simulate_biogeog_history: Simulate a biogeographical history, given a transition matrix...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Value Note Author(s) References See Also Examples

View source: R/BioGeoBEARS_simulate_v1.R

This function simulates a biogeographical history, given a Q transition matrix, a cladogenesis model giving the relative probability of different range inheritance scenarios, a phylogeny, and a 0-based index value deciding the starting state (which could be randomly generated according to a prior distribution of states).

1 2	simulate_biogeog_history(phy, Qmat, COO_probs_columnar, index_Qmat_0based_of_starting_state)

`phy`	An R `phylo` object.
`Qmat`	A (square, dense) Q transition matrix. Using a sparse matrix would require writing another function.
`COO_probs_columnar`	A speciation/cladogenesis transition matrix, in COO-like form, as produced by `rcpp_calc_anclikes_sp_COOweights_faster`.
`index_Qmat_0based_of_starting_state`	An integer index value, between 0 and `(numstates-1)`, which specifies what state will be the starting point for the simulation.

simulated_states_by_node A numeric matrix, giving the 0-based index of the state at each node and tip in the simulated history. Getting a more detailed history would require a version of stochastic mapping (Huelsenbeck et al. (2003), Bollback (2005), Bollback (2006)), but customized for the nonreversible and cladogenic aspects of biogeographical range evolution models.

Go BEARS!

Nicholas J. Matzke [email protected]

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

Huelsenbeck_etal_2003_stochastic_mapping

Bollback_2005

Bollback_2006_SIMMAP

Matzke_2012_IBS

rcpp_calc_anclikes_sp_COOweights_faster

testval=1

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges