Generates and manipulates the index of the transition rate parameters to be optimized.
TransMatMakerGeoHiSSE(hidden.areas=0, make.null=FALSE, include.jumps=FALSE,
separate.extirpation=FALSE)a numeric value with the number of hidden areas in
the model. The cannonical GeoSSE model has no hidden areas, so
'hidden.areas=0'. The default value is 0.
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.
allows for 0->1 and 1->0 transitions.
allows for 01->0 and 01->1 transitions.
Returns a rate matrix index.
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.