TipDatingBeast (version 1.1-0)

RandomDates: randomize dates among tips in the BEAST input file

Description

This function read an XML file (BEAST version 1), 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

RandomDates(name, reps = 20, writeTrees = T)

Arguments

name

The name of the original XML-formatted input file on which to apply the date-randomization procedure. Quote the name ("example"). The .xml extension should not be included.

reps

The number of repetions required by the user. There will be as many date-randomized datasets produced as the value of reps (default = 20).

writeTrees

This argument has no function in the current version (default = T).

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. and Khatchikian, C.E., 2017. TipDatingBeast: An R package to assist the implementation of phylogenetic tip-dating tests using BEAST. Molecular ecology resources, 17(4), pp.608-613. 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.
	# example file can be found in the example folder
	RandomDates("Flu-BEAST-1.8", reps = 20)
	# produce 20 replicate input files (.xml) in working directory
# }