TipDatingBeast (version 1.1-0)

PlotDRT: List taxa names present in the BEAST input file

Description

Once analyzed with BEAST, the PlotDRT function allows comparing the parameter estimates obtained with the original vs. the randomized datasets. This function requires uploading, reading and analyzing the "Log" files generated by BEAST. A Log file contains a row for each MCMC sampling and a column for each estimated parameter. When considered as frequency distributions, this file provides an estimate of the marginal posterior probability distribution for each parameter. The function "PlotDRT" enable a graphical comparison of the parameter estimates obtained with the original vs. the date-randomized datasets (whatever the shuffling procedure considered).

Usage

PlotDRT(name, reps, burnin = 0.1)

Arguments

name

The name of the original Log file (excluding the .log extension) to upload and compute the real parameter estimates on. The name of the Log files computed from the date-randomized datasets should look like "name.Rep[i].log"

reps

The number date-randomized log files

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 produce a two plots; one in normal scale, one in log scale.

Details

The function works only after all BEAST runs are completed

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
	PlotDRT("Flu_BEAST_1.8", reps = 20, burnin = 0.1)
	# produce DRT plot 
# }