Tracer

Tracer

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

At present there is no detailed manual for this application, you will simply have to 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 and the "Export Data" function can be used to export the data from the plots for use in another graphic package.

To export the currently displayed graphic use the "Export PDF" function in the "File" menu.

Version History

2013-12-11 - v1.6

Now supports skygrid analysis and does KDE density plots
New features:
  • Multilocus 'Skygrid' analysis option - use this option when analysing BEAST output generated under this model.
  • Density plots are now drawn as kernal density estimates instead of histograms.
  • Traces can be designated as integer or categorical with appropriate plots and statistics given.
Bugs fixed:
  • Minor bug fixes.
2009-11-30 - v1.5

A number of new features including drag-and-drop file import.
New features:
  • Can now import log files by dragging them into the left hand side of the window.
  • GMRF 'Skyride' analysis option - use this option when analysing BEAST output generated under this model (Minin, Bloomquist & Suchard, 2008, Mol Biol Evol 25:1459-71).
  • Burnins are shown on trace plots (in a paler colour).
  • The ESSs of 'Combined Traces' are now calculated explicitly rather than just summing the individual ESSs. This shows cases where individual traces are sampling different distributions.
Bugs fixed:
  • Fixed bug when selecting 'Combined Trace' on its own. A checkbox is available for hiding these.
  • By default the trace panel shows the complete trace rather than a sub-sample.
  • Fixed issues when columns had the same name - a suffix is now appended.
2008-11-29 - v1.4.1

A minor update with a few new features
New features:
  • Multiple trace files can now be selected in the Import dialog box
  • When selecting multiple trace files, the common set of traces are displayed (even if they are in a different order - as long as they are named the same) to make model comparisons easier.
Bugs fixed:
  • Fixed problem with freezing when selecting a static (non-changing) trace
  • Fixed some issues with setting up 'Temporal Analyses'
2007-10-11 - v1.4

A major update with many new features
New features:
  • Overlay distributions from different files and statistics
  • More control over plotting
  • Export of graphics as PDFs and raw data from most views
  • Calculation of Bayes Factors to compare runs with different models
  • Overlay demographics reconstructions including Skyline plots
  • Translucent points for joint-marginal densities
  • Faster and more accurate ESS analysis
Bugs fixed:
  • This is an almost complete re-write so all bugs are new
2005-09-29 - v1.3

Numerous bug fixes
Bugs fixed:
  • Fixes crashes when the wrong model is selected in Bayesian Skyline reconstruction.
  • Fixes crashes when solid intervals is chosen with zero values.
  • More reliably reveals statistics table when a log file is loaded.
  • Keeps log likelihood values in non-scientific format.
  • Can copy and paste from all tabs and windows.
  • Can export raw numerical data as text file.
2005-02-25 - v1.2.1

Adds new analyses and fixes a couple of bugs.
New features:
  • Now analyses the new Bayesian Skyline Plot.
  • More demographic model analyses.
  • Can now remove Traces from the table.
Bugs fixed:
A few minor bug fixes.
2004-10-28 - v1.2

Adds new analyses and fixes a couple of bugs.
New features:
  • Now analyses the new Bayesian Skyline Plot.
  • More demographic model analyses.
Bugs fixed:
  • Keeps a menu available on the mac even when all the windows have been closed.
  • Fixes a problem with the reporting of erroneous mean parameter values when multiple traces were combined after changing from default burn-in sizes.
2004-09-17 - v1.1.1

Now allows multiple Tracer windows.
New features:
  • Allows multiple Tracer windows using the "New" command.
2004-05-24 - v1.1

New version with a number of new features.
New features:
  • Added a new Analysis menu that has a single item: Demographic Analysis - this draws a plot of the posterior density of the demographic function over time.
  • Added a plot in the Estimates tab when multiple statistic traces are selected. It now shows a series of range bars for the HPD allowing comparison of related statistics.
  • Can optionally draw every point in the Trace plot or only a sample if the file is large.
  • Can now select multiple traces when multiple trace files are combined.
  • Improved legend display for plotting densities of multiple combined trace files.
Bugs fixed:
Minor bug fixes
2003-09-22 - v1.0.1

Fixed problem with taking too much CPU time and crashing on certain traces
New features:
Progress dialog box when loading large files
Bugs fixed:
  • Fixed problem with analysis thread using up way too much CPU time when not doing anything. This was more noticable on Windows machines.
  • Fixed problem with the program hanging when a parameter trace contained only one value over its entire length (mainly discrete parameters).
  • Switched to native look-and-feel on Windows.
2003-08-08 - v1.0

First released version
 
Andrew Rambaut, 2007