Package: parafac4microbiome 1.3.2.9000

parafac4microbiome: Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

Creation and selection of PARAllel FACtor Analysis (PARAFAC) models of longitudinal microbiome data. You can import your own data with our import functions or use one of the example datasets to create your own PARAFAC models. Selection of the optimal number of components can be done using assessModelQuality() and assessModelStability(). The selected model can then be plotted using plotPARAFACmodel(). The Parallel Factor Analysis method was originally described by Caroll and Chang (1970) <doi:10.1007/BF02310791> and Harshman (1970) <https://www.psychology.uwo.ca/faculty/harshman/wpppfac0.pdf>.

Authors:Geert Roelof van der Ploeg [aut, cre], Johan Westerhuis [ctb], Anna Heintz-Buschart [ctb], Age Smilde [ctb], University of Amsterdam [cph, fnd]

parafac4microbiome_1.3.2.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
parafac4microbiome/json (API)

# Install 'parafac4microbiome' in R:
install.packages('parafac4microbiome', repos = c('https://grvanderploeg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grvanderploeg/parafac4microbiome/issues

Pkgdown/docs site:https://grvanderploeg.com

Datasets:
  • Fujita2023 - Fujita2023 longitudinal microbiome data
  • Shao2019 - Shao2019 longitudinal microbiome data
  • vanderPloeg2024 - VanderPloeg2024 longitudinal multi-omics dataset

On CRAN:

Conda:

dimensionality-reductionmicrobiomemicrobiome-datamultiwaymultiway-algorithmsparallel-factor-analysis

7.24 score 9 stars 1 packages 107 scripts 224 downloads 30 exports 91 dependencies

Last updated from:b7b9770abc. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK272
source / vignettesOK326
linux-release-x86_64OK265
macos-release-arm64OK189
macos-oldrel-arm64OK186
windows-develOK251
windows-releaseOK226
windows-oldrelOK205
wasm-releaseOK165

Exports:%>%assessModelQualityassessModelStabilitycalculateFMScalculateSparsitycalculateVarExpcalcVarExpPerComponentcorcondiafac_to_vectflipLoadingsimportPhyloseqimportTreeSummarizedExperimentinitializePARAFACmultiwayCentermultiwayCLRmultiwayScaleparafacparafac_core_alsparafac_funplotModelMetricplotModelStabilityplotModelTCCsplotPARAFACmodelprocessDataCubereinflateFacreinflateTensorreshapeDatasortComponentstransformPARAFACloadingsvect_to_fac

Dependencies:abindbackportsbayesmbootbroomcarcarDatacliCMLScodetoolscolorspacecompositionscorrplotcowplotcpp11DEoptimRDerivdoBydoParalleldplyrfarverforeachforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobanditeratorslabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmultiwaynlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompracmapurrrquadprogquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrobustbaserstatixrTensorS7scalesSparseMstringistringrsurvivaltensorAtibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo

Fujita2023
Introduction | Processing the data cube | Determining the correct number of components | Jack-knifed models | Model selection
Rendered fromFujita2023.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-29

Introduction
Datasets | Analysis | Processing the data cube | Making a PARAFAC model | Plotting a PARAFAC model
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-29

Shao2019
Introduction | Processing the data cube | Determining the correct number of components | Jack-knifed models | Model selection
Rendered fromShao2019.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-29

vanderPloeg2024
Introduction | Processing the data cube | Determining the correct number of components | Model selection
Rendered fromvanderPloeg2024.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-29

Readme and manuals

Help Manual

Help pageTopics
Create randomly initialized models to determine the correct number of components by assessing model quality metrics.assessModelQuality
Bootstrapping procedure to determine PARAFAC model stability for a given number of components.assessModelStability
Calculate Factor Match Score for all initialized models.calculateFMS
Calculate sparsity across the feature mode of a multi-way array.calculateSparsity
Calculate the variation explained by a PARAFAC model.calculateVarExp
Calculate the variance explained of a PARAFAC model, per componentcalcVarExpPerComponent
Core Consistency Diagnostic (CORCONDIA) calculationcorcondia
Vectorize Fac objectfac_to_vect
Sign flip the loadings of many randomly initialized models to make consistent overview plots.flipLoadings
Fujita2023 longitudinal microbiome dataFujita2023
Import Phyloseq object for PARAFAC modellingimportPhyloseq
Import TreeSummarizedExperiment object for PARAFAC modellingimportTreeSummarizedExperiment
Initialize PARAFAC algorithm input vectorsinitializePARAFAC
Center a multi-way arraymultiwayCenter
Perform a centered log-ratio transform over a multi-way arraymultiwayCLR
Scale a multi-way arraymultiwayScale
Parallel Factor Analysisparafac
Internal PARAFAC alternating least-squares (ALS) core algorithmparafac_core_als
PARAFAC loss function calculationparafac_fun
Plot diagnostics of many initialized PARAFAC models.plotModelMetric
Plot a summary of the loadings of many initialized parafac models.plotModelStability
Plots Tucker Congruence Coefficients of randomly initialized models.plotModelTCCs
Plot a PARAFAC modelplotPARAFACmodel
Process a multi-way array of count data.processDataCube
Calculate Xhat from a model Fac objectreinflateFac
Create a tensor out of a set of matrices similar to a component model.reinflateTensor
Reorganize longitudinal microbiome into a data cube ready for PARAFAC modelling.reshapeData
Shao2019 longitudinal microbiome dataShao2019
Sort PARAFAC components based on variance explained per component.sortComponents
Transform PARAFAC loadings to an orthonormal basis. Note: this function only works for 3-way PARAFAC models.transformPARAFACloadings
vanderPloeg2024 longitudinal multi-omics datasetvanderPloeg2024
Convert vectorized output of PARAFAC to a Fac list object with all loadings per mode.vect_to_fac