TipDatingBeast (version 1.0-5)

TaxaOut: generates input files for leave-one-out analyses in BEAST

Description

This function produces input files to perform leave-one-out analyses using BEAST version 1 software. As many files as taxa present in the input file are produced; each one leaving each consecutive taxon out for analysis.

Usage

TaxaOut(name, lBound = 0, hBound = 1.0E100, writeTrees = T)

Arguments

name

The name of the original XML-formatted input file on which to apply the LOOCV procedure (the .xml extension should be excluded). This xml should be set up so that earlier dates have lower numerical values (i.e., set direction = "forwards" when setting up date in BEAUti). Place the name between quotes ("example").

lBound

The uniform prior lower bound for the age of the missing taxa (default = 0)

hBound

The uniform prior higher bound for the age of the missing taxa (default = 1.0E100)

writeTrees

Set to False (F) if you do not want the trees to be written when running the date-randomized datasets in BEAST. To proceed the LOOCV, only the log files are needed (default = T).

Value

The function returns as many files as taxa are present in the input file; each one leaving each consecutive taxon out for analysis.

Details

The function works only with a .xml file generated with BEAUti.

References

Rieux A & Khatchikian, C. Unpublished. Drummond AJ, Suchard MA, Xie D & Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology And Evolution 29: 1969-1973.

Examples

# NOT RUN {
    # using the example files "Flu_BEAST_1.8.xml" found in example folder.
	TaxaOut("Flu_BEAST_1.8")
	# produce 21 input files, each one without the corresponding taxon
# }