parse_lagrange_output: Parse the output file from python 'LAGRANGE'
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 C++ LAGRANGE run.

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  parse_lagrange_output(outfn, outputfiles = FALSE,
    results_dir = getwd(), new_splits_fn = FALSE,
    new_states_fn = TRUE, filecount = 0)

`outfn`	The C++ `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 `FALSE`.
`new_states_fn`	Should a text file containing a table of the states and their probabilities be output? Default `TRUE`, unlike python `LAGRANGE`, C++ `LAGRANGE` will output the states at the nodes.
`filecount`	The starting number for the filecount (relevant if one is processing many files).

This function parses the output of LAGRANGE, obtained by a command such as the following, run at a UNIX/Mac Terminal command line.

cd /Users/nick/Desktop/__projects/_2011-07-15_Hannah_spider_fossils/_data/lagrange_for_nick

./lagrange_cpp palp_no_Lacun_v1_2nd387.lg > lagrange_results_v1_2nd387.txt

C++ LAGRANGE can be obtained at https://code.google.com/p/lagrange/

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/

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