ListTaxa: List taxa names present in the BEAST input file

In TipDatingBeast: Using Tip Dates with Phylogenetic Trees in BEAST

Description

This function list the taxa names present in an input xml file for the BEAST version 1 software. The function is intended to help using the function "TaxonOut" as it allows the identification of the order of each taxa present in the input file.

Usage

ListTaxa(name)

Arguments

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

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: 
    # using the example files "Flu-BEAST-1.8.xml" found in example folder.
	# example file can be found in the example folder
	ListTaxa("Flu-BEAST-1.8")
	# list all 21 taxa in the file in the console 

## End(Not run)

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