twDEMC: parallel DEMC

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

Author
Thomas Wutzler
Date of publication
2015-02-12 17:02:03
Maintainer
Thomas Wutzler <twutz@bgc-jena.mpg.de>
License
GPL (>=2)
Version
0.9.214

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