Man pages for parafac4microbiome
Parallel Factor Analysis Modelling of Longitudinal Microbiome Data
| assessModelQuality | Create randomly initialized models to determine the correct... |
| assessModelStability | Bootstrapping procedure to determine PARAFAC model stability... |
| calculateFMS | Calculate Factor Match Score for all initialized models. |
| calculateSparsity | Calculate sparsity across the feature mode of a multi-way... |
| calculateVarExp | Calculate the variation explained by a PARAFAC model. |
| calcVarExpPerComponent | Calculate the variance explained of a PARAFAC model, per... |
| corcondia | Core Consistency Diagnostic (CORCONDIA) calculation |
| fac_to_vect | Vectorize Fac object |
| flipLoadings | Sign flip the loadings of many randomly initialized models to... |
| 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 |
| parafac4microbiome-package | parafac4microbiome: Parallel Factor Analysis Modelling of... |
| parafac_core_als | Internal PARAFAC alternating least-squares (ALS) core... |
| parafac_fun | PARAFAC loss function calculation |
| parafac_gradient | Calculate gradient of PARAFAC model. |
| pipe | Pipe operator |
| plotModelMetric | Plot diagnostics of many initialized PARAFAC models. |
| plotModelStability | Plot a summary of the loadings of many initialized parafac... |
| plotModelTCCs | Plots Tucker Congruence Coefficients of randomly initialized... |
| 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... |
| reshapeData | Reorganize longitudinal microbiome into a data cube ready for... |
| Shao2019 | Shao2019 longitudinal microbiome data |
| sortComponents | Sort PARAFAC components based on variance explained per... |
| transformPARAFACloadings | Transform PARAFAC loadings to an orthonormal basis. Note:... |
| vanderPloeg2024 | vanderPloeg2024 longitudinal dataset |
| vect_to_fac | Convert vectorized output of PARAFAC to a Fac list object... |
