Lines of Code
[root]/src/dr/inference/operators
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 386 (100.0%) | 16790 (100.0%) | 43.4 |
| msuchard | 77 (19.9%) | 6219 (37.0%) | 80.7 |
| alexei.drummond | 80 (20.7%) | 3997 (23.8%) | 49.9 |
| jheled | 78 (20.2%) | 2190 (13.0%) | 28.0 |
| baele.guy@gmail.com | 19 (4.9%) | 1705 (10.2%) | 89.7 |
| akaruiws | 18 (4.7%) | 1105 (6.6%) | 61.3 |
| Michael.DefoinPLatel | 4 (1.0%) | 429 (2.6%) | 107.2 |
| alexander.alekseyenko | 5 (1.3%) | 370 (2.2%) | 74.0 |
| rambaut | 23 (6.0%) | 236 (1.4%) | 10.2 |
| dong.w.xie | 72 (18.7%) | 186 (1.1%) | 2.5 |
| Sebastian.Hoehna | 3 (0.8%) | 163 (1.0%) | 54.3 |
| gcybis@yahoo.com.br | 3 (0.8%) | 124 (0.7%) | 41.3 |
| philippe.lemey@gmail.com | 1 (0.3%) | 46 (0.3%) | 46.0 |
| bloomquist | 2 (0.5%) | 16 (0.1%) | 8.0 |
| jen.tom | 1 (0.3%) | 4 (0.0%) | 4.0 |
Added missing CompoundParameter.fireParameterChangedEvent method, and demonstrating a nicer approach to multi-developer debugging.
28 lines of code changed in 2 files:
Reverted to how the parameters were set previously, the likelihoods were not being updated correctly.
26 lines of code changed in 1 file:
Stream-lining serial operations during multi-parameter updates
32 lines of code changed in 1 file:
Fixed Jacobian for log-transforms under new adaptive multivariate transition kernel for mixture models.
2 lines of code changed in 1 file:
Fixed the MH ratio for the independent coalescent sampler.
16 lines of code changed in 2 files:
Allows for an independent coalescent to be drawn given a list of taxa and a demographic model. The generated tree is then copied into the existing treeModel.
171 lines of code changed in 1 file:
Fix to issue 687; may need to port to 1.7 branch. RandomWalkOperator no longer reflects negative values when using default bounds.
5 lines of code changed in 2 files:
Fixed transform; they were missing Jacobians in computing densities.
9 lines of code changed in 1 file:
Added transformations to the syntax rules of the adaptable variance MVN operator.
5 lines of code changed in 1 file:
Fixed log determinate for large diagonal matrices; refactored transforms.
147 lines of code changed in 1 file:
More flexible version of the adaptable variance MVN operator with respect to the transformations, which can now be provided using XML specification.
160 lines of code changed in 1 file:
New version of the adaptable variance MVN operator. Transformation to the log scale is currently always performed, the Jacobian has been taken into account for the MH-ratio.
59 lines of code changed in 1 file:
Remove old version of the operator.
0 lines of code changed in 1 file:
Refactoring.
396 lines of code changed in 1 file:
Added option to specify the number of iterations using the initial covariance.
66 lines of code changed in 1 file:
Fixed typo.
1 lines of code changed in 2 files:
Cleaning up.
11 lines of code changed in 1 file:
Remaining part of an adaptive Metropolis (AM) algorithm/operator. Seems to be working but needs more testing. Also needs a rewrite to exploit symmetry and avoid redundant calculations.
156 lines of code changed in 1 file:
First part of an adaptive Metropolis (AM) algorithm/operator.
290 lines of code changed in 1 file:
First version of an independent sampler from a normal distribution model.
177 lines of code changed in 1 file:
Forgot to include the actual parameter in the XML rules.
8 lines of code changed in 2 files:
First version of an independent sampler from a gamma distribution.
163 lines of code changed in 1 file:
Updated PrecisionMatrixGibbsOperator for functionality within path sampling from posterior to prior. Should still cause errors in path sampling between two arbitrary models.
12 lines of code changed in 4 files:
Better mixing for hierarchical graph model
16 lines of code changed in 2 files:
Hierarchical model for discrete trait
108 lines of code changed in 1 file:
Commented out a couple of debug printfs
2 lines of code changed in 4 files:
trunk:solve Issue 451: BEAST suggests using a non-integer for randomWalkIntegerOperator
2 lines of code changed in 2 files:
Fixed integer overflow (when prior sampling) and mixed-math in RandomWalkOperator
5 lines of code changed in 1 file:
Change the performance suggestion.
5 lines of code changed in 1 file:
Tidy up more msatBMA related things.
72 lines of code changed in 3 files:
Tidy up MsatBMA related things.
131 lines of code changed in 2 files:
Trunk: revert an incorrect change on uniform and random walk integer operator on integer parameter part
13 lines of code changed in 3 files:
Trunk: add Uniform Integer Operator Test
18 lines of code changed in 2 files:
Trunk: solve Issue 435: UniformIntegerOperator did not include upper in the value:
int newValue = MathUtils.nextInt(upper - lower) + lower;
Because nextInt(n) gives value [0, n-1], if upper = 2 then newValue cannot have 2.
The correct code should be
int newValue = MathUtils.nextInt(upper - lower + 1) + lower;
29 lines of code changed in 1 file:
Trunk: make Integer Parameter to allow to pass Variable<Integer>.
66 lines of code changed in 7 files:
Implemented algorithm for a reflected random walk avoiding a loop. Refactored the old looping algorithm out into a method and created a unit test to compare the two. Currently for the test with a very large number of loop iterations, the results are different at the 4th decimal place, probably as a result of loss of precision in the repeated subtractions in the loop.
65 lines of code changed in 1 file:
Fixed an issue where an IntegerRandomWalkOperator was actually just generating a RandomWalkOperator (the wrong string was being used).
1 lines of code changed in 1 file:
add a new operator on sum constrained parameter, providing better mixing for multiscale parameters
132 lines of code changed in 1 file:
Better checking in generalized linear models to ensure that design matrices are of full rank.
7 lines of code changed in 2 files:
marc did something
46 lines of code changed in 1 file:
(144 more)