Semi-Supervised Bayesian Mixture Models Incorporating Batch Correction

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Documentation for package ‘batchmix’ version 2.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

batchmix-package	Bayesian Mixture Modelling for Joint Model-Based Clustering/Classification and Batch Correction
batchmix	Bayesian Mixture Modelling for Joint Model-Based Clustering/Classification and Batch Correction
batchmix,	Bayesian Mixture Modelling for Joint Model-Based Clustering/Classification and Batch Correction
BatchMixtureModel	Bayesian Mixture Modelling for Joint Model-Based Clustering/Classification and Batch Correction
batchSemiSupervisedMixtureModel	Batch semisupervised mixture model
calcAllocProb	Calculate allocation probabilities
checkDataGenerationInputs	Check data generation inputs
checkProposalWindows	Check proposal windows
collectAcceptanceRates	Collect acceptance rate
continueChain	Continue chain
continueChains	Continue chains
createSimilarityMat	Create Similarity Matrix
gammaLogLikelihood	Gamma log-likelihood
generateBatchData	Generate batch data
generateBatchDataLogPoisson	Generate batch data
generateBatchDataMVT	Generate batch data from a multivariate t distribution
generateBatchDataVaryingRepresentation	Generate batch data
generateGroupIDsInSimulator	Generate group IDs
generateInitialLabels	Generate initial labels
getLikelihood	Get likelihood
getSampledBatchScale	Get sampled batch shift
getSampledBatchShift	Get sampled batch shift
getSampledClusterMeans	Get sampled cluster means
invGammaLogLikelihood	Inverse gamma log-likelihood
invWishartLogLikelihood	Inverse-Wishart log-likelihood
minVI	Minimium VI
plotAcceptanceRates	Plot acceptance rates
plotLikelihoods	Plot likelihoods
plotSampledBatchMeans	Plot sampled batch means
plotSampledBatchScales	Plot sampled batch scales
plotSampledClusterMeans	Plot sampled cluster means
plotSampledParameter	Plot sampled vector parameter
predictClass	Predict class
predictFromMultipleChains	Predict from multiple MCMC chains
prepareInitialParameters	Prepare initial values
processMCMCChain	Process MCMC chain
processMCMCChains	Process MCMC chains
rStickBreakingPrior	Random Draw From Stick Breaking Prior
runBatchMix	Run Batch Mixture Model
runMCMCChains	Run MCMC Chains
sampleMVN	Sample mixture of multivariate normal distributions with batch effects
sampleMVT	Sample mixture of multivariate t-distributions with batch effects
samplePriorLabels	Sample prior labels
sampleSemisupervisedMVN	Sample semi-supervised MVN Mixture model
sampleSemisupervisedMVT	Sample semi-supervised MVT Mixture model
VI.lb	Minimum VI lower bound
wishartLogLikelihood	Wishart log-likelihood