parse_lagrange_python_output_old: Parse the output file from python 'LAGRANGE' - old version
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

Parse the output of a python LAGRANGE output file. This is an older version useful for automating the parsing of a large number of files.

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

`outfn`	The python `LAGRANGE` output text file.
`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 splits 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).

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/).

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

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Ree2009configurator

Matzke_2012_IBS

ReeSmith2008

get_lagrange_nodenums, LGpy_splits_fn_to_table

test=1

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