LGcpp_splits_fn_to_table2: Get the ML splits per node, from Python LAGRANGE output

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

View source: R/BioGeoBEARS_readwrite_v1.R

Description

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

Usage

1

Arguments

splits_fn

The filename of a Python LAGRANGE output file.

Details

LAGRANGE outputs just the splits making up the top 95 the probability, or 15 states, whichever comes 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.

Value

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

Note

Go BEARS!

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

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

1
test=1

Example output

Loading required package: rexpokit
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Rcpp
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges

BioGeoBEARS documentation built on May 29, 2017, 8:36 p.m.