Molecular data simulations to test molecular clock calibration strategies
This is the original R code to simulate molecular data in pure birth trees and choose calibrations randomly. See the settings.csv file for an example of the parameters that can be specified for the simulations.
The code has some comments on how to run the simulations in unix machines. In general, it needs a a folder with a settings.csv, and a paths.txt files, and a folder with the unzipped scode folder, which should be called 'scode'. To start the simulations and analyses, open terminal, cd to the folder that contains the scode folder and the settings.csv file, and type 'Rscript scode/A4.set.runs.R'.
The 'A4.set.runs.R' script will source the code in 'scode' and start producing folders for each of the simulation settings in 'settings.csv'. The 'paths.txt' file should have the paths for beast and logAnalyzer in the local machine, see the file attached for an example. Several instances of the script can be run, so that several of the settings can be simulated and analysed simultaneously.
Feel free to contact me for any details at: firstname.lastname@example.org
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