TipDatingBeast (version 0.1-6)

RandomDates2: randomize dates among tips in the BEAST input file

Description

This function read an XML file (BEAST version 2), randomize dates among all tips and produce a new XML input file with such randomization. The process is repeated up to the number of replicates (default is 20).

Usage

RandomDates2(name, reps = 20)

Arguments

name

Name of the input file should be a .xml file generated using BEAUTi. Quote the name ("example"). Do not included .xml.

reps

Number of replicates to be produced (default 20).

Value

• The function returns one or many files (the number is set by the "reps" argument; default is 20) In each new file, the date values are randomized among all tips.

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Rieux A & Khatchikian, C. Unpublished.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

# using the example files "Flu2.xml" found in example folder.
	# example file can be found in the example folder
	RandomDates("Flu2", 10)
	# produce 10 replicate input files (.xml) in working directory