launch.sampletrees: Launches the c++ sampletrees program using arguments...
In Rsampletrees: MCMC Sampling of Gene Genealogies Conditional on Genetic Data

Description Usage Arguments Details Value References Examples

This function performs the MCMC tree sampling by launching the c++ sampletrees program. Linking of the pre_sampletrees functions to the c++ sampletrees program is done using Rcpp package. For more information about the sampletrees program, please see the package vignette.

1	launch.sampletrees(args, addtrees=FALSE)

`args`	An object of class ‘pars’ with the arguments for the sampletrees run
`addtrees`	If TRUE, store the trees in the output object (default=FALSE)

Sampletrees is a computationally intensive program. As such, it will write important MCMC output to output files as a back-up. Upon completion of the tree sampling, launch.sampletrees will read the output into R as a treeoutput object.

An object of class ‘treeoutput’, which is a list made up of three components:

1) runinfo - a copy of argobj

2) rawdata

3) procdata

The component ‘rawdata’ consists of

`i`	Iteration numbers of the MCMC samples
`Theta`	A vector of sampled theta values (mutation rate)
`Rho`	A vector of sampled rho values (recombination rate)
`Trees`	Either a string containing the name of the tree file or a list of class ‘multiPhylo’ containing the trees (if addtrees=TRUE). See the ape package documentation for more information on the ‘multiPhylo’ class.

The component ‘procdata’ (processed data) is also a list, initially made up only of a matrix with the acceptance proportions for each update type. Tree statistics may be added to procdata by addTreeStat

Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016

## Not run: 
oldPath=getwd()
setwd(paste(path.package("Rsampletrees"),"/extdata/",sep=""))
runpars=readArgs("example_h_pars")
runtree=launch.sampletrees(runpars)
setwd(oldPath)

## End(Not run)