BioGeoBEARS (version 0.2.1)

LGcpp_splits_fn_to_table: Get the ML splits per node, from C++ LAGRANGE output

Description

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

Usage

LGcpp_splits_fn_to_table(splits_fn)

Arguments

splits_fn

The filename of a C++ LAGRANGE output file.

Value

splits A data.frame containing the node numbers, splits, and split probabilities.

Details

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

See LGpy_MLsplit_per_node for choosing the single ML split 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, LGpy_MLsplit_per_node

Examples

test=1

# splits_fn = "/Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/
# examples/Psychotria_M0/LAGRANGE_C++/Psychotria_M0_lgcpp_out_splits00001.txt"
# LGcpp_splits_fn_to_table(splits_fn)