Lines of Code
[root]/src/dr/evomodel/sitemodel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 86 (100.0%) | 2307 (100.0%) | 26.8 |
| alexei.drummond | 16 (18.6%) | 975 (42.3%) | 60.9 |
| akaruiws | 8 (9.3%) | 490 (21.2%) | 61.2 |
| rambaut | 26 (30.2%) | 423 (18.3%) | 16.2 |
| benjamin.redelings | 1 (1.2%) | 311 (13.5%) | 311.0 |
| jheled | 23 (26.7%) | 84 (3.6%) | 3.6 |
| msuchard | 4 (4.7%) | 17 (0.7%) | 4.2 |
| dong.w.xie | 8 (9.3%) | 7 (0.3%) | 0.8 |
BMA for nucleotide substition models and gamma site model.
262 lines of code changed in 1 file:
Classes for modelling the relative rates of loci.
115 lines of code changed in 3 files:
Prevent repetitive rate calculations.
16 lines of code changed in 1 file:
Automatically create bounds for the category parameter and correction to adding parameter to model.
6 lines of code changed in 1 file:
Parser and corrections for DiscretizedLociRates.
3 lines of code changed in 1 file:
Models the relative loci rates using the given discritized parametric distribution.
88 lines of code changed in 1 file:
Trunk refactoring: site model (split parsers).
7 lines of code changed in 8 files:
code police
8 lines of code changed in 1 file:
Implemented checks to see that all models, likelihood and parameters are being controlled by the MCMC. The checks are made in MCMCParser but the warnings are currently commented out.
48 lines of code changed in 2 files:
[NEW] Add a site model with free rate parameters.
It doesn't actually work yet, for some reason...
* dr/app/beast/development_parses.properties:
+ Add DirichletSiteModel
* src/dr/evomodel/sitemodel/DirichletSiteModel.java
+ New model class.
311 lines of code changed in 1 file:
generify and auto intelliJ
12 lines of code changed in 2 files:
code police
0 lines of code changed in 2 files:
Just added a comment explaning the lower bound on the gamma shape parameter.
6 lines of code changed in 1 file:
Hard lower bound on shape parameter of GammaSite*Model
1 lines of code changed in 1 file:
Overloaded several standard BEAST XML labels, so BEAGLE does not mask standard classes completely. A better solution is to have BeastParser do this automatically when it replaces parsers.
6 lines of code changed in 1 file:
Intellij Auto changes
24 lines of code changed in 4 files:
Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...
50 lines of code changed in 4 files:
more string constants
3 lines of code changed in 2 files:
I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.
0 lines of code changed in 2 files:
Integrated BEAGLE into BEAST (compiles and runs but crashes in native code).
52 lines of code changed in 5 files:
Created a SiteRateModel and a GammaSiteRate model. This new interface just provides relative rates and proportions for sites (so has no reference to substmodels or frequencymodels.
0 lines of code changed in 2 files:
Moved ParameterChangeType -> Parameter.ChangeType
17 lines of code changed in 4 files:
added variable size functionality to Parameter
742 lines of code changed in 4 files:
Code Police
4 lines of code changed in 2 files:
Simplified the SiteModel interface so it is no longer a wrapper for a substitution model to get transition probability matrix.
228 lines of code changed in 6 files:
Missing interface components fixed.
10 lines of code changed in 2 files:
Compiling - ready to start testing...
newtreelikelihood is a new approach to the likelihood core to minimize
communication between Java and native implementations. This should allow faster native code and use of GPUs. This is just a temporary parallel package whilst this is developed.
19 lines of code changed in 1 file:
Started work on a sequence simulator
33 lines of code changed in 1 file:
moved all distributions into their own sub-package in dr.math
87 lines of code changed in 1 file:
Be very afraid: I have tidied up double and string attribute parsing in various classes. Hopefully no logic was changed, and I avoided code that couldn't be understood in a brief moment.
1 lines of code changed in 2 files:
Be scared: I have tidied up integer attribute parsing in various classes. Also operator weights were integers in some places -- they should all be doubles now...
78 lines of code changed in 1 file:
Change method name to something I understand
4 lines of code changed in 1 file:
Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers
Renamed getSocketChild
Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute
4 lines of code changed in 1 file:
Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.
0 lines of code changed in 4 files:
Added a few more synchronisations to allow multithreading.
16 lines of code changed in 1 file:
Added a few more synchronisations to allow multithreading. This includes GammaSiteModel & HKY. Basically, any lazy calculations for instance variables in functions called by TreeLikelihood need to be synchronized.
21 lines of code changed in 1 file:
tidyup and generifying
24 lines of code changed in 7 files:
Issue a warning for attributes of elements in BEAST xml files which are not declared by the XML rules. This helps both users (like me) not to get stung by silent ignore of typos, and developers (like me) which need to debug rules for new elements.
Those changes involves fixing some elements rules, and additional cleanup.
1 lines of code changed in 1 file: