trans.vary=FALSE)

Arguments

hidden.traits	a numeric value with the number of hidden states in the model. The canonical BiSSE model has no hidden states, so 'hidden.traits=0'. The default value is 0.
make.null	Sets the transition matrix to the null model such that (1) transition rates are the same across all hidden states and (2) the transition rates between hidden states (such as 0A <-> 1A) are the same.
cat.trans.vary	sets transition among hidden categories to vary.

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 she might have. The resulting matrix is to be plugged directly into hisse.

Value

Returns a rate matrix index.

hisse documentation built on Feb. 16, 2023, 10:26 p.m.