coef.nmf                Extract coefficients from NMF models
fitted.nmf              Extract fitted values from NMF models
nmf.cluster.criteria    Sample-clustering quality across ranks
nmf.cluster.flow        Cluster-flow (alluvial) diagram across a
                        sequence of fits
nmf.ffb                 NMF-FFB Main Estimation Algorithm (formerly
                        NMF-SEM)
nmf.ffb.DOT             Generate a Graphviz DOT Diagram for an NMF-FFB
                        Model
nmf.ffb.cv              Cross-Validation for NMF-FFB
nmf.ffb.inference       Statistical inference for NMF-FFB via X-fixed
                        full pair bootstrap
nmf.ffb.split           Heuristic Variable Splitting for NMF-FFB
nmf.rrr                 Three-Layer Non-negative Matrix Factorization
                        (NMF-AE)
nmf.rrr.DOT             DOT graph visualization for nmfae objects
nmf.rrr.cv              Sample-wise k-fold Cross-Validation for nmfae
nmf.rrr.ecv             Element-wise Cross-Validation for nmfae (Wold's
                        CV)
nmf.rrr.heatmap         Heatmap visualization of nmfae factor matrices
nmf.rrr.inference       Statistical Inference for NMF-AE Parameter
                        Matrix
nmf.rrr.kernel.beta.cv
                        Optimize kernel beta for nmfae by
                        cross-validation
nmf.rrr.rank            Rank selection for nmfae (paired rank, concise
                        diagnostics)
nmf.rrr.rename          Rename decoder and encoder bases
nmf.rrr.signed          Signed-Bottleneck NMF-AE: Three-Layer NMF-AE
                        with Signed Bottleneck
nmf.rrr.signed.ecv      Element-wise Cross-Validation for
                        Signed-Bottleneck NMF-AE
nmf.rrr.signed.heatmap
                        Heatmap visualization of nmfae.signed factor
                        matrices
nmf.rrr.signed.inference
                        Statistical Inference for Signed-Bottleneck
                        NMF-AE Signed Bottleneck
nmf.rrr.signed.rank     Rank selection for nmfae.signed (paired rank,
                        concise diagnostics)
nmf.rrr.signed.rename   Rename Resp/Cov labels on nmfae.signed objects
nmfkc                   Optimize NMF with kernel covariates (Full
                        Support for Missing Values)
nmfkc.DOT               Generate Graphviz DOT Scripts for NMF or
                        NMF-with-Covariates Models
nmfkc.ar                Construct observation and covariate matrices
                        for a vector autoregressive model
nmfkc.ar.DOT            Generate a Graphviz DOT Diagram for NMF-AR /
                        NMF-VAR Models
nmfkc.ar.degree.cv      Optimize lag order for the autoregressive model
nmfkc.ar.predict        Forecast future values for NMF-VAR model
nmfkc.ar.stationarity   Check stationarity of an NMF-VAR model
nmfkc.ard               Automatic relevance determination for NMF rank
                        (experimental)
nmfkc.bicv              Bi-cross-validation for NMF rank selection
nmfkc.class             Create a class (one-hot) matrix from a
                        categorical vector
nmfkc.consensus         Consensus-clustering rank selection for NMF
                        (Brunet 2004)
nmfkc.criterion         Compute model selection criteria for a fitted
                        nmfkc model
nmfkc.cv                Perform k-fold cross-validation for NMF with
                        kernel covariates
nmfkc.cv.methods        Print/plot methods for nmfkc cross-validation
                        objects
nmfkc.denormalize       Denormalize a matrix from [0,1] back to its
                        original scale
nmfkc.ecv               Perform Element-wise Cross-Validation (Wold's
                        CV)
nmfkc.inference         Statistical inference for the parameter matrix
                        C (Theta)
nmfkc.kernel            Create a kernel matrix from covariates
nmfkc.kernel.beta.cv    Optimize beta of the Gaussian kernel function
                        by cross-validation
nmfkc.kernel.beta.nearest.med
                        Estimate Gaussian/RBF kernel parameter beta
                        from covariates (supports landmarks)
nmfkc.kernel.gaussian   Create a Gaussian kernel matrix from covariates
nmfkc.net               Symmetric NMF for networks (tri / bi / signed)
