# Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

## Documentation for package ‘parafac4microbiome’ version 1.3.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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.