Rsampletrees (version 1.0.3)

readOutput: Read in sampletrees output

Description

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.

Usage

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

Arguments

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)

Value

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

Details

One of either argobj or argfile must not be NULL.

References

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

See Also

addTreeStat, addTrees

Examples

# NOT RUN {
#\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)

#}
# }