Lines of Code
[root]/src/dr/app/beauti/tipdatepanel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 46 (100.0%) | 1479 (100.0%) | 32.1 |
| dong.w.xie | 28 (60.9%) | 863 (58.4%) | 30.8 |
| rambaut | 17 (37.0%) | 603 (40.8%) | 35.4 |
| alexei.drummond | 1 (2.2%) | 13 (0.9%) | 13.0 |
BEAUti: added Pagel's Lambda transform of tree shape to measure phylogenetic signal in continuous traits. Check box in sites panel for continuous trait partition. Lambda appears in priors table and operators table.
28 lines of code changed in 4 files:
Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.
92 lines of code changed in 1 file:
Improved tip date parsing - now can read variable precision dates.
17 lines of code changed in 1 file:
Adding date precision to the BEAUti/Pathogen date guessing panel
10 lines of code changed in 1 file:
Cleaned up the tipdate sampling options (the joint prior model wasn't generating code so hid this option). Removed requirement for taxon sets to be at least 2 taxa.
2 lines of code changed in 1 file:
Added button to allow the setting of dates for selected taxa
165 lines of code changed in 2 files:
Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.
1 lines of code changed in 1 file:
Trunk: make clock model group working in GUI, but operators and generator not working yet.
5 lines of code changed in 1 file:
Trunk: big change of implementing clock model group, including to correct some auto GUI event regarding "fix mean" and calibration. Not finished yet.
1 lines of code changed in 1 file:
Trunk: more work on micro-sat data in BEAUti.
4 lines of code changed in 1 file:
Improvements to the Guess Dates Dialog to allow for parsing of calendar dates.
268 lines of code changed in 1 file:
Cleaning up BEAUti a bit.
2 lines of code changed in 1 file:
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).
1 lines of code changed in 1 file:
Fixed issue 369: http://code.google.com/p/beast-mcmc/issues/detail?id=369
6 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.
11 lines of code changed in 2 files:
TRUNK: modification of Discrete Trait in BEAUti, and change default prior of all clock rates into Gamma(0.001, 1000)
20 lines of code changed in 1 file:
TRUNK: merge Issue 294 from branch
2 lines of code changed in 1 file:
TRUNK: BEAUti make taxonList static.
20 lines of code changed in 1 file:
Trunk refactoring: make evoxml parsers more organized.
2 lines of code changed in 1 file:
Trunk: start merge BEAUti from branch 1.5 in
7 lines of code changed in 2 files:
BEAUTi: keep reducing ModelOptions by create enum DateUnitsType, and fix the bug of r2223.
13 lines of code changed in 1 file:
BEAUTi: fix more bugs regarding calibration calculation, and prior options.
10 lines of code changed in 1 file:
BEAUTi: fix more bugs regarding calibration GUI event and log.
2 lines of code changed in 1 file:
BEAUTi: add some GUI event, and reset panel.
10 lines of code changed in 1 file:
BEAUTi: bug fixing for clock setting in calibrication.
2 lines of code changed in 1 file:
BEAUTi: cotinue Issue #100 and Issue #124.
1) add some events in GUI to fire Tip Calibration and Node Calibration;
2) tidy up 5 FixRateType;
3) TODO: the calculation of ini rate and root height for Node Calibration.
2 lines of code changed in 1 file:
BEAUTi: cotinue Issue #100 and Issue #124.
1) implement isTipCalibration() by whether maximumTipHeight > 0;
2) if isTipCalibration(), then Tip Dates check box is checked;
3) if any calibration, then fix mean check box in clock panel is disabled.
4 lines of code changed in 1 file:
BEAUTi:
1) cotinue Issue #100;
2) start Issue #124.
1 lines of code changed in 1 file:
BEAUTi big refactory: move all enum into dr.app.beauti.enumTypes to spearate logic from GUI.
Note: some BEAST classes are using BEAUTi enum.
2 lines of code changed in 1 file:
BEAUTi: continue Issue #100:
1) if FIX_MEAN_RATE, then do delta exchange for all clock rates, which has to be multi-clock rates situation;
2) if ESTIMATE, then has scale op for each non-fixed rate except fixed rate, updown op for each non-fixed rate and tree, updownAll op for all non-fixed rates and all trees;
3) need TODO prior parameters calculations in selectParameters and selectOperators;
2 lines of code changed in 1 file:
BEAUTi: Issue #100,
1) complete GUI, and a further improvement will be continued;
2) need to add allClockRate delta operator, and implement it in BeastGenerator.
6 lines of code changed in 1 file:
Big Change of BEAUTI:
1) implement FixRateType containing estimate, fix mean, fix 1st partition to replace fixSubstitionRate;
2) comment out "mu" for no condon model;
3) correct *BEAST xml by adding updown operators;
4) fix bug to import NEXUS file when it contains subsititution model.
8 lines of code changed in 1 file:
BEAUTi: if tip dates then uncheck fix rate in Model panel.
1 lines of code changed in 1 file:
intellij tidy
13 lines of code changed in 1 file:
BEAUTi: rename partition series classes, and final relation is PartitionData => PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior.
0 lines of code changed in 1 file:
BEAUTi: before implement new model in BEAST, disable Yule and Birth Death for gene tree in Tree panel, when checked "use tip dates" in Tip Dates panel.
4 lines of code changed in 1 file:
Refactory BEAUTI package structure, add few panel packages and util package.
1 lines of code changed in 1 file:
Create dr.app.beauti.tipdatepanel package to make clear structure.
734 lines of code changed in 3 files: