twDEMC: parallel DEMC
Version 0.9.214

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

Browse man pages Browse package API and functions Browse package files

AuthorThomas Wutzler
Date of publication2015-02-12 17:02:03
MaintainerThomas Wutzler <twutz@bgc-jena.mpg.de>
LicenseGPL (>=2)
Version0.9.214
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("twDEMC", repos="http://R-Forge.R-project.org")

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 Source code
as.mcmc.list.twDEMCPops Man page Source code
calcBaseTemp Man page Source code
calcBaseTempSk Man page Source code
calcComponentTemp Man page Source code
calcDEMCTemp Man page Source code
calcDEMCTempProp Man page Source code
calcFLogDen Source code
calcM0twDEMC Man page Source code
calcStreamTemp Man page Source code
calcTemperatedLogDen Man page
calcTemperatedLogDen.default Man page
calcTemperatedLogDen.twDEMCPops Man page
calcTemperatedLogDenChains.array Man page
calcTemperatedLogDenChains.twDEMC Man page
colNames Source code
combinePops.twDEMC Man page
combineTwDEMCPops Man page Source code
completeBlockInfo Source code
completeDInfo Source code
completePopDescription Source code
completeResCompVec Man page Source code
concatChainsTwDEMCPops Source code
concatPops Man page
concatPops.twDEMCPops Man page
concatTwDEMCRuns Source code
constrainCfStack Man page Source code
constrainNStack Man page Source code
cut2dim2 Source code
cut2dim3 Source code
dDistr Man page Source code
debug.divideTwDEMC Source code
den2dCor Man page Source code
denBoth Man page Source code
denRich Man page Source code
denRichPrior Man page Source code
denSparse Man page Source code
denSparsePrior Man page Source code
depr.useWithMatrix.sumLogDenComp Source code
dinvchisq Man page Source code
dummyTwDEMCModel Man page Source code
generateXPropThin Source code
getBestModelIndex Man page Source code
getBestModelIndices Man page Source code
getCurrentBaseTemp.twDEMCPops Man page
getCurrentTemp.twDEMC Man page
getCurrentTemp.twDEMCPops Man page
getNBlocks.twDEMC Man page
getNBlocks.twDEMCPops Man page
getNChains.twDEMC Man page
getNChains.twDEMCPops Man page
getNChainsPop.twDEMC Man page
getNChainsPop.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
getNSamples.twDEMC Man page
getNSamples.twDEMCPops Man page
getNSamplesSpace.twDEMCPops Man page
getNSpaces.twDEMCPops Man page
getParBoundsPop.twDEMCPops Man page
getParBoundsPops Source code
getResFLogDenNames Source code
getRescompNameBlock Source code
getSpacesPop.twDEMCPops Man page
iSample2time Man page Source code
initZtwDEMCExt.matrix Man page
initZtwDEMCExt.twDEMC Man page
initZtwDEMCNormal Man page Source code
initZtwDEMCSub.matrix Man page
initZtwDEMCSub.twDEMC Man page
isLogDenDrift Man page Source code
logDenGaussian Man page Source code
marginals1d Man page Source code
marginals2d Man page Source code
marginals3d Man page Source code
mcmcListApply Man page Source code
modTwTwoDenEx1 Man page Source code
normConstLaplace Man page Source code
normConstLaplaceBridge Man page Source code
ofLnormMLE Source code
orderLogDen Man page Source code
parBoundsEnvelope Source code
plotChainPopMoves Man page Source code
plotThinned Man page Source code
plotThinned.mcmc.list Man page Source code
popApplyTwDEMC Man page Source code
popMeansTwDEMC Man page Source code
replaceZinitCases Man page Source code
replaceZinitNonFiniteLogDens Man page Source code
replaceZinitNonFiniteLogDensLastStep Man page Source code
rinvchisq Man page Source code
sampleStates Source code
sampleStatesConditional Source code
squeeze.twDEMCPops Man page
stackChains.array Man page
stackChains.mcmc.list Man page
stackChains.twDEMC Man page
stackChains.twDEMCPops Man page
stackChainsPop.twDEMC Man page
stackChainsPop.twDEMCPops Man page
stackChainsWithinPop Source code
stackPops.twDEMCPops Man page
stackPopsInSpace.twDEMCPops Man page
subChains.twDEMC Man page
subPops.twDEMCPops Man page
subset.twDEMC Man page
subset.twDEMCPops Man page
subsetF.twDEMCPops Man page
subsetTail.twDEMCPops Man page
subsetTwDEMCPop Source code
sumLogDenCompBlocks Man page Source code
thin.twDEMC Man page
thin.twDEMCPops Man page
thinN.mcmc.list Man page
time2iSample Man page Source code
tmp.f Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
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 Source code
twCalcLogDens Source code
twCalcLogDensPar Man page Source code
twCoefLnorm Man page Source code
twCoefLnormCi Man page Source code
twCoefLnormMLE Man page Source code
twCoefLnormMLE_depr Source code
twConstrainPoptDistr Man page Source code
twDEMC-package} \alias{twDEMC Man page
twDEMCBlock.array Man page
twDEMCBlock.twDEMC Man page
twDEMCBlock.twDEMCPops Man page
twDEMCBlockInt Man page Source code
twDEMCSA Man page Source code
twDEMCSACont Man page Source code
twDEMCStackToChains Source code
twLinreg1 Man page
twQuantiles2Coef Man page Source code
twRunDEMCSA Man page Source code
twTwoDenEx1 Man page
twVarDistrVec Man page Source code
twdemcEx1 Man page
unstackPopsTwDEMCPops Source code
updateBlockTwDEMC Man page Source code
updateBlocksTwDEMC Source code
updateIntervalTwDEMCChain Source code
updateIntervalTwDEMCParChains Source code
updateSigmaByGibbsSamplingInvchisq Man page Source code
xStepParallel Source code
xStepSnooker Source code

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
twDEMC documentation built on May 21, 2017, 1:32 a.m.