List taxa names present in the BEAST input file
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.
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".
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
The function works only with a .xml file generated with BEAUti
The function returns the names and order of the taxa present in an input xml file for the BEAST software.
Rieux A & Khatchikian, C. Unpublished. 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.
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## Not run: # example create with example file PlotLOOCV("Flu_BEAST_1.8", burnin = 0.1) # produce LOOCV plot ## End(Not run)