Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 293 (100.0%) | 11183 (100.0%) | 38.1 |
| alexei.drummond | 39 (13.3%) | 2412 (21.6%) | 61.8 |
| dong.w.xie | 128 (43.7%) | 2335 (20.9%) | 18.2 |
| msuchard | 20 (6.8%) | 2274 (20.3%) | 113.7 |
| philippe.lemey@gmail.com | 12 (4.1%) | 1422 (12.7%) | 118.5 |
| jheled | 28 (9.6%) | 1262 (11.3%) | 45.0 |
| rambaut | 28 (9.6%) | 760 (6.8%) | 27.1 |
| baele.guy@gmail.com | 18 (6.1%) | 435 (3.9%) | 24.1 |
| dong.w.xie@gmail.com | 10 (3.4%) | 102 (0.9%) | 10.2 |
| tbcbedford@gmail.com | 5 (1.7%) | 62 (0.6%) | 12.4 |
| victor.obolonkin@gmail.com | 1 (0.3%) | 51 (0.5%) | 51.0 |
| alexander.alekseyenko | 2 (0.7%) | 33 (0.3%) | 16.5 |
| benjamin.redelings | 1 (0.3%) | 25 (0.2%) | 25.0 |
| Michael.DefoinPLatel | 1 (0.3%) | 10 (0.1%) | 10.0 |
Bug fix when using prior sampling to estimate (log) marginal likelihoods.
3 lines of code changed in 2 files:
tracer: big correction of tracer code for my previous development on "Conditional Posterior Distributions", which fixed bugs in GUI especially in Filter, and use EDT thread.
102 lines of code changed in 10 files:
Additional output column for stepping-stone column
12 lines of code changed in 2 files:
Additional output column for path sampling
12 lines of code changed in 2 files:
Added calculation of the arithmetic mean estimator (AME).
27 lines of code changed in 1 file:
Fixed indexing issue in the stepping-stone sampling estimator.
6 lines of code changed in 1 file:
tweaking dnds trace analysis
72 lines of code changed in 2 files:
Minor change (mainly for testing purposes).
26 lines of code changed in 2 files:
Ensuring backwards compatability of MarginalLikelihoodAnalysis with harmonicOnly setting.
8 lines of code changed in 1 file:
adjusted toString method for harmonic mean and AICM
19 lines of code changed in 1 file:
adjusted toString method for stepping stone sampling
3 lines of code changed in 1 file:
adjusted toString method for path sampling
1 lines of code changed in 1 file:
Adding a CnCs counting class
718 lines of code changed in 1 file:
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.
2 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 3 files:
adding a trace analysis for syn and nonsyn counts
445 lines of code changed in 1 file:
Update to allow multiple input files with marginal likelihood samples to be processed.
67 lines of code changed in 1 file:
Removed some unnecessary comments.
0 lines of code changed in 1 file:
Update to allow multiple input files with marginal likelihood samples to be processed.
57 lines of code changed in 1 file:
Code to calculate the marginal likelihood using stepping-stone sampling (Xie et al., 2011), after the marginal likelihood estimator code has been run.
200 lines of code changed in 1 file:
adding custom burn-in to DnDsPerSiteAnalysis
27 lines of code changed in 1 file:
Fixed issue 471: http://code.google.com/p/beast-mcmc/issues/detail?id=471
11 lines of code changed in 1 file:
Fixed a burn-in issue with the path sampling analysis (previous version discards 20% of the samples leading to an incorrect marginal likelihood).
2 lines of code changed in 1 file:
Trunk: a small correction of TraceAnalysis
3 lines of code changed in 1 file:
Trunk: update TraceAnalysis
74 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.
4 lines of code changed in 2 files:
Trunk: more updates for GetDateFromTree and LogAnalyser
23 lines of code changed in 1 file:
Trunk: add a new tool to LogAnalyser
69 lines of code changed in 4 files:
Trunk: fix the trace bug
18 lines of code changed in 2 files:
Trunk: fix a critical bug for new Tracer, Issue 459: new Tracer gives different statistics to previous version
1 lines of code changed in 1 file:
more DnDsPerSiteAnalysis tweaking
4 lines of code changed in 1 file:
mor DnDsPerSiteAnalysis tweaking
55 lines of code changed in 1 file:
DnDsPerSiteAnalysis tweaking
110 lines of code changed in 1 file:
Trunk new Trace: fix some bugs.
24 lines of code changed in 5 files:
Trunk new Trace: more corrections to use 2d ArrayList ArrayList<ArrayList> not List[].
5 lines of code changed in 2 files:
Trunk new Trace: fix bug of returning double format for integer value, because Integer is stored as Double in Trace.
13 lines of code changed in 2 files:
Trunk new Trace: if combined traces exists, the filter has to be applied to all log files including combined traces, as Alexei advised.
1 lines of code changed in 1 file:
Trunk new Trace: fix filter not working bug.
2 lines of code changed in 1 file:
Trunk new Tracer: fix the bug of missing possible values displayed in FilterDiscretePanel after filter applied.
29 lines of code changed in 2 files:
Trunk new Trace: make trace type change function working.
42 lines of code changed in 4 files:
(106 more)