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. |