Directory src/dr/evomodel/continuous/

Total Files:
33
Deleted Files:
8
Lines of Code:
1520

[root]/src/dr/evomodel/continuous
                    directory in repo plink (1 files, 67 lines)

Lines of Code

src/dr/evomodel/continuous/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 413 (100.0%) 21545 (100.0%) 52.1
msuchard 227 (55.0%) 12448 (57.8%) 54.8
rambaut 112 (27.1%) 5479 (25.4%) 48.9
alexei.drummond 39 (9.4%) 2408 (11.2%) 61.7
gcybis@yahoo.com.br 2 (0.5%) 595 (2.8%) 297.5
jheled 22 (5.3%) 388 (1.8%) 17.6
mandevsgill 5 (1.2%) 165 (0.8%) 33.0
philippe.lemey@gmail.com 4 (1.0%) 57 (0.3%) 14.2
tbcbedford@gmail.com 2 (0.5%) 5 (0.0%) 2.5

Most Recent Commits

mandevsgill 2013-05-16 07:51 Rev.: 5653

A few more minor changes (essentially all operations involving meanCache and storedMeanCache now done by cacheHelper). Rewritten code does not break anything.

0 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (new)
mandevsgill 2013-05-14 17:55 Rev.: 5649

Some very minor changes

160 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (+160 -10)
mandevsgill 2013-05-11 05:09 Rev.: 5645

Starting on diffusion with drift

5 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (new)
msuchard 2013-05-07 07:43 Rev.: 5635

Fixing transformed trees when random

121 lines of code changed in 16 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+4 -4), FullyConjugateMultivariateTraitLikelihood.java (new), IntegratedMultivariateTraitLikelihood.java (+2 -3), MissingTraits.java (new), MultinomialLatentLiabilityLikelihood.java (+25 -1), NonPhylogeneticMultivariateTraitLikelihood.java (new), OrderedLatentLiabilityLikelihood.java (+25 -1), SampledMultivariateTraitLikelihood.java (+27 -1), SemiConjugateMultivariateTraitLikelihood.java (new)
msuchard 2013-05-06 15:27 Rev.: 5631

Finally interfacing multivariate traits, although they are now generally integrated out.

46 lines of code changed in 4 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+10 -14), DiffusionRateStatistic.java (+33 -7), IntegratedMultivariateTraitLikelihood.java (+3 -2)
gcybis@yahoo.com.br 2013-05-01 19:07 Rev.: 5624

Latent Liability model

595 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: MultinomialLatentLiabilityLikelihood.java (+298), OrderedLatentLiabilityLikelihood.java (+297)
msuchard 2013-01-18 06:54 Rev.: 5333

Fixing jitter in IMTL

5 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (+5 -3)
msuchard 2013-01-10 05:20 Rev.: 5302

Added unit-IntervalLatentLiabilityLikelihood for VNTRs; plan to refactor to remove duplicated code once more fully tested.

553 lines of code changed in 4 files:

  • src/dr/evomodel/continuous: BinaryLatentLiabilityLikelihood.java (new 254), IntegratedMultivariateTraitLikelihood.java (+7 -4), IntervalLatentLiabilityLikelihood.java (new 292), LatentLiabilityLikelihood.java (del)
msuchard 2012-12-08 08:56 Rev.: 5280

Delegated handling of missing values in IntegratedMultivariateTraitLikelihood with a view towards enabling partially missing values

184 lines of code changed in 5 files:

  • src/dr/evomodel/continuous: DebugableIntegratedMultivariateTraitLikelihood.java (+38 -13), IntegratedMultivariateTraitLikelihood.java (+20 -26), MissingTraits.java (+125), NonPhylogeneticMultivariateTraitLikelihood.java (+1 -1)
msuchard 2012-11-30 06:37 Rev.: 5263

Fixed zero-branch length bug in IntegratedMultivariateTraitLikelihood and harmonized behavior of NonPhylogeneticMultivariateTraitLikelihood for model selection.

53 lines of code changed in 3 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+35 -6), IntegratedMultivariateTraitLikelihood.java (+5 -1), NonPhylogeneticMultivariateTraitLikelihood.java (+13 -1)
msuchard 2012-06-30 12:04 Rev.: 5059

Checking equations for Pybus et al. manuscript

70 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: FullyConjugateMultivariateTraitLikelihood.java (+58), IntegratedMultivariateTraitLikelihood.java (+12)
msuchard 2012-03-27 07:45 Rev.: 4895

Implementing transformed trees and Pagel's lambda estimator

29 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (+29 -4)
tbcbedford@gmail.com 2011-11-22 02:04 Rev.: 4468

Fixed bug in calculation of log density in BiasedMultivariateDiffusionModel. Branches should properly scale with time now. This seems to be working.

5 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: BiasedMultivariateDiffusionModel.java (new)
msuchard 2011-09-26 10:31 Rev.: 4333

Can specify non-integer degrees-of-freedom for Wishart distributions

11 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: NonPhylogeneticMultivariateTraitLikelihood.java (+11 -1)
msuchard 2011-09-24 14:39 Rev.: 4332

Fixed degrees-of-freedom in Wishart statistics for NonPhylogeneticMultivariateTraitLikelihood

28 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: NonPhylogeneticMultivariateTraitLikelihood.java (+28 -5)
msuchard 2011-09-24 11:56 Rev.: 4331

Enabled Gibbs sampling of precision matrix in NonPhylogeneticMultivariateTraitLikelihood

69 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: FullyConjugateMultivariateTraitLikelihood.java (+3 -2), NonPhylogeneticMultivariateTraitLikelihood.java (+66 -18)
msuchard 2011-09-21 22:54 Rev.: 4329

Fixed store/restore in WeightedMixtureModel

0 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: NonPhylogeneticMultivariateTraitLikelihood.java (-1)
msuchard 2011-09-16 13:42 Rev.: 4318

Playing with rescaling for the non-phylogenetic model

27 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: NonPhylogeneticMultivariateTraitLikelihood.java (+27 -5)
msuchard 2011-09-12 21:59 Rev.: 4306

Implemented a null model to test for phylogenetic correlation of continuous traits

254 lines of code changed in 7 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+19 -10), DebugableIntegratedMultivariateTraitLikelihood.java (-11), FullyConjugateMultivariateTraitLikelihood.java (+2 -2), IntegratedMultivariateTraitLikelihood.java (+7 -3), NonPhylogeneticMultivariateTraitLikelihood.java (+214 -6), SemiConjugateMultivariateTraitLikelihood.java (+12 -1), StarTreeMultivariateTraitLikelihood.java (del)
msuchard 2011-08-24 12:38 Rev.: 4238

Latent liability model appears to work well.

40 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: LatentLiabilityLikelihood.java (new 40)
rambaut 2011-08-24 04:15 Rev.: 4235

Moved antigenic stuff into its own package.

0 lines of code changed in 3 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (del), DiscreteAntigenicTraitLikelihood.java (del), MultidimensionalScalingLikelihood.java (del)
msuchard 2011-08-20 14:02 Rev.: 4222

Implemented Joe Felsenstein's latent liability model with a single new class to BEAST.

243 lines of code changed in 3 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+21), IntegratedMultivariateTraitLikelihood.java (-15), LatentLiabilityLikelihood.java (+222)
rambaut 2011-08-20 10:29 Rev.: 4221

Fixed up a few things.

551 lines of code changed in 3 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (new 317), DiscreteAntigenicTraitLikelihood.java (new 29), MultidimensionalScalingLikelihood.java (new 205)
rambaut 2011-08-20 03:58 Rev.: 4216

Various bits

6 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: DiscreteAntigenicTraitLikelihood.java (+6 -3)
rambaut 2011-08-19 00:53 Rev.: 4201

Work on discrete Antigenic MDS

11 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: DiscreteAntigenicTraitLikelihood.java (+10 -6), MultidimensionalScalingLikelihood.java (+1 -1)
rambaut 2011-08-10 23:50 Rev.: 4179

Some refactoring of MatrixParameter (renamed getNumberOfParameters to getParameterCount). Also allowed MultivariateNormalPrior take a matrix parameter and assume the individual parameters within this represent independent draws from the MVN.

34 lines of code changed in 4 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+1 -2), DiscreteAntigenicTraitLikelihood.java (+32 -4), InhibitionAssayLikelihood.java (+1 -1)
rambaut 2011-08-10 04:21 Rev.: 4172

Discrete AG model...

55 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: DiscreteAntigenicTraitLikelihood.java (+55 -9)
rambaut 2011-08-09 22:39 Rev.: 4171

First attempt at a discrete antigenic cluster classifier.

400 lines of code changed in 3 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+26 -18), DiscreteAntigenicTraitLikelihood.java (+335), MultidimensionalScalingLikelihood.java (+39 -18)
rambaut 2011-08-05 04:24 Rev.: 4156

16 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+2 -2), AntigenicTraitLikelihood.java (+14 -8)
rambaut 2011-08-02 19:00 Rev.: 4151

Improvements and tweaks to Antigenic MDS

5 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+5 -3)
rambaut 2011-08-01 21:27 Rev.: 4149

Improvements and tweaks to Antigenic MDS

102 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+95 -29), MultidimensionalScalingLikelihood.java (+7 -73)
rambaut 2011-07-31 11:53 Rev.: 4146

Seem to have got the Antigenic MDS working correctly with threshold assay values and replicate measurements.

136 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+103 -102), MultidimensionalScalingLikelihood.java (+33 -33)
rambaut 2011-07-30 03:57 Rev.: 4145

Slowly beating this code into shape

154 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+107 -90), MultidimensionalScalingLikelihood.java (+47 -59)
rambaut 2011-07-29 02:16 Rev.: 4132

Resuming work on this...

3 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: MultidimensionalScalingLikelihood.java (+3 -3)
rambaut 2011-07-23 04:00 Rev.: 4116

uncommitting an erroneous revision

0 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: CartogramDiffusionModel.java (new)
rambaut 2011-07-01 04:13 Rev.: 4084

Fixing some issues with row/column indexing in the sparse matrix

18 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+12 -33), MultidimensionalScalingLikelihood.java (+6 -31)
msuchard 2011-06-29 15:07 Rev.: 4077

Added skeleton class for non-phylogenetic trait model for model comparison

50 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+4 -2), NonPhylogeneticMultivariateTraitLikelihood.java (+46)
rambaut 2011-06-28 04:17 Rev.: 4073

Implementing paired virus-antiserum measurements (for when a titre is available for a serum raised against the virus being tested - this will be assume to be drawn from an identical distribution across all such pairs).

44 lines of code changed in 2 files:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+13 -4), MultidimensionalScalingLikelihood.java (+31 -2)
rambaut 2011-06-21 03:41 Rev.: 4051

Reads text based files which map repeated assays to antisera and viruses to corresponding antisera (these will be assumed to be drawn from an independent distribution independent of location).

103 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+103 -32)
rambaut 2011-06-21 02:54 Rev.: 4050

2 lines of code changed in 1 file:

  • src/dr/evomodel/continuous: AntigenicTraitLikelihood.java (+2 -10)

(172 more)

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