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 0based 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 
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 COOlike form, as produced by

index_Qmat_0based_of_starting_state 
An integer
index value, between 0 and 
simulated_states_by_node
A numeric matrix, giving
the 0based 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/matzke2013internationalbiogeographysocietyposter 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
1  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
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