Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

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Documentation for package ‘parafac4microbiome’ version 1.3.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
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
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.
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 multi-omics dataset
vect_to_fac	Convert vectorized output of PARAFAC to a Fac list object with all loadings per mode.