Directory src/dr/evomodel/epidemiology/casetocase/

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mdhall272@gmail.com 2013-05-17 04:53 Rev.: 5656

Bug fix

0 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (changed)

mdhall272@gmail.com 2013-05-16 02:58 Rev.: 5651

More comments

0 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractCase.java (new), AbstractOutbreak.java (changed)

mdhall272@gmail.com 2013-05-16 02:54 Rev.: 5650

Minor fixes and comment changes

18 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractOutbreak.java (+1), CaseToCaseTransmissionLikelihood.java (+12 -7), SimpleOutbreak.java (+5 -2)

mdhall272@gmail.com 2013-05-09 00:22 Rev.: 5639

efficiency improvements & other misc small fixes

23 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+21 -17), Morelli12Outbreak.java (new), SimpleOutbreak.java (+1 -4)

mdhall272@gmail.com 2013-05-03 02:53 Rev.: 5626

Added simpler outbreak class (no latent periods).

616 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractOutbreak.java (+6 -6), CaseToCaseTransmissionLikelihood.java (+149 -69), Morelli12Outbreak.java (+102 -29), SimpleOutbreak.java (+359)

mdhall272@gmail.com 2013-05-02 00:45 Rev.: 5625

Now fairly confident geographical analysis has to be done in post-processing - removed.

13 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+3 -1), Morelli12Outbreak.java (+10 -80)

mdhall272@gmail.com 2013-04-30 03:37 Rev.: 5620

Added spatial kernel function; fixed bug.

107 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+26 -12), Morelli12Outbreak.java (+81 -21)

mdhall272@gmail.com 2013-04-27 00:31 Rev.: 5616

bug fixed

27 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+27 -6)

mdhall272@gmail.com 2013-04-26 22:23 Rev.: 5615

bug fixed

31 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+31 -18)

mdhall272@gmail.com 2013-04-26 20:36 Rev.: 5614

Done up to tracking down a few bugs

235 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractOutbreak.java (+4 -2), CaseToCaseTransmissionLikelihood.java (+208 -156), Morelli12Outbreak.java (+23 -27)

mdhall272@gmail.com 2013-04-24 05:20 Rev.: 5605

Big and hopefully final rewrite

351 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractOutbreak.java (+9 -17), CaseToCaseTransmissionLikelihood.java (+235 -190), Morelli12Outbreak.java (+107 -132)

mdhall272@gmail.com 2013-04-13 03:20 Rev.: 5589

C2CTL now implements treeTraitProvider and outputs painted trees

90 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractCase.java (+6 -11), AbstractOutbreak.java (+3 -1), CaseToCaseTransmissionLikelihood.java (+78 -19), Morelli12Outbreak.java (+2 -19), TransmissionTreeOperator.java (+1 -2)

mdhall272@gmail.com 2013-04-10 23:57 Rev.: 5578

Finished combining the classes.

23 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+23 -49), FelsensteinCaseToCaseTransmissionLikelihood.java (del)

mdhall272@gmail.com 2013-04-10 04:06 Rev.: 5575

continuing the clean-up

422 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+352 -163), FelsensteinCaseToCaseTransmissionLikelihood.java (new 70)

mdhall272@gmail.com 2013-04-09 04:42 Rev.: 5568

FC2CTL reworked to calculate overall likelihoods and randomly pick a transmission tree when MCMC samples are taken, similarly to discrete traits. Still probably too slow unless the likelihood function can be solved analytically. Will probably fold that class into the main C2CTL as a variant.

90 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology/casetocase: FelsensteinCaseToCaseTransmissionLikelihood.java (+85 -70), Morelli12Outbreak.java (+4 -4), TransmissionTreeOperator.java (+1 -1)

mdhall272@gmail.com 2013-04-08 21:15 Rev.: 5563

Nomenclature change, continued

4 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (-1), Morelli12Outbreak.java (+4 -4)

mdhall272@gmail.com 2013-04-08 20:41 Rev.: 5562

Nomenclature change

507 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractCaseSet.java (del), AbstractOutbreak.java (+59), CaseToCaseTransmissionLikelihood.java (+6 -6), FelsensteinCaseToCaseTransmissionLikelihood.java (+5 -5), Morelli12FarmCaseSet.java (del), Morelli12Outbreak.java (+437)

mdhall272@gmail.com 2013-04-06 03:57 Rev.: 5558

Tidying up

23 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: Morelli12FarmCaseSet.java (new 23)

mdhall272@gmail.com 2013-04-06 03:48 Rev.: 5557

Made the case class an inner class of the case set class, which is much neater.

294 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractCase.java (+1 -4), Morelli12FarmCase.java (del), Morelli12FarmCaseSet.java (+288 -23), TransmissionTreeOperator.java (+5 -5)

mdhall272@gmail.com 2013-02-21 22:19 Rev.: 5446

Working as intended. All classes necessary for TT=TMRCA model (sans geography) now complete.

3 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: TransmissionTreeOperator.java (+3 -2)

mdhall272@gmail.com 2013-02-21 21:46 Rev.: 5445

Cleaning up (fixing SVN tree conflict?)

