readOutput: Read in sampletrees output
In Rsampletrees: MCMC Sampling of Gene Genealogies Conditional on Genetic Data

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

This function is used to read in results from a run of sampletrees. Either the object with the settings for the run or the file containing these settings is passed to the function. A new object is created that contains a component that stores the run settings, plus additional components storing the output, the sampled values for theta and rho, and a matrix with acceptance proportions. Note that the trees themselves are by default not read in as these files can be very large.

1	readOutput(treeobj=NULL, argobj=NULL, argfile=NULL, addtrees=FALSE)

`treeobj`	A ‘treeoutput’ object from a previous sampletrees runs
`argobj`	A settings object of class ‘pars’ describing the sampletrees run
`argfile`	A file containing the settings describing the sampletrees run
`addtrees`	If TRUE, store the trees in the output object (default=FALSE)

One of either argobj or argfile must not be NULL.

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

Kelly Burkett

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

addTreeStat, addTrees

#\dontrun{
#system.file("Examples/example_g_pars", package="Rsampletrees")
filename=paste(path.package("Rsampletrees"),"/extdata/example_g_pars",sep="")
runpars=readArgs(filename, check=FALSE)

# Must change the path so that the output can be found
runname=paste(path.package("Rsampletrees"),"extdata",runpars$RunName, sep="/")
#paste(system.file(package="Rsampletrees"),runpars$RunName, sep="/")
runpars=changeArgs(runpars, RunName=runname)

# Read in the output
results=readOutput(argobj=runpars)

#}