`transMatMakerGeoHiSSE.Rd`

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

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

- 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.

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`

.

Returns a rate matrix index.