BioGeoBEARS (version 0.2.1)

LGcpp_states_fn_to_table: Get the ML states per node, from C++ LAGRANGE output

Description

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

Usage

LGcpp_states_fn_to_table(states_fn)

Arguments

states_fn

The filename of a C++ LAGRANGE output file.

Value

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

Details

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.

References

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

Matzke_2012_IBS

ReeSmith2008

See Also

get_lagrange_nodenums, LGcpp_MLstate_per_node

Examples

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)