TipDatingBeast (version 1.1-0)

PlotLOOCV: List taxa names present in the BEAST input file

Description

The LOOCV (Leave-one-out-cross-validation) is a statistical procedure aiming to detect whether some particular sequences, when used as calibration in a tip dating analyse, could lead to systematic bias. Once the XMLs produced with the "TaxaOut" function analyzed with BEAST, the PlotLOOCV function allows a graphical comparison of the estimated vs true sequence ages. Similarly to the PlotDRT function, PlotLOOCV requires uploading, reading and analysing the "Log" files generated by BEAST.

Usage

PlotLOOCV(name, burnin = 0.1)

Arguments

name

the name of the original XML file (excluding the .xml extension). In the same folder, should be present the i LogFiles generated from the i XMLs produced with the "TaxaOut" function (i being the number of Taxa in the dataset). The name of the Log files should look like "name.Taxon[i].log".

burnin

the fraction of the first MCMC sampling to exclude from the Log files when computing the parameter estimates distribution (default = 0.1, which means 10

Value

The function returns the names and order of the taxa present in an input xml file for the BEAST software.

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 {
	# example create with example file
	PlotLOOCV("Flu_BEAST_1.8", burnin = 0.1)
	# produce LOOCV plot 
# }