Package: nmfkc 0.8.2

nmfkc: Non-Negative Matrix Factorization with Kernel Covariates

Performs Non-negative Matrix Factorization (NMF) with Kernel Covariates. Given an observation matrix and kernel covariates, it optimizes both a basis matrix and a parameter matrix. Notably, if the kernel matrix is an identity matrix, the method simplifies to standard NMF. Also provides NMF with Random Effects (NMF-RE) via nmfre(), which estimates a mixed-effects model combining covariate-driven scores with unit-specific random effects together with wild bootstrap inference, and NMF-based Structural Equation Modeling (NMF-SEM) via nmf.sem(), which fits a two-block input-output model for blind source separation and path analysis. References: Satoh (2025) <doi:10.48550/arXiv.2403.05359>; Satoh (2025) <doi:10.48550/arXiv.2510.10375>; Satoh (2025) <doi:10.48550/arXiv.2512.18250>; Satoh (2026) <doi:10.48550/arXiv.2603.01468>; Satoh (2026) <doi:10.1007/s42081-025-00314-0>.

Authors:Kenichi Satoh [aut, cre]

nmfkc_0.8.2.tar.gz
nmfkc_0.8.2.zip(r-4.7)nmfkc_0.8.2.zip(r-4.6)nmfkc_0.8.2.zip(r-4.5)
nmfkc_0.8.2.tgz(r-4.6-any)nmfkc_0.8.2.tgz(r-4.5-any)
nmfkc_0.8.2.tar.gz(r-4.7-any)nmfkc_0.8.2.tar.gz(r-4.6-any)
nmfkc_0.8.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
nmfkc/json (API)
NEWS

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

Bug tracker:https://github.com/ksatohds/nmfkc/issues

Pkgdown/docs site:https://ksatohds.github.io

On CRAN:

Conda:

7.03 score 6 stars 13 scripts 498 downloads 63 exports 0 dependencies

Last updated from:f8de7ccad7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK169
source / vignettesOK291
linux-release-x86_64OK180
macos-release-arm64OK164
macos-oldrel-arm64OK112
windows-develOK117
windows-releaseOK131
windows-oldrelOK133
wasm-releaseOK114

Exports:nmf.cluster.criterianmf.cluster.flownmf.ffbnmf.ffb.cvnmf.ffb.DOTnmf.ffb.inferencenmf.ffb.splitnmf.semnmf.sem.cvnmf.sem.DOTnmf.sem.inferencenmf.sem.splitnmfaenmfae.cvnmfae.DOTnmfae.ecvnmfae.heatmapnmfae.inferencenmfae.kernel.beta.cvnmfae.ranknmfae.renamenmfae.signednmfae.signed.ecvnmfae.signed.heatmapnmfae.signed.inferencenmfae.signed.ranknmfae.signed.renamenmfkcnmfkc.arnmfkc.ar.degree.cvnmfkc.ar.DOTnmfkc.ar.predictnmfkc.ar.stationaritynmfkc.ardnmfkc.bicvnmfkc.classnmfkc.consensusnmfkc.criterionnmfkc.cvnmfkc.denormalizenmfkc.DOTnmfkc.ecvnmfkc.inferencenmfkc.kernelnmfkc.kernel.beta.cvnmfkc.kernel.beta.nearest.mednmfkc.kernel.gaussiannmfkc.netnmfkc.net.DOTnmfkc.net.ecvnmfkc.net.inferencenmfkc.net.ranknmfkc.normalizenmfkc.ranknmfkc.residual.plotnmfkc.signednmfkc.signed.cvnmfkc.signed.ecvnmfkc.signed.ranknmfkc.signed.rffnmfrenmfre.dfU.scannmfre.inference

Dependencies:

Choosing the NMF rank on data with a known true rank

Rendered fromrank-selection-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-06-14
Started: 2026-06-14

Classification with NMF-LAB

Rendered fromclassification-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-03-29
Started: 2025-10-13

Introduction to nmfkc

Rendered fromintroduction-to-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2025-11-24
Started: 2025-10-13

NMF-FFB with nmfkc

Rendered fromnmf-sem-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-05-03
Started: 2025-12-20

NMF-RE: Mixed-Effects Modeling with nmfkc

Rendered fromnmf-re-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-03-29
Started: 2026-03-02

Soft community detection in networks with nmfkc.net

Rendered fromnetwork-community-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-06-14
Started: 2026-06-14

Time Series Analysis with NMF-VAR

Rendered fromtimeseries-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-03-29
Started: 2025-10-13

Topic Modeling with nmfkc

Rendered fromtopic-modeling-with-nmfkc.Rmdusingknitr::rmarkdownon Jun 14 2026.