nmfkc.net.DOT           Generate a Graphviz DOT Diagram for a Symmetric
                        NMF Network
nmfkc.net.ecv           Element-wise cross-validation for nmfkc.net
                        (upper-triangle folds)
nmfkc.net.inference     Statistical Inference for Symmetric NMF
                        Parameters
nmfkc.net.rank          Rank selection for nmfkc.net (concise
                        diagnostics)
nmfkc.normalize         Normalize a matrix to the range [0,1]
nmfkc.rank              Rank selection diagnostics with graphical
                        output
nmfkc.residual.plot     Plot Diagnostics: Original, Fitted, and
                        Residual Matrices as Heatmaps
nmfkc.signed            NMF-KC with signed covariate matrix
nmfkc.signed.cv         Column-wise k-fold cross-validation for
                        nmfkc.signed
nmfkc.signed.ecv        Element-wise cross-validation for nmfkc.signed
nmfkc.signed.rank       Rank selection for nmfkc.signed (concise
                        diagnostics)
nmfkc.signed.rff        Random Fourier Features for nmfkc.signed()
nmfre                   Non-negative Matrix Factorization with Random
                        Effects
nmfre.ecv               NMF-RE element-wise cross-validation for rank
                        selection
nmfre.inference         Statistical inference for the coefficient
                        matrix C from NMF-RE
plot.nmf.cluster.criteria
                        Plot clustering-quality criteria across a
                        sequence of fits
plot.nmf.cluster.flow   Plot a cluster-flow (alluvial) diagram
plot.nmf.rank           Plot a rank-selection (nmf.rank) object
plot.nmfae              'plot.nmfae' displays the convergence
                        trajectory of the objective function across
                        iterations. The title shows the achieved R^2.
plot.nmfkc              Plot method for objects of class 'nmfkc'
plot.nmfkc.DOT          Plot method for nmfkc.DOT objects
plot.nmfkc.ard          Plot method for nmfkc.ard objects
plot.nmfkc.consensus    Plot a consensus rank-selection
                        (nmfkc.consensus) object
plot.nmfkc.signed       Plot method for nmfkc.signed (convergence)
plot.nmfre              Plot convergence diagnostics for NMF models
plot.nmfre.ecv          Plot method for nmfre.ecv objects
predict.nmfkc           Prediction method for objects of class 'nmfkc'
predict.nmfkc.signed    Predict method for nmfkc.signed
predict.nmfre           Predict method for nmfre objects
print.nmf.cluster.criteria
                        Print method for nmf.cluster.criteria objects
print.nmf.cluster.flow
                        Print method for nmf.cluster.flow objects
print.nmf.inference     Print method for NMF inference objects
print.nmf.rank          Print method for rank-selection (nmf.rank)
                        objects
print.nmfkc.ard         Print method for nmfkc.ard objects
print.nmfkc.consensus   Print method for nmfkc.consensus objects
print.nmfre.ecv         Print method for nmfre.ecv objects
print.summary.nmf.sem   Print method for summary.nmf.sem objects
print.summary.nmfkc     Print method for 'summary.nmfkc' objects
print.summary.nmfkc.inference
                        Print method for summary.nmfkc.inference
                        objects
print.summary.nmfkc.net
                        Print method for summary.nmfkc.net objects
print.summary.nmfkc.net.inference
                        Print method for summary.nmfkc.net.inference
                        objects
print.summary.nmfkc.net.signed
                        Print method for summary.nmfkc.net.signed
                        objects
print.summary.nmfkc.signed
                        Print method for summary.nmfkc.signed
residuals.nmf           Extract residuals from NMF models
summary.nmf.sem         Summary method for nmf.sem objects
summary.nmfkc           Summary method for objects of class 'nmfkc'
summary.nmfkc.inference
                        Summary method for nmfkc.inference objects
summary.nmfkc.net       Summary method for nmfkc.net objects
summary.nmfkc.net.inference
                        Summary method for nmfkc.net.inference objects
summary.nmfkc.net.signed
                        Summary method for nmfkc.net.signed objects
summary.nmfkc.signed    Summary method for nmfkc.signed
summary.nmfre           Summary method for objects of class 'nmfre'
