Tracer

Mục lục bài viết

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.community/tracer

Compiled binaries (for Mac, Windows and Linux) are available from the Tracer GitHub repository.

Source code is available from GitHub.

Version History

2018-05-01 – v1.7.1

Tracer is no longer distributed from this website.

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