Directory src/dr/evomodel/epidemiology/

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danny.wilson@gmail.com 2012-08-09 04:56 Rev.: 5119

Submitting classes for epidemiological inference under deterministic SIS and SIR models to dr.evomodel.epidemiology

1452 lines of code changed in 8 files:

• src/dr/evomodel/epidemiology: LambertW.java (new 254), LogisticGrowthN0.java (new 147), LogisticGrowthN0Model.java (new 88), LogisticGrowthN0ModelParser.java (new 80), ODEDemographicFunction.java (new 397), SIRepidemic.java (new 282), SIRepidemicModel.java (new 117), SIRepidemicModelParser.java (new 87)

rambaut 2012-08-08 23:06 Rev.: 5116

Adding attributions.

12 lines of code changed in 10 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+3), DynamicalSystem.java (+3), DynamicalVariable.java (new), SIRModel.java (new), SIRModelParser.java (+3)

rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

4 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology: SIRModel.java (+4)

tbcbedford@gmail.com 2012-01-26 05:27 Rev.: 4613

I cleaned up some things and moved to a proportional framework. S, I and R are now 0 to 1 and sum to 1. There is an additional host population size parameter that scales each of these proportions. I use a delta exchange operator on the proportions.

Also, I fixed most of the mixing issues in a (stupidly) trivial fashion. I had assumed that smaller scaleFactors result in smaller operations. Starting scaleFactors off at 0.99 for recoveryRate and reproductiveNumber fixes most everything.

53 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+3 -3), SIRModel.java (+41 -47), SIRModelParser.java (+9 -16)

tbcbedford@gmail.com 2012-01-25 04:00 Rev.: 4610

Some cleanup of time keeping.

66 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalSystem.java (+35 -9), DynamicalVariable.java (+27 -25), SIRModel.java (+4 -4)

tbcbedford@gmail.com 2012-01-25 03:45 Rev.: 4609

Streamlining Timeseries Statistics.

27 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology: SIRModel.java (+27 -81)

tbcbedford@gmail.com 2012-01-24 04:06 Rev.: 4606

Rather than a custom logger, I've switched to statistics that describe time series. Have separate statistics for susceptibles, infecteds, recovereds and effective population size through time. Need to implement user-defined ranges and step sizes in the XML.

107 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalLogger.java (del), DynamicalLoggerParser.java (del), SIRModel.java (+107 -5)

tbcbedford@gmail.com 2012-01-24 02:41 Rev.: 4603

Starting to implement a time series logger.

284 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalLogger.java (new 100), DynamicalLoggerParser.java (new 169), SIRModel.java (+15)

tbcbedford@gmail.com 2012-01-24 02:03 Rev.: 4602

Reparameterized transmission rate to R0. This allows me to put a lower limit of 1.0 on R0. Appears to working with simulated data. Need to assume a value on recovery rate for identifiability. Still getting poor acceptance probabilites. However, have had success with an operator that scales S, I and R simultaneously.

scale(sir.reproductiveNumber) 0.0036
scale(sir.susceptibles) 0.0099
scale(sir.infecteds) 0.1221
scale(sir.recovereds) 0.0106
up:sir.susceptibles sir.infecteds sir.recovereds down: 0.3145

35 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+3 -3), DynamicalSystem.java (+13), SIRModel.java (+14 -12), SIRModelParser.java (+5 -5)

tbcbedford@gmail.com 2012-01-23 23:50 Rev.: 4601

I had moved this to forward time. It didn't work very well at all. Too difficult to choose good initial parameter values. Switch back to backward time. Now working on multivariate operators.

70 lines of code changed in 5 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+1 -1), DynamicalSystem.java (+1 -1), DynamicalVariable.java (+1 -1), SIRModel.java (+66 -2), SIRModelParser.java (+1 -1)

tbcbedford@gmail.com 2012-01-21 01:26 Rev.: 4597

Rolling back SIRModel likelihood.

1 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology: SIRModel.java (+1 -65)

tbcbedford@gmail.com 2012-01-21 00:31 Rev.: 4596

Convergence issues had been an identifiability problem. Was going to an initial state with non-zero recovereds. I fixed this here by adding a likelihood to the model that prefers zero recovereds. However, this is causing massively slow mixing, because changing any one of the epidemiological parameters pushes the initial recovereds off their mark. Will attempt to move to a forward-simulation approach.

99 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology: SIRModel.java (+99 -7)

tbcbedford@gmail.com 2012-01-19 05:00 Rev.: 4593

Fixed issue with initial state. However, now there seems to be convergence issues.

44 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalSystem.java (+8 -8), DynamicalVariable.java (+21 -19), SIRModel.java (+15 -9)

tbcbedford@gmail.com 2012-01-19 02:15 Rev.: 4592

Identified bug in DynamicalVariable reset. Everything looks more-or-less in order. Testing now.

16 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalSystem.java (+3 -3), DynamicalVariable.java (+7 -5), SIRModel.java (+6 -5)

tbcbedford@gmail.com 2012-01-19 01:29 Rev.: 4591

I've implemented store/restore in DynamicalSystem and called this from SIRModel. No longer having errors, but something is still wrong.

117 lines of code changed in 4 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+10), DynamicalSystem.java (+33 -10), DynamicalVariable.java (+41), SIRModel.java (+33 -54)

tbcbedford@gmail.com 2012-01-18 23:21 Rev.: 4590

Streamlined Variable and Force constructors in DynamicalSystem. Interfaced SIRModel with DynamicalSystem. Doing just-in-time extension of timeseries when getValue is called. Compiles and runs, but gives a state-not-restored-correctly error.

164 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+15 -5), DynamicalSystem.java (+95 -38), SIRModel.java (+54 -40)

tbcbedford@gmail.com 2012-01-18 03:33 Rev.: 4578

Implemented linear interpolation for getValue and trapezoidal rule for getIntegral.

71 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology: DynamicalSystem.java (+3 -2), DynamicalVariable.java (+68 -2)

tbcbedford@gmail.com 2012-01-18 00:58 Rev.: 4577

Implemented helper classes for dynamical systems. This is designed to simulate partial differential system via the simple Euler method. After forward calculation, can ask for the value at any point in time via fast binary search.

236 lines of code changed in 6 files:

• src/dr/evomodel/epidemiology: DynamicalForce.java (+49), DynamicalSystem.java (+106), DynamicalVariable.java (+73), HybridTauleapSEIR.java (del), SEIRState.java (del), SIRModel.java (+8 -6)

tbcbedford@gmail.com 2012-01-17 01:51 Rev.: 4575

Updated skeleton of SIRModel. Includes S, I and R parameters and doesn't crash. Returns dummy likelihood.

90 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology: SIRModel.java (+67 -14), SIRModelParser.java (+23 -5)

tbcbedford@gmail.com 2011-12-07 05:20 Rev.: 4516

Small cleanup and starting to store trajectory with HybridTauleapSEIR class.

80 lines of code changed in 1 file:

• src/dr/evomodel/epidemiology: HybridTauleapSEIR.java (new 80)

tbcbedford@gmail.com 2011-12-07 04:53 Rev.: 4515

Integreting Denise's code for forward simulation of SIR trajectories.

507 lines of code changed in 3 files:

• src/dr/evomodel/epidemiology: HybridTauleapSEIR.java (+477), SEIRState.java (new 23), SIRModel.java (+7 -3)

rambaut 2011-10-25 01:35 Rev.: 4371

Start towards implementing Volz et al (2009) Genetics

245 lines of code changed in 2 files:

• src/dr/evomodel/epidemiology: SIRModel.java (+183), SIRModelParser.java (+62)