Semi-Supervised Bayesian Mixture Models Incorporating Batch Correction


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Documentation for package ‘batchmix’ version 1.0.1

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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
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
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
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
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
wishartLogLikelihood Wishart log-likelihood