LGcpp_states_fn_to_table: Get the ML states per node, from C++ LAGRANGE output
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_readwrite_v1.R

C++ LAGRANGE outputs a list of states and state probabilities for each node. This function converts them to a table.

1	LGcpp_states_fn_to_table(states_fn)

states_fn

The filename of a C++ LAGRANGE output file.

LAGRANGE outputs just the states making up the top 95 first.

See LGcpp_MLstate_per_node for choosing the single ML state at each node, and see get_lagrange_nodenums for connecting these node numbers to APE node numbers.

states A data.frame containing the node numbers, states, and state probabilities.

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

get_lagrange_nodenums, LGcpp_MLstate_per_node

test=1

# states_fn = "/Dropbox/_njm/__packages/BioGeoBEARS_setup/
# inst/extdata/examples/Psychotria_M0/LAGRANGE_C++/
# Psychotria_M0_lgcpp_out_states00001.txt"
# LGcpp_states_fn_to_table(states_fn)