simulated_indexes_to_tipranges_object: Convert simulated Qmat 0-based indexes to a tipranges object
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 takes simulated state indices (ranging from 0 to numstates-1, i.e. number of possible geographic ranges-1) and converts them to a tipranges object. This can then be converted into a C++-LAGRANGE-style PHYLIP geographic ranges file.

1 2	simulated_indexes_to_tipranges_object(simulated_states_by_node, areas_list, states_list, trfn)

`simulated_states_by_node`	The simulated states/geographic ranges, in 0-based index form, ordered as the tips & nodes are ordered in a `pruningwise`-ordered `phylo` object in `APE`.
`areas_list`	A list of the desired area names/abbreviations/letters.
`states_list`	A list of the possible states/geographic ranges, in 0-based index form.
`trfn`	The filename of the source Newick tree.

tipranges_object An object of class tipranges.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Matzke_2012_IBS

ReeSmith2008

SmithRee2010_CPPversion

define_tipranges_object, getareas_from_tipranges_object, simulated_indexes_to_tipranges_file

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