Last update: 2026-06-14
Started: 2025-10-13

Readme and manuals

Help Manual

Help pageTopics
Extract coefficients from NMF modelscoef.nmf coef.nmf.sem
Extract fitted values from NMF modelsfitted.nmf fitted.nmf.sem fitted.nmfae
Sample-clustering quality across ranksnmf.cluster.criteria
Cluster-flow (alluvial) diagram across a sequence of fitsnmf.cluster.flow
NMF-FFB Main Estimation Algorithm (formerly NMF-SEM)nmf.ffb nmf.sem
Cross-Validation for NMF-FFBnmf.ffb.cv nmf.sem.cv
Generate a Graphviz DOT Diagram for an NMF-FFB Modelnmf.ffb.DOT nmf.sem.DOT
Statistical inference for NMF-FFB via X-fixed full pair bootstrapnmf.ffb.inference nmf.sem.inference
Heuristic Variable Splitting for NMF-FFBnmf.ffb.split nmf.sem.split
Three-Layer Non-negative Matrix Factorization (NMF-AE)nmfae
Sample-wise k-fold Cross-Validation for nmfaenmfae.cv
DOT graph visualization for nmfae objectsnmfae.DOT
Element-wise Cross-Validation for nmfae (Wold's CV)nmfae.ecv
Heatmap visualization of nmfae factor matricesnmfae.heatmap
Statistical Inference for NMF-AE Parameter Matrixnmfae.inference
Optimize kernel beta for nmfae by cross-validationnmfae.kernel.beta.cv
Rank selection for nmfae (paired rank, concise diagnostics)nmfae.rank
Rename decoder and encoder basesnmfae.rename
Signed-Bottleneck NMF-AE: Three-Layer NMF-AE with Signed Bottlenecknmfae.signed
Element-wise Cross-Validation for Signed-Bottleneck NMF-AEnmfae.signed.ecv
Heatmap visualization of nmfae.signed factor matricesnmfae.signed.heatmap
Statistical Inference for Signed-Bottleneck NMF-AE Signed Bottlenecknmfae.signed.inference
Rank selection for nmfae.signed (paired rank, concise diagnostics)nmfae.signed.rank
Rename Dec/Enc labels on nmfae.signed objectsnmfae.signed.rename
Optimize NMF with kernel covariates (Full Support for Missing Values)nmfkc
Construct observation and covariate matrices for a vector autoregressive modelnmfkc.ar
Optimize lag order for the autoregressive modelnmfkc.ar.degree.cv
Generate a Graphviz DOT Diagram for NMF-AR / NMF-VAR Modelsnmfkc.ar.DOT
Forecast future values for NMF-VAR modelnmfkc.ar.predict
Check stationarity of an NMF-VAR modelnmfkc.ar.stationarity
Automatic relevance determination for NMF rank (experimental)nmfkc.ard
Bi-cross-validation for NMF rank selectionnmfkc.bicv
Create a class (one-hot) matrix from a categorical vectornmfkc.class
Consensus-clustering rank selection for NMF (Brunet 2004)nmfkc.consensus
Compute model selection criteria for a fitted nmfkc modelnmfkc.criterion
Perform k-fold cross-validation for NMF with kernel covariatesnmfkc.cv
Denormalize a matrix from [0,1] back to its original scalenmfkc.denormalize
Generate Graphviz DOT Scripts for NMF or NMF-with-Covariates Modelsnmfkc.DOT
Perform Element-wise Cross-Validation (Wold's CV)nmfkc.ecv
Statistical inference for the parameter matrix C (Theta)nmfkc.inference
Create a kernel matrix from covariatesnmfkc.kernel
Optimize beta of the Gaussian kernel function by cross-validationnmfkc.kernel.beta.cv
Estimate Gaussian/RBF kernel parameter beta from covariates (supports landmarks)nmfkc.kernel.beta.nearest.med
Create a Gaussian kernel matrix from covariatesnmfkc.kernel.gaussian
Symmetric NMF for networks (tri / bi / signed)nmfkc.net
Generate a Graphviz DOT Diagram for a Symmetric NMF Networknmfkc.net.DOT
Element-wise cross-validation for nmfkc.net (upper-triangle folds)nmfkc.net.ecv
Statistical Inference for Symmetric NMF Parametersnmfkc.net.inference
Rank selection for nmfkc.net (concise diagnostics)nmfkc.net.rank
Normalize a matrix to the range [0,1]nmfkc.normalize
Rank selection diagnostics with graphical outputnmfkc.rank
Plot Diagnostics: Original, Fitted, and Residual Matrices as Heatmapsnmfkc.residual.plot
