Lines of Code
[root]/src/dr/app/tracer/analysis
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 156 (100.0%) | 9749 (100.0%) | 62.4 |
| rambaut | 72 (46.2%) | 5743 (58.9%) | 79.7 |
| alexei.drummond | 22 (14.1%) | 2636 (27.0%) | 119.8 |
| dong.w.xie | 42 (26.9%) | 1216 (12.5%) | 28.9 |
| tbcbedford@gmail.com | 11 (7.1%) | 87 (0.9%) | 7.9 |
| dong.w.xie@gmail.com | 5 (3.2%) | 47 (0.5%) | 9.4 |
| jheled | 2 (1.3%) | 16 (0.2%) | 8.0 |
| msuchard | 2 (1.3%) | 4 (0.0%) | 2.0 |
tracer: doWork in EBSP needs to be reviewed, it seems a copy of BSP.
1 lines of code changed in 2 files:
Porting fixes from 1.7.3 back into the trunk
11 lines of code changed in 2 files:
trunk: merge Issue 284:Tracer doing BSP will throw an exception if the log file/tree file are out of sync
46 lines of code changed in 3 files:
Fixed typo.
2 lines of code changed in 2 files:
Updated the text describing AICM and Bayes factor model comparison. Always doing comparisons on ln scale. Also, in keeping with previous behavior, simple harmonic mean estimator is never used. Options are: "aicm" and "harmonic mean". Harmonic mean gives smoothed estimator.
26 lines of code changed in 3 files:
Model comparison now defaults to comparing all open trace files, rather than all selected trace files. To me this seems like a more expected behavior. I tried to implement a checkbox in the dialog box for "Use selected trace files only". However, this was difficult because the List<TraceList> that's passed in from TracerFrame doesn't have information about what is currently selected.
2 lines of code changed in 1 file:
Ratios of AICMs are not Bayes factors.
3 lines of code changed in 1 file:
Bayes factors are not odds.
3 lines of code changed in 1 file:
Moving naming from "Bayes Factors" to "Model Comparison"
5 lines of code changed in 2 files:
Full width table by default.
0 lines of code changed in 1 file:
Implementing AICM in Tracer. The Bayes factor dialog now has a drop-down menu with AICM as the default option.
52 lines of code changed in 2 files:
trunk: add EBSP analysis in Tracer, but doWork() not working yet.
877 lines of code changed in 1 file:
Working towards Tracer 1.6. Switched trace 'types' (in the GUI) to 'real', 'integer' and 'categorical' as the previous ones were in programmers' jargon. These buttons also are now disabled when no trace is selected. Also disabled the confirmation box for setting types - if you press the button, then you probably intended to do it (this is a static switch at the top of the TracerFrame.java).
Cleaned up some issues with the generification of 'Variate' - in particular some methods in the plotting were not being overridden.
In 'distribution' tab, for real traces, KDEs are now the default. Histogram estimates can also be shown.
Options for plotting are now stored for specific traces (for example, if you set a manual range for a trace it is now remembered and used for this trace only).
Cleaned up some odd code in Skyline plotting (causing an erroneous warning box to appear).
Removed a few exclamation marks from dialog box messages and cleaned up the text.
114 lines of code changed in 14 files:
Trunk: add two epoch in Tracer Demo reconstruction
46 lines of code changed in 1 file:
Trunk new Trace: more corrections to use 2d ArrayList ArrayList<ArrayList> not List[].
50 lines of code changed in 2 files:
Trunk new Trace: fix BSP plot in analysis, which should use 2d ArrayList ArrayList<ArrayList> not List[].
10 lines of code changed in 1 file:
Trunk new Trace: finally get rid of array copying functions getValues(?, [], ?) from Trace, which is memory consuming. Please use List<T> for your futher programming in Tracer.
74 lines of code changed in 6 files:
Trunk new Trace: remove static convert method from Trace.
0 lines of code changed in 1 file:
Trunk new Trace: 1) Try to replace Double[] as List<Double>, which save some memory, but it still crashes after loading a big log; 2) use traceType to detemine type, instead of prime type (T) of List<T> in Trace, and integer is stored as List<Double> currently for simlple solution of plotting.
10 lines of code changed in 5 files:
Trunk: starts using List instead array in Trace, and return List for getValues.
11 lines of code changed in 5 files:
Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.
62 lines of code changed in 9 files:
Trunk: new Tracer dev: make it complied, but there is still casting problem.
8 lines of code changed in 1 file:
Trunk: correction of r3529
4 lines of code changed in 1 file:
Trunk: solve Issue 393: Fix the message of the Bayes factor report in Tracer
3 lines of code changed in 1 file:
Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.
42 lines of code changed in 13 files:
TRUNK: new tracer dev merged from branch TRACER_NEW_DEV.
28 lines of code changed in 7 files:
What is a marginal likelihood?
1 lines of code changed in 1 file:
Trunk: merge r2706
33 lines of code changed in 1 file:
Added drag and drop of log files into Tracer.
4 lines of code changed in 1 file:
Work on next version of Tracer. Implemented a 'GMRF Skyride' analysis. Implemented feature request <http://code.google.com/p/beast-mcmc/issues/detail?id=191> to display burnins in different colour.
705 lines of code changed in 1 file:
LineagesThroughTimeDialog now reports 1 lineage for times above the root of a tree. This is nicer than the conditional version when comparing against known analytical results for lineage through time plots.
3 lines of code changed in 1 file:
Fixes Constant-Exponential reconstruction in Tracer which was out of sync with current BEAST parameterization.
12 lines of code changed in 1 file:
Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.
476 lines of code changed in 8 files:
UniformRootPrior works on trees with contemporaneous tips but not dated tips.
18 lines of code changed in 1 file:
Small additions to Tracer
24 lines of code changed in 1 file:
Added a 'DemographicLogger' - this is a logger for recording reconstructions (popsizes + change points) for skyline, skyride type models. The logger takes a class that implements 'DemographicReconstructor' interface. For BSPs this is the BayesianSkylineLikelihood itself.
The actual reconstruction has not been implemented for BSP yet.
Added an Exponential-growth BSP model.
21 lines of code changed in 1 file:
added new tests for wide exchange operator in ExchangeOperatorTest and YuleModelTest... I would encourage other BEAST developers to consider writing JUnit tests... they are easy and fun!
35 lines of code changed in 1 file:
Renamed ADNADamageModel to SequenceErrorModel. Intend to make it more general.
2 lines of code changed in 1 file:
More additions and improvements to Tracer
304 lines of code changed in 5 files:
Added a 'Trait through time' plot. Give the name of any trait stored in the tree (including 'rate').
588 lines of code changed in 2 files:
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