TipDatingBeast (version 1.1-0)

TaxonOut: single Taxon out input file for leave-one-out analysis in BEAST

Description

This function produces a single input file for leave-one-out analyses using BEAST version 1 software. In this analysis, the date of the chosen taxon is estimated using the remaining taxa dates. The function "ListTaxa" is intended to help identifying the order (parameter "takeOut") of the taxon desired for the leave-out-analysis.

Usage

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

Arguments

name

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

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)

takeOut

Taxon order for the take-one-out analysis.

writeTrees

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

Value

The function returns a single file to perform a leave-one-out analyses using BEAST software for the specific taxon.

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 using the 5th taxon ("CHICKEN_HONGKONG_915_1997")
	TaxonOut("Flu_BEAST_1.8", takeOut = 5)
	# produce a single input files without the corresponding taxon ("CHICKEN_HONGKONG_915_1997")
# }