Directory src/dr/inference/markovchain/

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Sibon.Li@gmail.com 2012-09-18 19:14 Rev.: 5170

Changes to MarkovChainDelegate to allow it better access and privileges to MarkovChain

1 lines of code changed in 2 files:

• src/dr/inference/markovchain: MarkovChainDelegate.java (+1 -1)

rambaut 2012-08-18 21:54 Rev.: 5145

If +Inf or NaN in MarkovChain, it now converts these to -Inf so it can continue if the user has chosen to ignore errors.

10 lines of code changed in 2 files:

• src/dr/inference/markovchain: MarkovChain.java (new)

rambaut 2012-08-18 02:25 Rev.: 5139

Porting r5138 from 1.7 branch

16 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+16 -6)

rambaut 2012-08-17 21:06 Rev.: 5137

Changed compound likelihood to return the actual special values (i.e. +Inf, NaN or -Inf) up the chain. Added 'todo' comment in MarkovChain suggesting a check for +Inf and NaN. Need to review this idea.

5 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+5)

sibon.li 2012-04-07 06:46 Rev.: 4920

Added an interface for delegating tasks in the Markov Chain

72 lines of code changed in 2 files:

• src/dr/inference/markovchain: MarkovChain.java (+26), MarkovChainDelegate.java (+46)

msuchard 2012-03-26 15:04 Rev.: 4888

Added ability to co-opt an existing root height in StarTreeModel

9 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+9 -9)

rambaut 2012-03-08 04:52 Rev.: 4787

Finally fixed the diagnostics strings displayed after an incorrect restore so that they are genuinely before and after (as opposed to both after).

9 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+9 -5)

rambaut 2012-03-08 04:40 Rev.: 4786

Commented out a couple of debug printfs

4 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+4 -1)

rambaut 2012-03-04 01:01 Rev.: 4761

Removing wrongly located files.

0 lines of code changed in 1 file:

• src/dr/inference/markovchain: BlueBeastMarkovChain.java (del)

rambaut 2012-03-04 00:59 Rev.: 4760

Reverting changes in 4754 - MarkovChain is not designed for subclassing.

19 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+19 -19)

sibon.li 2012-03-03 21:38 Rev.: 4758

Commented out all of my last commit until issues resolved

536 lines of code changed in 1 file:

• src/dr/inference/markovchain: BlueBeastMarkovChain.java (new 536)

sibon.li 2012-03-03 16:23 Rev.: 4755

Added classes to enable implicit convergence assessment checks using BLUE

595 lines of code changed in 1 file:

• src/dr/inference/markovchain: BlueBeastMarkovChain.java (+595)

sibon.li 2012-03-03 16:18 Rev.: 4754

Changes to encapsulation in MCMC.java and MarkovChain.java. MarkovChain.java no longer final and some private variables changed to protected

20 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+20 -20)

rambaut 2011-11-15 09:26 Rev.: 4424

Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.

11 lines of code changed in 3 files:

• src/dr/inference/markovchain: MarkovChain.java (+8 -8), MarkovChainListener.java (new)

rambaut 2010-11-16 05:18 Rev.: 3721

Cleaned up full evaluation test error reporting.

5 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+5 -7)

rambaut 2010-11-16 05:14 Rev.: 3720

Started work on caching in ATL

2 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+2 -2)

rambaut 2009-12-05 05:33 Rev.: 2656

Fix for dynamic scaling with BEAGLE?

17 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+17 -14)

rambaut 2009-10-29 05:18 Rev.: 2482

Added some simple timing round the evaluation just after each operator which is stored by the operator and reported in the operator analysis table. On this note, I have added an attribute to <mcmc operatorAnalaysis="analysis.file"> which gives the name of the file to write the analysis to. If this isn't there then the file isn't written. We need to add this to BEAUti to use the same file name stem as the log and trees file (with an extension '.ops'?).

