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Walter edited this page Jul 16, 2017 · 21 revisions

Tracer

Copyright by Andrew Rambaut, Marc Suchard & Alexei Drummond

Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC, Migrate, RevBayes, and possibly other MCMC programs.

Although Tracer can be used with programs other than BEAST, users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.

You can join the mailing list here: http://groups.google.com/group/beast-users

The latest release for Tracer is here: https://github.com/beast-dev/tracer/releases/latest

The website for BEAST (and Tracer) is here: http://beast.bio.ed.ac.uk/

Besides this wiki, there are few more tutorials available for this application, such as analysing BEAST output. Some of BEAST tutorials also demonstrate how to use Tracer. Alternatively, you can simply play around and see what happens, basically select the trace file in the top left of the window, the individual parameter in the bottom left and the analysis appears on the right.

There are 4 analysis tabs to choose from:

  • Estimates - this shows the mean, stdev, confidence intervals and other statistics about the selected parameter. A frequency distribution will also be plotted.
  • Density - this shows the Bayesian posterior density plot for the selected parameter.
  • Joint-Marginal - this only appears if exactly 2 parameters are choosen (hold down shift to select multiple parameters). It then plots one against the other to look at their joint-marginal distribution.
  • Trace - this shows the trace of the parameter against state or generation number. Use this to check mixing, choose a suitable burn-in and look for trends that might suggest problems with convergence.

Multiple parameters can be selected by holding down the shift key. This will overlay the plots for the different parameters allowing comparisons to be made. You can also select multiple trace files as well to compare different runs. If multiple trace files have the same trace names then a "Combined" trace will automatically appear. This can be selected as well as the individual trace files.

You can also perform the following analyses by selecting an option from the Analysis menu:

  • Demographic reconstruction
  • Bayesian Skyline reconstruction
  • Extended Bayesian Skyline reconstruction
  • GMRF Skyride reconstruction
  • SkyGrid reconstruction
  • Lineages through time
  • Conditional posterior

The "Reload Trace File" function in "File" menu allows you to monitor the log during the MCMC runtime. The "Print" function in the "File" menu will print the current graph or table. The "Export Data" function can be used to export the data from the plots for use in another graphic package, and "Export Statistic Summary" exports the summary into a tab-delimited file. To export the currently displayed graphic use the "Export PDF" function in the "File" menu.

Citation

The recommended citation for this program is:

Rambaut A, Suchard MA, Xie D & Drummond AJ (2014) Tracer v1.6, Available from http://beast.bio.ed.ac.uk/Tracer

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