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

Files in this package

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

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

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