NMF-KC with signed covariate matrixnmfkc.signed
Column-wise k-fold cross-validation for nmfkc.signednmfkc.signed.cv
Element-wise cross-validation for nmfkc.signednmfkc.signed.ecv
Rank selection for nmfkc.signed (concise diagnostics)nmfkc.signed.rank
Random Fourier Features for nmfkc.signed()nmfkc.signed.rff
Non-negative Matrix Factorization with Random Effectsnmfre
Scan dfU cap rates for NMF-REnmfre.dfU.scan
Statistical inference for the coefficient matrix C from NMF-REnmfre.inference
Plot clustering-quality criteria across a sequence of fitsplot.nmf.cluster.criteria
Plot a cluster-flow (alluvial) diagramplot.nmf.cluster.flow
Plot a rank-selection (nmf.rank) objectplot.nmf.rank
'plot.nmfae' displays the convergence trajectory of the objective function across iterations. The title shows the achieved R^2.plot.nmfae
Plot method for nmfae.cv objectsplot.nmfae.cv
Plot method for nmfae.ecv objectsplot.nmfae.ecv
Plot method for nmfae.kernel.beta.cv objectsplot.nmfae.kernel.beta.cv
Plot method for nmfae.signed (convergence)plot.nmfae.signed
Plot method for objects of class 'nmfkc'plot.nmfkc
Plot method for nmfkc.ard objectsplot.nmfkc.ard
Plot a consensus rank-selection (nmfkc.consensus) objectplot.nmfkc.consensus
Plot method for nmfkc.DOT objectsplot.nmfkc.DOT
Plot method for nmfkc.signed (convergence)plot.nmfkc.signed
Plot convergence diagnostics for NMF modelsplot.nmf.sem plot.nmfre
Plot method for predict.nmfae objectsplot.predict.nmfae
Predict method for nmfae objectspredict.nmfae
Predict method for nmfae.signedpredict.nmfae.signed
Prediction method for objects of class 'nmfkc'predict.nmfkc
Predict method for nmfkc.signedpredict.nmfkc.signed
Print method for nmf.cluster.criteria objectsprint.nmf.cluster.criteria
Print method for nmf.cluster.flow objectsprint.nmf.cluster.flow
Print method for NMF inference objectsprint.nmf.inference
Print method for rank-selection (nmf.rank) objectsprint.nmf.rank
Print method for nmfkc.ard objectsprint.nmfkc.ard
Print method for nmfkc.consensus objectsprint.nmfkc.consensus
Print method for summary.nmf.sem objectsprint.summary.nmf.sem
Print method for summary.nmfae objectsprint.summary.nmfae
Print method for summary.nmfae.inference objectsprint.summary.nmfae.inference
Print method for summary.nmfae.signedprint.summary.nmfae.signed
Print method for summary.nmfae.signed.inference objectsprint.summary.nmfae.signed.inference
Print method for 'summary.nmfkc' objectsprint.summary.nmfkc
Print method for summary.nmfkc.inference objectsprint.summary.nmfkc.inference
Print method for summary.nmfkc.net objectsprint.summary.nmfkc.net
Print method for summary.nmfkc.net.inference objectsprint.summary.nmfkc.net.inference
Print method for summary.nmfkc.net.signed objectsprint.summary.nmfkc.net.signed
Print method for summary.nmfkc.signedprint.summary.nmfkc.signed
Extract residuals from NMF modelsresiduals.nmf residuals.nmf.sem residuals.nmfae residuals.nmfre
Summary method for nmf.sem objectssummary.nmf.sem
Summary method for nmfae objectssummary.nmfae
Summary method for nmfae.inference objectssummary.nmfae.inference
Summary method for nmfae.signedsummary.nmfae.signed
Summary method for nmfae.signed.inference objectssummary.nmfae.signed.inference
Summary method for objects of class 'nmfkc'summary.nmfkc
Summary method for nmfkc.inference objectssummary.nmfkc.inference
Summary method for nmfkc.net objectssummary.nmfkc.net
Summary method for nmfkc.net.inference objectssummary.nmfkc.net.inference
Summary method for nmfkc.net.signed objectssummary.nmfkc.net.signed
Summary method for nmfkc.signedsummary.nmfkc.signed
Summary method for objects of class 'nmfre'summary.nmfre