simulate_biogeog_history: Simulate a biogeographical history, given a transition matrix and cladogenesis model

Description

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).

Usage

simulate_biogeog_history(phy, Qmat, COO_probs_columnar, index_Qmat_0based_of_starting_state)

Arguments

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.

Value

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.

References

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

Examples

Run this code

testval=1