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  "Title": "Semi-Supervised Bayesian Mixture Models Incorporating Batch\nCorrection",
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  "Description": "Semi-supervised and unsupervised Bayesian mixture models\nthat simultaneously infer the cluster/class structure and a\nbatch correction. Densities available are the multivariate\nnormal and the multivariate t. The model sampler is implemented\nin C++. This package is aimed at analysis of low-dimensional\ndata generated across several batches. See Coleman et al.\n(2022) <doi:10.1101/2022.01.14.476352> for details of the\nmodel.",
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    "batchSemiSupervisedMixtureModel",
    "calcAllocProb",
    "checkDataGenerationInputs",
    "checkProposalWindows",
    "collectAcceptanceRates",
    "continueChain",
    "continueChains",
    "createSimilarityMat",
    "gammaLogLikelihood",
    "generateBatchData",
    "generateBatchDataLogPoisson",
    "generateBatchDataMVT",
    "generateBatchDataVaryingRepresentation",
    "generateGroupIDsInSimulator",
    "generateInitialLabels",
    "getLikelihood",
    "getSampledBatchScale",
    "getSampledBatchShift",
    "getSampledClusterMeans",
    "invGammaLogLikelihood",
    "invWishartLogLikelihood",
    "minVI",
    "plotAcceptanceRates",
    "plotLikelihoods",
    "plotSampledBatchMeans",
    "plotSampledBatchScales",
    "plotSampledClusterMeans",
    "plotSampledParameter",
    "predictClass",
    "predictFromMultipleChains",
    "prepareInitialParameters",
    "processMCMCChain",
    "processMCMCChains",
    "rStickBreakingPrior",
    "runBatchMix",
    "runMCMCChains",
    "sampleMVN",
    "sampleMVT",
    "samplePriorLabels",
    "sampleSemisupervisedMVN",
    "sampleSemisupervisedMVT",
    "VI.lb",
    "wishartLogLikelihood"
  ],
  "_help": [
    {
      "page": "batchmix-package",
      "title": "Bayesian Mixture Modelling for Joint Model-Based Clustering/Classification and Batch Correction",
      "topics": [
        "batchmix-package",
        "batchmix"
      ]
    },
    {
      "page": "batchSemiSupervisedMixtureModel",
      "title": "Batch semisupervised mixture model",
      "topics": [
        "batchSemiSupervisedMixtureModel"
      ]
    },
    {
      "page": "calcAllocProb",
      "title": "Calculate allocation probabilities",
      "topics": [
        "calcAllocProb"
      ]
    },
    {
      "page": "checkDataGenerationInputs",
      "title": "Check data generation inputs",
      "topics": [
        "checkDataGenerationInputs"
      ]
    },
    {
      "page": "checkProposalWindows",
      "title": "Check proposal windows",
      "topics": [
        "checkProposalWindows"
      ]
    },
    {
      "page": "collectAcceptanceRates",
      "title": "Collect acceptance rate",
      "topics": [
        "collectAcceptanceRates"
      ]
    },
    {
      "page": "continueChain",
      "title": "Continue chain",
      "topics": [
        "continueChain"
      ]
    },
    {
      "page": "continueChains",
      "title": "Continue chains",
      "topics": [
        "continueChains"
      ]
    },
    {
      "page": "createSimilarityMat",
      "title": "Create Similarity Matrix",
      "topics": [
        "createSimilarityMat"
      ]
    },
    {
      "page": "gammaLogLikelihood",
      "title": "Gamma log-likelihood",
      "topics": [
        "gammaLogLikelihood"
      ]
    },
    {
      "page": "generateBatchData",
      "title": "Generate batch data",
      "topics": [
        "generateBatchData"
      ]
    },
    {
      "page": "generateBatchDataLogPoisson",
      "title": "Generate batch data",
      "topics": [
        "generateBatchDataLogPoisson"
      ]
    },
    {
      "page": "generateBatchDataMVT",
      "title": "Generate batch data from a multivariate t distribution",
      "topics": [
        "generateBatchDataMVT"
      ]
    },
    {
      "page": "generateBatchDataVaryingRepresentation",
      "title": "Generate batch data",
      "topics": [
        "generateBatchDataVaryingRepresentation"
      ]
    },
    {
      "page": "generateGroupIDsInSimulator",
      "title": "Generate group IDs",
      "topics": [
        "generateGroupIDsInSimulator"
      ]
    },
    {
      "page": "generateInitialLabels",
      "title": "Generate initial labels",
      "topics": [
