Lines of Code
[root]/src/dr/app/beauti/enumTypes
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 71 (100.0%) | 1036 (100.0%) | 14.5 |
| dong.w.xie | 46 (64.8%) | 994 (95.9%) | 21.6 |
| rambaut | 25 (35.2%) | 42 (4.1%) | 1.6 |
This is a very large commit. It addresses some architectural issues in BEAUti that were going to hinder implementation of continuous traits.
The main thing it does is to isolate creating and importing traits from creating partitions on those traits. A button on the data panel explicitly specifies that a trait should be used as a data partition (i.e., have a TreeLikelihood). This allows traits to be used for other purposes (such as defining Species in *BEAST). This has also allowed considerable simplification of code and tidying up.
There are a number of bug fixes as well over v1.6.0 that I will add to the issue list to keep track of them. Given the complex nature of these changes, I do not think these should be ported to the 1.6.0 branch but perhaps the bugs can be fixed.
These changes will have introduced bugs and possibly cause issues with XML generation that now need to be fixed (I will attempt to catch as many as possible).
0 lines of code changed in 17 files:
Trunk: merge change.
2 lines of code changed in 2 files:
Trunk: merge issue 416, 417 and 418.
25 lines of code changed in 1 file:
Trunk: EBSP missing P.
1 lines of code changed in 2 files:
Trunk: merge Issue 410: "Improper priors" on posterior statistics from branch 1.6.
12 lines of code changed in 1 file:
Trunk: solve Issue 392: BEAUti: wrong validation to apply Normal prior to tmrca
2 lines of code changed in 1 file:
Reordered the PriorType Enum so that UNDEFINED is first. This is so it doesn't appear as an option in the RootHeightPriorCombo. The user shouldn't be able to select it as an option.
4 lines of code changed in 1 file:
Implemented a new option for default priors - an UNDEFINED prior. This comes up as red in the priors table and the XML will not generate until this is set (even to a uniform[0,+Inf] would be OK). At present, the only parameters to use this option are the rate parameters for discrete traits (i.e., 1 character partitions).
12 lines of code changed in 1 file:
Restored improper uniform priors on rate parameters but added a red colour to the prior table to warn about this.
9 lines of code changed in 1 file:
Renamed an internal constant from JEFFREYS_PRIOR to ONE_OVER_X_PRIOR
5 lines of code changed in 1 file:
Firstly, made writeComment take a VarArg number of strings to allow for multi-line comments. Comments now have a blank line before them to break up the XML visually.
Secondly, removed the 'booleanLikelihood' for LogisticModel as this was nasty. Instead, proper priors need to be put on the t50 parameter (a gamma is given as default). Also added gamma default prior to the doubling time parameter (and picked a larger initial value to help with numerical issues in logistic and expansion model).
Thirdly, normalized the generation of discrete trait models to always use generalSubstitutionModel.
Have generated all these model and tested that they run (but not that they produce reasonable results).
4 lines of code changed in 1 file:
Trunk: solve Issue 347: change BEAUti default prior of ucld.stdv and kappa, and fix few little bugs.
2 lines of code changed in 2 files:
This is rather a large update as I was making changes in a branch and have merged them back in. This allows any trait name to be created (not just 'Location' and 'Species'). The idea is that the discrete model is not phylogoegraphy specific - you can model any discrete change. Have added a check box to say use *BEAST - at this point you should create a Species trait. Have cleaned up a few othe UI issues. Almost certainly there will be XML generation issues as a result and we should concentrate on testing and fixing these.
2 lines of code changed in 1 file:
Trunk; BEAUti add Random Local Clock, but it seems BEAST model has bug
2 lines of code changed in 1 file:
TRUNK: beauti: add newick format starting tree generator.
2 lines of code changed in 2 files:
Added a few models of sequence (tip) error to model the action of hypermutation by APOBEC editing in HIV.
6 lines of code changed in 2 files:
TRUNK: BEAUti discrete traits prior and operator panels are working.
20 lines of code changed in 1 file:
TRUNK: BEAUti a correction of *BEAST pop size model type.
3 lines of code changed in 2 files:
TRUNK: BEAUti Phylogeographic initial dev done for gui.
5 lines of code changed in 2 files:
Trunk refactoring: 2nd part of operators (split parsers).
2 lines of code changed in 1 file:
Trunk refactoring: finish tree operators (split parsers)..
2 lines of code changed in 1 file:
Trunk: start merge BEAUti from branch 1.5 in
69 lines of code changed in 2 files:
BEAUTi: correct spell and remove Warning message.
1 lines of code changed in 2 files:
BEAUTi: Issue 140: more options for *beast.
But Population Size Model – Constant does not work yet.
45 lines of code changed in 1 file:
BEAUTi:
1) solve Issue 135: Laplace prior has not been implemented in PriorParsers, but appearing in BEAUTi;
2) solve Issue 158: We should have the Inverse Gamma distribution in Beauti.
13 lines of code changed in 1 file:
BEAUTi: solve Issue 156: LogNormal in prior panel in Beauti.
1 lines of code changed in 1 file:
BEAUTi: continue to reduce ModelOptions
47 lines of code changed in 1 file:
BEAUTi: start to create Builder parttern in Parameter, and simplify prior's parameters.
16 lines of code changed in 1 file:
BEAUTi: add enum BinaryModelType.
43 lines of code changed in 1 file:
BEAUTi: add some useful message.
4 lines of code changed in 1 file:
BEAUTi:
1) cotinue Issue #100;
2) start Issue #124.
5 lines of code changed in 1 file:
Fix the problem of BEAST using BEAUTi code, finding from r2123.
0 lines of code changed in 2 files:
BEAUTi big refactory: move all enum into dr.app.beauti.enumTypes to spearate logic from GUI.
Note: some BEAST classes are using BEAUTi enum.
670 lines of code changed in 13 files: