twDEMC: parallel DEMC

Parallel version of a DEMC differential evolution markov chain. DEMC is a variant of MCMC monte carlo markov chain.

AuthorThomas Wutzler
Date of publication2015-02-12 17:02:03
MaintainerThomas Wutzler <twutz@bgc-jena.mpg.de>
LicenseGPL (>=2)
Version0.9.214

View on R-Forge

Man pages

as.mcmc.list.twDEMC: as mcmc list twDEMC

as.mcmc.list.twDEMCPops: as mcmc list twDEMCPops

calcBaseTemp: calcBaseTemp

calcBaseTempSk: calcBaseTempSk

calcComponentTemp: calcComponentTemp

calcDEMCTemp: calcDEMCTemp

calcDEMCTempProp: calcDEMCTempProp

calcM0twDEMC: calcM0twDEMC

calcStreamTemp: calcStreamTemp

calcTemperatedLogDen: calcTemperatedLogDen

calcTemperatedLogDenChains.array: calcTemperatedLogDenChains array

calcTemperatedLogDenChains.twDEMC: calcTemperatedLogDenChains twDEMC

calcTemperatedLogDen.default: calcTemperatedLogDen default

calcTemperatedLogDen.twDEMCPops: calcTemperatedLogDen twDEMCPops

combinePops.twDEMC: combinePops twDEMC

combineTwDEMCPops: combineTwDEMCPops

completeResCompVec: completeResCompVec

concatPops: concatPops

concatPops.twDEMCPops: concatPops twDEMCPops

constrainCfStack: constrainCfStack

constrainNStack: constrainNStack

dDistr: dDistr

den2dCor: den2dCor

denBoth: denBoth

denRich: denRich

denRichPrior: denRichPrior

denSparse: denSparse

denSparsePrior: denSparsePrior

dinvchisq: dinvchisq

dummyTwDEMCModel: dummyTwDEMCModel

getBestModelIndex: getBestModelIndex

getBestModelIndices: getBestModelIndices

getCurrentBaseTemp.twDEMCPops: getCurrentBaseTemp twDEMCPops

getCurrentTemp.twDEMC: getCurrentTemp twDEMC

getCurrentTemp.twDEMCPops: getCurrentTemp twDEMCPops

getNBlocks.twDEMC: getNBlocks twDEMC

getNBlocks.twDEMCPops: getNBlocks twDEMCPops

getNChainsPop.twDEMC: getNChainsPop twDEMC

getNChainsPop.twDEMCPops: getNChainsPop twDEMCPops

getNChains.twDEMC: getNChains twDEMC

getNChains.twDEMCPops: getNChains twDEMCPops

getNGen.twDEMC: getNGen twDEMC

getNGen.twDEMCPops: getNGen twDEMCPops

getNParms.twDEMC: getNParms twDEMC

getNParms.twDEMCPops: getNParms twDEMCPops

getNPops.twDEMC: getNPops twDEMC

getNPops.twDEMCPops: getNPops twDEMCPops

getNSamplesSpace.twDEMCPops: getNSamplesSpace twDEMCPops

getNSamples.twDEMC: getNSamples twDEMC

getNSamples.twDEMCPops: getNSamples twDEMCPops

getNSpaces.twDEMCPops: getNSpaces twDEMCPops

getParBoundsPop.twDEMCPops: getParBoundsPop twDEMCPops

getSpacesPop.twDEMCPops: getSpacesPop twDEMCPops

initZtwDEMCExt.matrix: initZtwDEMCExt matrix

initZtwDEMCExt.twDEMC: initZtwDEMCExt twDEMC

initZtwDEMCNormal: initZtwDEMCNormal

initZtwDEMCSub.matrix: initZtwDEMCSub matrix

initZtwDEMCSub.twDEMC: initZtwDEMCSub twDEMC

iSample2time: iSample2time

isLogDenDrift: isLogDenDrift

logDenGaussian: logDenGaussian

marginals1d: marginals1d

marginals2d: marginals2d

marginals3d: marginals3d

mcmcListApply: mcmcListApply

modTwTwoDenEx1: modTwTwoDenEx1

normConstLaplace: normConstLaplace

normConstLaplaceBridge: normConstLaplaceBridge

orderLogDen: orderLogDen

plotChainPopMoves: plotChainPopMoves

plotThinned: plotThinned

plotThinned.mcmc.list: plotThinned mcmc list

popApplyTwDEMC: popApplyTwDEMC

popMeansTwDEMC: popMeansTwDEMC

replaceZinitCases: replaceZinitCases

replaceZinitNonFiniteLogDens: replaceZinitNonFiniteLogDens

replaceZinitNonFiniteLogDensLastStep: replaceZinitNonFiniteLogDensLastStep

rinvchisq: rinvchisq

squeeze.twDEMCPops: squeeze twDEMCPops

stackChains.array: stackChains array

stackChains.mcmc.list: stackChains mcmc list

stackChainsPop.twDEMC: stackChainsPop twDEMC

stackChainsPop.twDEMCPops: stackChainsPop twDEMCPops

stackChains.twDEMC: stackChains twDEMC

stackChains.twDEMCPops: stackChains twDEMCPops

stackPopsInSpace.twDEMCPops: stackPopsInSpace twDEMCPops

stackPops.twDEMCPops: stackPops twDEMCPops

subChains.twDEMC: subChains twDEMC

subPops.twDEMCPops: subPops twDEMCPops

subsetF.twDEMCPops: subsetF twDEMCPops

subsetTail.twDEMCPops: subsetTail twDEMCPops

subset.twDEMC: subset twDEMC

subset.twDEMCPops: subset twDEMCPops

sumLogDenCompBlocks: sumLogDenCompBlocks

thinN.mcmc.list: thinN mcmc list

thin.twDEMC: thin twDEMC

thin.twDEMCPops: thin twDEMCPops

time2iSample: time2iSample

transNormPopt.default: transNormPopt default

transOrigPopt.array: transOrigPopt array

transOrigPopt.default: transOrigPopt default

transOrigPopt.matrix: transOrigPopt matrix

transOrigPopt.mcmc.list: transOrigPopt mcmc list

transOrigPopt.twDEMC: transOrigPopt twDEMC

twCalcLogDenPar: twCalcLogDenPar

twCalcLogDensPar: twCalcLogDensPar

twCoefLnorm: twCoefLnorm

twCoefLnormCi: twCoefLnormCi

twCoefLnormMLE: twCoefLnormMLE

twConstrainPoptDistr: twConstrainPoptDistr

twDEMCBlock.array: twDEMCBlock array

twDEMCBlockInt: twDEMCBlockInt

twDEMCBlock.twDEMC: twDEMCBlock twDEMC

twDEMCBlock.twDEMCPops: twDEMCBlock twDEMCPops

twdemcEx1: Example DEMC result

twDEMC-package: parallel DEMC

twDEMCSA: twDEMCSA

twDEMCSACont: twDEMCSACont

twLinreg1: Artificial data and parameters for DEMC-Example

twQuantiles2Coef: twQuantiles2Coef

twRunDEMCSA: twRunDEMCSA

twTwoDenEx1: Example model for artificial inverse experiment with two...

twVarDistrVec: twVarDistrVec

updateBlockTwDEMC: updateBlockTwDEMC

updateSigmaByGibbsSamplingInvchisq: updateSigmaByGibbsSamplingInvchisq

Functions

as.mcmc.list.twDEMC Man page
as.mcmc.list.twDEMCPops Man page
calcBaseTemp Man page
calcBaseTempSk Man page
calcComponentTemp Man page
calcDEMCTemp Man page
calcDEMCTempProp Man page
calcM0twDEMC Man page
calcStreamTemp Man page
calcTemperatedLogDen Man page
calcTemperatedLogDenChains.array Man page
calcTemperatedLogDenChains.twDEMC Man page
calcTemperatedLogDen.default Man page
calcTemperatedLogDen.twDEMCPops Man page
combinePops.twDEMC Man page
combineTwDEMCPops Man page
completeResCompVec Man page
concatPops Man page
concatPops.twDEMCPops Man page
constrainCfStack Man page
constrainNStack Man page
dDistr Man page
den2dCor Man page
denBoth Man page
denRich Man page
denRichPrior Man page
denSparse Man page
denSparsePrior Man page
dinvchisq Man page
dummyTwDEMCModel Man page
getBestModelIndex Man page
getBestModelIndices Man page
getCurrentBaseTemp.twDEMCPops Man page
getCurrentTemp.twDEMC Man page
getCurrentTemp.twDEMCPops Man page
getNBlocks.twDEMC Man page
getNBlocks.twDEMCPops Man page
getNChainsPop.twDEMC Man page
getNChainsPop.twDEMCPops Man page
getNChains.twDEMC Man page
getNChains.twDEMCPops Man page
getNGen.twDEMC Man page
getNGen.twDEMCPops Man page
getNParms.twDEMC Man page
getNParms.twDEMCPops Man page
getNPops.twDEMC Man page
getNPops.twDEMCPops Man page
getNSamplesSpace.twDEMCPops Man page
getNSamples.twDEMC Man page
getNSamples.twDEMCPops Man page
getNSpaces.twDEMCPops Man page
getParBoundsPop.twDEMCPops Man page
getSpacesPop.twDEMCPops Man page
initZtwDEMCExt.matrix Man page
initZtwDEMCExt.twDEMC Man page
initZtwDEMCNormal Man page
initZtwDEMCSub.matrix Man page
initZtwDEMCSub.twDEMC Man page
iSample2time Man page
isLogDenDrift Man page
logDenGaussian Man page
marginals1d Man page
marginals2d Man page
marginals3d Man page
mcmcListApply Man page
modTwTwoDenEx1 Man page
normConstLaplace Man page
normConstLaplaceBridge Man page
orderLogDen Man page
plotChainPopMoves Man page
plotThinned Man page
plotThinned.mcmc.list Man page
popApplyTwDEMC Man page
popMeansTwDEMC Man page
replaceZinitCases Man page
replaceZinitNonFiniteLogDens Man page
replaceZinitNonFiniteLogDensLastStep Man page
rinvchisq Man page
squeeze.twDEMCPops Man page
stackChains.array Man page
stackChains.mcmc.list Man page
stackChainsPop.twDEMC Man page
stackChainsPop.twDEMCPops Man page
stackChains.twDEMC Man page
stackChains.twDEMCPops Man page
stackPopsInSpace.twDEMCPops Man page
stackPops.twDEMCPops Man page
subChains.twDEMC Man page
subPops.twDEMCPops Man page
subsetF.twDEMCPops Man page
subsetTail.twDEMCPops Man page
subset.twDEMC Man page
subset.twDEMCPops Man page
sumLogDenCompBlocks Man page
thinN.mcmc.list Man page
thin.twDEMC Man page
thin.twDEMCPops Man page
time2iSample Man page
transNormPopt.default Man page
transOrigPopt.array Man page
transOrigPopt.default Man page
transOrigPopt.matrix Man page
transOrigPopt.mcmc.list Man page
transOrigPopt.twDEMC Man page
twCalcLogDenPar Man page
twCalcLogDensPar Man page
twCoefLnorm Man page
twCoefLnormCi Man page
twCoefLnormMLE Man page
twConstrainPoptDistr Man page
twDEMCBlock.array Man page
twDEMCBlockInt Man page
twDEMCBlock.twDEMC Man page
twDEMCBlock.twDEMCPops Man page
twdemcEx1 Man page
twDEMC-package} \alias{twDEMC Man page
twDEMCSA Man page
twDEMCSACont Man page
twLinreg1 Man page
twQuantiles2Coef Man page
twRunDEMCSA Man page
twTwoDenEx1 Man page
twVarDistrVec Man page
updateBlockTwDEMC Man page
updateSigmaByGibbsSamplingInvchisq Man page

