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Walter edited this page Apr 27, 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 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

There are few tutorials available for this application, such as analysing BEAST output. You also can simply play around and see what happens. Basically you can 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 select the "Demographic Analysis" from the Analysis menu - This plots the distribution of demographic population sizes over time for a number of models (constant size, exponential growth & logistic growth) that are available in BEAST. This involves you selecting the traces for each parameter of the model. You should only select the model that was actually run under BEAST (e.g., if you ran an exponential growth model, you shouldn't plot the constant population size model).

The "Analysis" menu also contains options for performing Bayesian Skyline reconstructions and for calculating Bayes Factors between runs.

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.

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