PlotLOOCV: List taxa names present in the BEAST input file

In TipDatingBeast: Using Tip Dates with Phylogenetic Trees in BEAST

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

Details

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

Value

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

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 

## End(Not run)

TipDatingBeast documentation built on Oct. 30, 2019, 11:40 a.m.