Files

DESCRIPTION
NAMESPACE
R
R/S3twDEMC.R R/S3twDEMCPops.R R/den2dCor.R R/denSparceRichBoth.R R/initZ.R R/invChiSquare.R R/logDenGaussion.R R/marginals.R R/normConst.R R/plotTwDEMC.R R/sa.R R/tempDec.R R/transScale.R R/twCalcLogDenPar.R R/twDEMCBlocks.R R/twMisc.R R/util.R R/zz.R
TODO.txt
build
build/vignette.rds
data
data/twLinreg1.RData
data/twTwoDenEx1.RData
data/twdemcEx1.RData
depr
depr/acceptedPosY.R depr/memoize.R depr/multiModal.R depr/tempDec.R
inst
inst/SigmaBlockEx1
inst/SigmaBlockEx1/fitSigmaBlock.R
inst/TwoDenEx1
inst/TwoDenEx1/TwoDenEx1.R inst/TwoDenEx1/fitTwoDenEx1.R inst/TwoDenEx1/fitTwoDenEx1_bak.R
inst/develop
inst/develop/ClusterControlFlow.graphml
inst/doc
inst/doc/SamplingObsUncertainty.R
inst/doc/SamplingObsUncertainty.Rmd
inst/doc/SamplingObsUncertainty.html
inst/doc/SimpleSingleModel.R
inst/doc/SimpleSingleModel.Rmd
inst/doc/SimpleSingleModel.html
inst/doc/TwoDen.R
inst/doc/TwoDen.Rmd
inst/doc/TwoDen.html
inst/genData
inst/genData/genDataLin1.R inst/genData/genDataTwTwoDenEx4.R inst/genData/genDataTwdemcEx1.R inst/genData/twDEMC-package.Rd inst/genData/twLinreg1.Rd inst/genData/twTwoDenEx1.Rd inst/genData/twdemcEx1.Rd
inst/scratch
inst/scratch/divideTwDEMS_beforeT.R inst/scratch/thetaHatRaftery07.R
inst/unitTests
inst/unitTests/TODO_runitdivideTwDEMC.R inst/unitTests/runitS3twDEMC.R inst/unitTests/runitcalcDEMCTemp.R inst/unitTests/runitconstrainNStack.R inst/unitTests/runitinitZ.R inst/unitTests/runitlogDenGaussian.R inst/unitTests/runitreplaceZinitNonFiniteLogLiks.R inst/unitTests/runitrunTwDEMC.R inst/unitTests/runittransOrigPopt.R inst/unitTests/runittwCalcLogDenPar.R inst/unitTests/runittwDEMC.R inst/unitTests/runittwDEMCMulti.R inst/unitTests/runittwDEMCPops.R inst/unitTests/runittwDEMCSA.R
man
man/as.mcmc.list.twDEMC.Rd man/as.mcmc.list.twDEMCPops.Rd man/calcBaseTemp.Rd man/calcBaseTempSk.Rd man/calcComponentTemp.Rd man/calcDEMCTemp.Rd man/calcDEMCTempProp.Rd man/calcM0twDEMC.Rd man/calcStreamTemp.Rd man/calcTemperatedLogDen.Rd man/calcTemperatedLogDen.default.Rd man/calcTemperatedLogDen.twDEMCPops.Rd man/calcTemperatedLogDenChains.array.Rd man/calcTemperatedLogDenChains.twDEMC.Rd man/combinePops.twDEMC.Rd man/combineTwDEMCPops.Rd man/completeResCompVec.Rd man/concatPops.Rd man/concatPops.twDEMCPops.Rd man/constrainCfStack.Rd man/constrainNStack.Rd man/dDistr.Rd man/den2dCor.Rd man/denBoth.Rd man/denRich.Rd man/denRichPrior.Rd man/denSparse.Rd man/denSparsePrior.Rd man/dinvchisq.Rd man/dummyTwDEMCModel.Rd man/getBestModelIndex.Rd man/getBestModelIndices.Rd man/getCurrentBaseTemp.twDEMCPops.Rd man/getCurrentTemp.twDEMC.Rd man/getCurrentTemp.twDEMCPops.Rd man/getNBlocks.twDEMC.Rd man/getNBlocks.twDEMCPops.Rd man/getNChains.twDEMC.Rd man/getNChains.twDEMCPops.Rd man/getNChainsPop.twDEMC.Rd man/getNChainsPop.twDEMCPops.Rd man/getNGen.twDEMC.Rd man/getNGen.twDEMCPops.Rd man/getNParms.twDEMC.Rd man/getNParms.twDEMCPops.Rd man/getNPops.twDEMC.Rd man/getNPops.twDEMCPops.Rd man/getNSamples.twDEMC.Rd man/getNSamples.twDEMCPops.Rd man/getNSamplesSpace.twDEMCPops.Rd man/getNSpaces.twDEMCPops.Rd man/getParBoundsPop.twDEMCPops.Rd man/getSpacesPop.twDEMCPops.Rd man/iSample2time.Rd man/initZtwDEMCExt.matrix.Rd man/initZtwDEMCExt.twDEMC.Rd man/initZtwDEMCNormal.Rd man/initZtwDEMCSub.matrix.Rd man/initZtwDEMCSub.twDEMC.Rd man/isLogDenDrift.Rd man/logDenGaussian.Rd man/marginals1d.Rd man/marginals2d.Rd man/marginals3d.Rd man/mcmcListApply.Rd man/modTwTwoDenEx1.Rd man/normConstLaplace.Rd man/normConstLaplaceBridge.Rd man/orderLogDen.Rd man/plotChainPopMoves.Rd man/plotThinned.Rd man/plotThinned.mcmc.list.Rd man/popApplyTwDEMC.Rd man/popMeansTwDEMC.Rd man/replaceZinitCases.Rd man/replaceZinitNonFiniteLogDens.Rd man/replaceZinitNonFiniteLogDensLastStep.Rd man/rinvchisq.Rd man/squeeze.twDEMCPops.Rd man/stackChains.array.Rd man/stackChains.mcmc.list.Rd man/stackChains.twDEMC.Rd man/stackChains.twDEMCPops.Rd man/stackChainsPop.twDEMC.Rd man/stackChainsPop.twDEMCPops.Rd man/stackPops.twDEMCPops.Rd man/stackPopsInSpace.twDEMCPops.Rd man/subChains.twDEMC.Rd man/subPops.twDEMCPops.Rd man/subset.twDEMC.Rd man/subset.twDEMCPops.Rd man/subsetF.twDEMCPops.Rd man/subsetTail.twDEMCPops.Rd man/sumLogDenCompBlocks.Rd man/thin.twDEMC.Rd man/thin.twDEMCPops.Rd man/thinN.mcmc.list.Rd man/time2iSample.Rd man/transNormPopt.default.Rd man/transOrigPopt.array.Rd man/transOrigPopt.default.Rd man/transOrigPopt.matrix.Rd man/transOrigPopt.mcmc.list.Rd man/transOrigPopt.twDEMC.Rd man/twCalcLogDenPar.Rd man/twCalcLogDensPar.Rd man/twCoefLnorm.Rd man/twCoefLnormCi.Rd man/twCoefLnormMLE.Rd man/twConstrainPoptDistr.Rd man/twDEMC-package.Rd man/twDEMCBlock.array.Rd man/twDEMCBlock.twDEMC.Rd man/twDEMCBlock.twDEMCPops.Rd man/twDEMCBlockInt.Rd man/twDEMCSA.Rd man/twDEMCSACont.Rd man/twLinreg1.Rd man/twQuantiles2Coef.Rd man/twRunDEMCSA.Rd man/twTwoDenEx1.Rd man/twVarDistrVec.Rd man/twdemcEx1.Rd man/updateBlockTwDEMC.Rd man/updateSigmaByGibbsSamplingInvchisq.Rd
scratch
scratch/applyLB.R scratch/demcStep_commonTemp.R scratch/ggplot.R scratch/ofMultiSum.R scratch/scratch.R scratch/twDEMC_multiMetSum.R scratch/twDEMC_repeatT.R scratch/twDEMC_seq.R
tests
tests/doRUnit.R
vignettes
vignettes/SamplingObsUncertainty.Rmd
vignettes/SimpleSingleModel.Rmd
vignettes/TwoDen.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.