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