Directory src/dr/inference/prior/

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jheled 2009-09-07 13:28 Rev.: 2211

comment out unused code

458 lines of code changed in 22 files:

• src/dr/inference/prior: AbstractParameterPrior.java (+48 -52), CompositePrior.java (new), ContinuousVariablePrior.java (+84 -84), ExponentialParameterPrior.java (+42 -42), GammaParameterPrior.java (new), LogPriorStatistic.java (+19 -19), NormalParameterPrior.java (+50 -50), ParameterPrior.java (+17 -17), Prior.java (new), SimplePrior.java (new), UniformParameterPrior.java (new)

jheled 2009-09-04 10:29 Rev.: 2195

code police

3 lines of code changed in 1 file:

• src/dr/inference/prior: Prior.java (+3 -3)

alexei.drummond 2009-07-18 18:12 Rev.: 1871

First step in development of a generic version of Parameter, called Variable for now. Parameter now implements Variable<Double> but eventually all dr.inference.* will be based on Variable rather than Parameter. At least that is the idea anyway...

34 lines of code changed in 1 file:

• src/dr/inference/prior: Prior.java (+34 -33)

jheled 2009-04-24 12:36 Rev.: 1629

Inverse gamma distribution

2 lines of code changed in 1 file:

• src/dr/inference/prior: GammaParameterPrior.java (+2 -1)

alexei.drummond 2008-08-12 21:16 Rev.: 1112

moved all distributions into their own sub-package in dr.math

80 lines of code changed in 2 files:

• src/dr/inference/prior: GammaParameterPrior.java (+40 -34), NormalParameterPrior.java (+40 -34)

rambaut 2008-04-07 16:59 Rev.: 804

Tweak to NexusImporter to read root node attribute values.

0 lines of code changed in 3 files:

• src/dr/inference/prior: ImmigrationIntegrationForAlternativeSplicingPrior.java (del), alsDefaultPrior.java (del), alsPriorLambdaIntegrator.java (del)

alexander.alekseyenko 2008-03-29 22:36 Rev.: 793

Fixed a small bug in sclatedTreeLengthRateModel.
Made stuff for ALS model more generic.
Created a default prior for ALS model and a class that integrates over the acquisition rate. Modified the example file accordingly.

405 lines of code changed in 3 files:

• src/dr/inference/prior: AlternativeSplicingPrior.java (del), alsDefaultPrior.java (new 219), alsPriorLambdaIntegrator.java (new 186)

alexander.alekseyenko 2008-03-27 11:46 Rev.: 784

Added classes necessary for MSSD a.k.a. Aquisition-Loss-Substitution (ALS) a.k.a. Immigration-Mutation-Death model functionality. Added prior and integrated immigration prior correction for alternative splicing creation and loss model.
AscertainedSitePatterns -- can handle ascertainment of two types
MutationDeathType -- extends a datatype with an additional state for the death state. Slightly differently (more clean?) structured than the other datatypes in the project. Let me know if you like it.
MutationDeathModel -- extends an arbitrary SubstitutionModel to include an additional absorbing death state.
ScaledTreeLengthRateModel -- Scales the sum of all edges to a specified value (like 1.0 in my case)

testBinary.xml -- a small example of who all of this stuff work
Changes:
BeastParser: added the parsers here
SitePatterns: made comparePatterns() protected instead of private
FrequencyModel: added a function to get the frequency parameter

395 lines of code changed in 2 files:

• src/dr/inference/prior: AlternativeSplicingPrior.java (new 216), ImmigrationIntegrationForAlternativeSplicingPrior.java (new 179)

jheled 2007-01-25 10:36 Rev.: 172

comments & cosmetic changes

8 lines of code changed in 2 files:

• src/dr/inference/prior: Prior.java (+1 -1), UniformParameterPrior.java (+7 -7)