10 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+10)

rambaut 2009-10-03 00:23 Rev.: 2341

Replaced 'preBurnin' with an autoOptimizeDelay (coercionDelay). The rationale for this is that the preBurnin meant that the initial state was not in the log files, it was unecessary and it cause a small inefficiency as the JIT compiler re-optimized after the preburnin chain had finished. We also didn't see warning messages until after the pre-burnin period. There is a new attribute to the MCMC parser - autoOptimizeDelay (to which the old preBurnin attribute now maps so old XML will run).

8 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+8 -7)

jheled 2009-09-09 08:26 Rev.: 2227

generify and auto intelliJ

5 lines of code changed in 2 files:

• src/dr/inference/markovchain: Profiler.java (new)

jheled 2009-09-01 09:58 Rev.: 2171

casting problem

10 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+10 -4)

jheled 2009-08-27 15:29 Rev.: 2152

Even slower at startup - have more detailed printouts

4 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+4)

msuchard 2009-08-15 13:46 Rev.: 2076

BEAGLE GammaSiteModel now accepts a mutationRate for compatibility with some BEAST XML.

2 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+2 -2)

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...

5 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+5 -7)

alexei.drummond 2009-07-15 16:25 Rev.: 1860

refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying

37 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+37 -42)

jheled 2009-07-15 13:44 Rev.: 1858

comment out operator experimental code

60 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+60 -57)

rambaut 2009-05-16 22:04 Rev.: 1720

Made the threshold at which the full evaluation test fail into a static constant at the top of the class.

4 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+4 -2)

jheled 2009-05-16 13:05 Rev.: 1719

Control number of operator evaluation checks via minOpsFullEvaluations.

Add 'minOpsFullEvaluations="0" fullEvaluation="0"' to the <mcmc> attributes to disable checks altogether.

6 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+6 -4)

msuchard 2009-05-16 06:35 Rev.: 1716

Temporary solution before full code review: if fullEvaluationCount == 0, then switch off usingFullEvaluation

2 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+2)

jheled 2009-04-20 09:10 Rev.: 1606

Check evaluation after accept move as well. chaeck until at least N (=1) accpets and rejects for each operator.

22 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+22 -23)

rambaut 2009-04-18 22:06 Rev.: 1595

Slight modification of when the fullEvaluation test is performed.

1 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+1 -5)

Sebastian.Hoehna 2009-04-15 01:05 Rev.: 1573

Tidying up to resolve more the confusion between the Gibbs and Metropolized Gibbs Proposals.

2 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+2 -18)

Sebastian.Hoehna 2009-04-14 23:42 Rev.: 1572

Change name of SimpleGibbsOperator to SimpleMetropolizedGibbsOperator to avoid confusion.

4 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+4 -4)

rambaut 2009-04-14 09:53 Rev.: 1570

Full evaluation continues until every operator has done at least one operation. If an error has occurred in this time, then a runtime exception is thrown.

32 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+32 -15)

rambaut 2009-04-13 11:09 Rev.: 1566

Cleaned up MarkovChain a little more. There were some debug printfs surrounded by if statements. Made the flag that turned these on into a static final - this should mean the if statements will not be compiled in if false.

Added comment about odd coding surrounding Gibbs operators - don't want to fiddle but looks suspect to me.

16 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+16 -13)

rambaut 2009-04-12 23:21 Rev.: 1558

Added an additional test of full evaluation of the likelihood after an operator. This should detect operators that don't fully flag up what to update.

I also removed a likelihood.makeDirty() call that was removing efficiency savings on restore. This was presumably a work around for a bug in another class. We should expect the test of full evaluation after restore test to fail on some models (but who knows what? This call was masking the test of correct restore). Benchmark.xml works with this call removed.

25 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+25 -7)

jheled 2009-04-09 14:42 Rev.: 1549

cosmetic

266 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+266 -272)

Sebastian.Hoehna 2009-03-04 10:01 Rev.: 1478

Added some stuff to get the MGS working.

288 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+288 -239)

rambaut 2009-01-10 05:23 Rev.: 1404

Fixed problem generating XML to sample from the prior in BEAUti.

8 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+8 -1)

jheled 2008-12-01 14:55 Rev.: 1346

automatic code improvments (intellij)

1 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+1 -1)

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