Package index
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Fujita2023 - Fujita2023 longitudinal microbiome data
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Shao2019 - Shao2019 longitudinal microbiome data
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assessModelQuality() - Create randomly initialized models to determine the correct number of components by assessing model quality metrics.
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assessModelStability() - Bootstrapping procedure to determine PARAFAC model stability for a given number of components.
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calcVarExpPerComponent() - Calculate the variance explained of a PARAFAC model, per component
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calculateFMS() - Calculate Factor Match Score for all initialized models.
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calculateSparsity() - Calculate sparsity across the feature mode of a multi-way array.
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calculateVarExp() - Calculate the variation explained by a PARAFAC model.
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corcondia() - Core Consistency Diagnostic (CORCONDIA) calculation
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fac_to_vect() - Vectorize Fac object
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flipLoadings() - Sign flip the loadings of many randomly initialized models to make consistent overview plots.
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importPhyloseq() - Import Phyloseq object for PARAFAC modelling
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importTreeSummarizedExperiment() - Import TreeSummarizedExperiment object for PARAFAC modelling
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initializePARAFAC() - Initialize PARAFAC algorithm input vectors
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multiwayCLR() - Perform a centered log-ratio transform over a multi-way array
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multiwayCenter() - Center a multi-way array
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multiwayScale() - Scale a multi-way array
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parafac() - Parallel Factor Analysis
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parafac_core_als() - Internal PARAFAC alternating least-squares (ALS) core algorithm
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parafac_fun() - PARAFAC loss function calculation
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plotModelMetric() - Plot diagnostics of many initialized PARAFAC models.
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plotModelStability() - Plot a summary of the loadings of many initialized parafac models.
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plotModelTCCs() - Plots Tucker Congruence Coefficients of randomly initialized models.
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plotPARAFACmodel() - Plot a PARAFAC model
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processDataCube() - Process a multi-way array of count data.
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reinflateFac() - Calculate Xhat from a model Fac object
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reinflateTensor() - Create a tensor out of a set of matrices similar to a component model.
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reshapeData() - Reorganize longitudinal microbiome into a data cube ready for PARAFAC modelling.
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sortComponents() - Sort PARAFAC components based on variance explained per component.
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transformPARAFACloadings() - Transform PARAFAC loadings to an orthonormal basis. Note: this function only works for 3-way PARAFAC models.
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vanderPloeg2024 - vanderPloeg2024 longitudinal multi-omics dataset
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vect_to_fac() - Convert vectorized output of PARAFAC to a Fac list object with all loadings per mode.