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Walter edited this page Apr 26, 2017
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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.
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.
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'
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
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.
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.
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.
Now allows multiple Tracer windows.
New features:
- Allows multiple Tracer windows using the "New" command.
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
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.
First released version