transMatMakerGeoHiSSE: Transition Rate matrix generator for the GeoHiSSE model

TransMatMakerGeoHiSSER Documentation

Transition Rate matrix generator for the GeoHiSSE model

Description

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

Usage

TransMatMakerGeoHiSSE(hidden.traits=0, make.null=FALSE, include.jumps=FALSE, 
	separate.extirpation=FALSE)

Arguments

hidden.traits

a numeric value with the number of hidden trait in the model. The cannonical GeoSSE model has no hidden areas, so 'hidden.traits=0'. The default value is 0.

make.null

Sets the transition matrix to the null model such that (1) transition rates from endemic to widespread areas (A -> AB and B -> AB) are the same across all hidden areas and (2) the transition rates between hidden areas (such as 0A <-> 1A) are the same for all areas.

include.jumps

allows for 0->1 and 1->0 transitions.

separate.extirpation

allows for 01->0 and 01->1 transitions.

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 GeoHiSSE.

Value

Returns a rate matrix index.


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