32 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: TransmissionTreeOperator.java (+32 -22)

mdhall272@gmail.com 2013-02-21 21:43 Rev.: 5444

Cleaning up

2 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+2 -2)

mdhall272@gmail.com 2013-02-20 23:30 Rev.: 5440

Added method to check transmission network makes sense

27 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+27), TransmissionTreeOperator.java (-2)

mdhall272@gmail.com 2013-02-20 22:15 Rev.: 5439

Parser done

62 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+1 -2), TransmissionTreeOperator.java (+61 -11)

mdhall272@gmail.com 2013-02-20 06:36 Rev.: 5438

Operator wrapping a phylogenetic tree operator that changes transmission tree accordingly (TT=TMRCA only). Still needs testing and parser.

98 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+4), TransmissionTreeOperator.java (+94 -3)

mdhall272@gmail.com 2013-02-15 03:14 Rev.: 5399

Efficiency savings

11 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: NodePaintingSwitchOperator.java (new)

mdhall272@gmail.com 2013-02-15 02:49 Rev.: 5398

Efficiency savings

56 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+56 -35)

mdhall272@gmail.com 2013-02-14 23:44 Rev.: 5396

New case and case set classes with likelihood functions borrowed from Morelli et al, PLoS Comp Biol, 2012

597 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+1 -1), LesionDatedFarmCase.java (del), LesionDatedFarmCaseSet.java (del), Morelli12FarmCase.java (new 327), Morelli12FarmCaseSet.java (+172), TransmissionTreeOperator.java (+97)

mdhall272@gmail.com 2013-01-30 07:18 Rev.: 5360

Moving on to the next tree operator.

159 lines of code changed in 8 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+4), NodePaintingSwitchOperator.java (-3), TransmissionExchangeOperatorA.java (+32 -16), TransmissionExchangeOperatorB.java (+68 -11), TransmissionWilsonBaldingA.java (new 27), TransmissionWilsonBaldingB.java (new 28)

mdhall272@gmail.com 2013-01-30 05:19 Rev.: 5359

Finished off transmission tree operators and began on special cases of the existing phylogenetic tree operators

151 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+10 -1), NodePaintingCreepOperator.java (new), NodePaintingSwitchOperator.java (+3 -2), TransmissionExchangeOperatorA.java (+86), TransmissionExchangeOperatorB.java (+40)

mdhall272@gmail.com 2013-01-29 06:57 Rev.: 5353

Cleaned up comments.

12 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: NodePaintingCreepOperator.java (+8 -5), NodePaintingSwitchOperator.java (+4 -5)

mdhall272@gmail.com 2013-01-29 06:36 Rev.: 5352

Silly mistake rectified.

3 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+3), NodePaintingCreepOperator.java (-2)

mdhall272@gmail.com 2013-01-29 06:03

Further work on TT>=TMRCA. Sacrificing efficiency for more intuitive code for now.

258 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+189 -49), NodePaintingCreepOperator.java (+60 -3), NodePaintingSwitchOperator.java (+9 -17)

mdhall272@gmail.com 2013-01-28 22:41 Rev.: 5344

Finished rewriting for TT>=TMRCA version (needs testing).

16 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: NodePaintingSwitchOperator.java (+16 -10)

mdhall272@gmail.com 2013-01-28 22:14 Rev.: 5343

Rewriting for TT>=TMRCA version

30 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: NodePaintingSwitchOperator.java (+30 -4)

mdhall272@gmail.com 2013-01-25 04:56 Rev.: 5337

Started adding the operators to allow the transmission times to occur after TMRCAs.

179 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+63 -6), NodePaintingCreepOperator.java (+93), NodePaintingSwitchOperator.java (+23 -20)

mdhall272@gmail.com 2013-01-17 04:53 Rev.: 5328

Un-mothballing the label-switching version (Felsenstein very slow) and renaming to reflect this.

916 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+408 -169), FelsensteinCaseToCaseTransmissionLikelihood.java (+489), LesionDatedFarmCase.java (new 5), LesionDatedFarmCaseSet.java (new 9), NodePaintingSwitchOperator.java (+5 -5), OldCaseToCaseTransmissionLikelihood.java (del)

mdhall272@gmail.com 2013-01-16 02:36 Rev.: 5326

Done but not tested.

118 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+118 -3)

mdhall272@gmail.com 2013-01-15 06:03 Rev.: 5320

Began work on new version using modified Felsenstein pruning algorithm rather than sampling the network simultaneously.

821 lines of code changed in 5 files:

• src/dr/evomodel/epidemiology/casetocase: AbstractCaseSet.java (new 6), CaseToCaseTransmissionLikelihood.java (+94 -447), LesionDatedFarmCaseSet.java (+9 -9), NodePaintingSwitchOperator.java (+5 -5), OldCaseToCaseTransmissionLikelihood.java (new 707)

mdhall272@gmail.com 2012-12-03 22:12 Rev.: 5270

Another small tip date-related modification.

12 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology/casetocase: CaseToCaseTransmissionLikelihood.java (+11 -10), LesionDatedFarmCase.java (+1 -1)

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