Parallel Factor Analysis Modelling of Longitudinal Microbiome Data


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Documentation for package ‘parafac4microbiome’ version 1.0.3

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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.
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.
calcVarExpPerComponent Calculate the variance explained of a PARAFAC model, per component
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.
Fujita2023 Fujita2023 longitudinal microbiome data
importMicrobiotaProcess Import MicrobiotaProcess object for PARAFAC modelling
importPhyloseq Import Phyloseq object for PARAFAC modelling
importTreeSummarizedExperiment Import TreeSummarizedExperiment object for PARAFAC modelling
initializePARAFAC Initialize PARAFAC algorithm input vectors
multiwayCenter Center a multi-way array
multiwayCLR Perform a centered log-ratio transform over 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
parafac_gradient Calculate gradient of PARAFAC model.
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.
Shao2019 Shao2019 longitudinal microbiome data
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 microbiome data
vect_to_fac Convert vectorized output of PARAFAC to a Fac list object with all loadings per mode.