BioGeoBEARS (version 0.2.1)

parse_lagrange_python_output: Parse the output file from python LAGRANGE

Description

Parse the output of a python LAGRANGE.

Usage

parse_lagrange_python_output(outfn = "output.results.txt", outputfiles = FALSE, results_dir = getwd(), new_splits_fn = TRUE, new_states_fn = FALSE, filecount = 0, append = FALSE)

Arguments

outfn

The python LAGRANGE output text file.

outputfiles

Should parsed output be written to files? Default FALSE.

results_dir

The directory outfn is in.

new_splits_fn

Should a text file containing a table of the splits and their probabilities be output? Default TRUE.

new_states_fn

Should a text file containing a table of the states and their probabilities be output? Default FALSE, as I don't believe python LAGRANGE will output the states at the nodes (C++ LAGRANGE will, however).

filecount

The starting number for the filecount (relevant if one is processing many files).

append

Should results be appended to preexisting file? (default FALSE)

Value

sumstats A data.frame containing the summary statistics (LnL, d and e rates, etc.) The splits filename is output to screen.

Details

Python LAGRANGE is run from a UNIX/Terminal command-line with a command such as "python lagrangefilename.py". You will need to have the "lagrange" python directory in your working directory.

The input file can be obtained from http://www.reelab.net/lagrange/configurator/index (Ree (2009)).

Python comes installed on many machines, or can be downloaded from the Enthought Python Distribution (https://www.enthought.com/products/epd/).

References

https://code.google.com/p/lagrange/ https://www.enthought.com/products/epd/ http://www.reelab.net/lagrange/configurator/index

Ree2009configurator

Matzke_2012_IBS

ReeSmith2008

See Also

get_lagrange_nodenums, LGpy_splits_fn_to_table

Examples

test=1