        "generateInitialLabels"
      ]
    },
    {
      "page": "getLikelihood",
      "title": "Get likelihood",
      "topics": [
        "getLikelihood"
      ]
    },
    {
      "page": "getSampledBatchScale",
      "title": "Get sampled batch shift",
      "topics": [
        "getSampledBatchScale"
      ]
    },
    {
      "page": "getSampledBatchShift",
      "title": "Get sampled batch shift",
      "topics": [
        "getSampledBatchShift"
      ]
    },
    {
      "page": "getSampledClusterMeans",
      "title": "Get sampled cluster means",
      "topics": [
        "getSampledClusterMeans"
      ]
    },
    {
      "page": "invGammaLogLikelihood",
      "title": "Inverse gamma log-likelihood",
      "topics": [
        "invGammaLogLikelihood"
      ]
    },
    {
      "page": "invWishartLogLikelihood",
      "title": "Inverse-Wishart log-likelihood",
      "topics": [
        "invWishartLogLikelihood"
      ]
    },
    {
      "page": "minVI",
      "title": "Minimium VI",
      "topics": [
        "minVI"
      ]
    },
    {
      "page": "plotAcceptanceRates",
      "title": "Plot acceptance rates",
      "topics": [
        "plotAcceptanceRates"
      ]
    },
    {
      "page": "plotLikelihoods",
      "title": "Plot likelihoods",
      "topics": [
        "plotLikelihoods"
      ]
    },
    {
      "page": "plotSampledBatchMeans",
      "title": "Plot sampled batch means",
      "topics": [
        "plotSampledBatchMeans"
      ]
    },
    {
      "page": "plotSampledBatchScales",
      "title": "Plot sampled batch scales",
      "topics": [
        "plotSampledBatchScales"
      ]
    },
    {
      "page": "plotSampledClusterMeans",
      "title": "Plot sampled cluster means",
      "topics": [
        "plotSampledClusterMeans"
      ]
    },
    {
      "page": "plotSampledParameter",
      "title": "Plot sampled vector parameter",
      "topics": [
        "plotSampledParameter"
      ]
    },
    {
      "page": "predictClass",
      "title": "Predict class",
      "topics": [
        "predictClass"
      ]
    },
    {
      "page": "predictFromMultipleChains",
      "title": "Predict from multiple MCMC chains",
      "topics": [
        "predictFromMultipleChains"
      ]
    },
    {
      "page": "prepareInitialParameters",
      "title": "Prepare initial values",
      "topics": [
        "prepareInitialParameters"
      ]
    },
    {
      "page": "processMCMCChain",
      "title": "Process MCMC chain",
      "topics": [
        "processMCMCChain"
      ]
    },
    {
      "page": "processMCMCChains",
      "title": "Process MCMC chains",
      "topics": [
        "processMCMCChains"
      ]
    },
    {
      "page": "rStickBreakingPrior",
      "title": "Random Draw From Stick Breaking Prior",
      "topics": [
        "rStickBreakingPrior"
      ]
    },
    {
      "page": "runBatchMix",
      "title": "Run Batch Mixture Model",
      "topics": [
        "runBatchMix"
      ]
    },
    {
      "page": "runMCMCChains",
      "title": "Run MCMC Chains",
      "topics": [
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      ]
    },
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      "title": "Sample mixture of multivariate normal distributions with batch effects",
      "topics": [
        "sampleMVN"
      ]
    },
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      "page": "sampleMVT",
      "title": "Sample mixture of multivariate t-distributions with batch effects",
      "topics": [
        "sampleMVT"
      ]
    },
    {
      "page": "samplePriorLabels",
      "title": "Sample prior labels",
      "topics": [
        "samplePriorLabels"
      ]
    },
    {
      "page": "sampleSemisupervisedMVN",
      "title": "Sample semi-supervised MVN Mixture model",
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        "sampleSemisupervisedMVN"
      ]
    },
    {
      "page": "sampleSemisupervisedMVT",
      "title": "Sample semi-supervised MVT Mixture model",
      "topics": [
        "sampleSemisupervisedMVT"
      ]
    },
    {
      "page": "VI.lb",
      "title": "Minimum VI lower bound",
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      ]
    },
    {
      "page": "wishartLogLikelihood",
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    }
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