AIC.PLNfit              Akaike Information Criterion for a fitted PLN
                        model
AIC.ZIPLNfit            Akaike Information Criterion for a fitted ZIPLN
                        model
BIC.PLNfit              Bayesian Information Criterion for a fitted PLN
                        model
BIC.ZIPLNfit            Bayesian Information Criterion for a fitted
                        ZIPLN model
ICL                     Integrated Classification Likelihood
Networkfamily           An R6 Class to virtually represent a collection
                        of network fits
PLN                     Poisson lognormal model
PLNLDA                  Poisson lognormal model towards Linear
                        Discriminant Analysis
PLNLDA_param            Control of a PLNLDA fit
PLNLDAfit               An R6 Class to represent a PLNfit in a LDA
                        framework
PLNLDAfit_diagonal      An R6 Class to represent a PLNfit in a LDA
                        framework with diagonal covariance
PLNPCA                  Poisson lognormal model towards Principal
                        Component Analysis
PLNPCA_param            Control of PLNPCA fit
PLNPCAfamily            An R6 Class to represent a collection of
                        PLNPCAfit
PLNPCAfit               An R6 Class to represent a PLNfit in a PCA
                        framework
PLN_param               Control of a PLN fit
PLNfamily               An R6 Class to represent a collection of PLNfit
PLNfit                  An R6 Class to represent a PLNfit in a
                        standard, general framework
PLNfit_diagonal         An R6 Class to represent a PLNfit in a
                        standard, general framework, with diagonal
                        residual covariance
PLNfit_fixedcov         An R6 Class to represent a PLNfit in a
                        standard, general framework, with fixed
                        (inverse) residual covariance
PLNfit_genpop           An R6 Class to represent a PLNfit with a
                        residual covariance structured by a fixed
                        correlation matrix (e.g. a genetic relationship
                        matrix), motivated by population genetics
PLNfit_spherical        An R6 Class to represent a PLNfit in a
                        standard, general framework, with spherical
                        residual covariance
PLNmixture              Poisson lognormal mixture model
PLNmixture_param        Control of a PLNmixture fit
PLNmixturefamily        An R6 Class to represent a collection of
                        PLNmixturefit
PLNmixturefit           An R6 Class to represent a PLNfit in a mixture
                        framework
PLNnetwork              Sparse Poisson lognormal model for network
                        inference
PLNnetwork_param        Control of PLNnetwork fit
PLNnetworkfamily        An R6 Class to represent a collection of
                        'PLNnetworkfit's
PLNnetworkfit           An R6 Class to represent a PLNfit in a sparse
                        inverse covariance framework
ZIPLN                   Zero Inflated Poisson lognormal model
ZIPLN_param             Control of a ZIPLN fit
ZIPLNfit                An R6 Class to represent a ZIPLNfit
ZIPLNfit_diagonal       An R6 Class to represent a ZIPLNfit in a
                        standard, general framework, with diagonal
                        residual covariance
ZIPLNfit_fixed          An R6 Class to represent a ZIPLNfit in a
                        standard, general framework, with fixed
                        (inverse) residual covariance
ZIPLNfit_sparse         An R6 Class to represent a ZIPLNfit in a
                        standard, general framework, with sparse
                        inverse residual covariance
ZIPLNfit_spherical      An R6 Class to represent a ZIPLNfit in a
                        standard, general framework, with spherical
                        residual covariance
ZIPLNnetwork            Zero Inflated Sparse Poisson lognormal model
                        for network inference
ZIPLNnetwork_param      Control of ZIPLNnetwork fit
ZIPLNnetworkfamily      An R6 Class to represent a collection of
                        ZIPLNnetwork
barents                 Barents fish data set
coef.PLNLDAfit          Extracts model coefficients from objects
                        returned by 'PLNLDA()'
coef.PLNfit             Extract model coefficients
coef.PLNmixturefit      Extract model coefficients
coef.ZIPLNfit           Extract model coefficients
coefficient_path        Extract the regularization path of a PLNnetwork
                        fit
compute_PLN_starting_point
                        Helper function for PLN initialization.
compute_ZIPLN_starting_point
                        Helper function for ZIPLN initialization.
compute_offset          Compute offsets from a count data using one of
                        several normalization schemes
extract_probs           Extract edge selection frequency in bootstrap
                        subsamples
fitted.PLNfit           Extracts model fitted values from objects
                        returned by 'PLN()' and its variants
fitted.PLNmixturefit    Extracts model fitted values from objects
                        returned by 'PLNmixture()' and its variants
fitted.ZIPLNfit         Extracts model fitted values from objects
                        returned by 'ZIPLN()' and its variants
getBestModel.PLNPCAfamily
                        Best model extraction from a collection of
                        models
getModel.PLNPCAfamily   Model extraction from a collection of models
logLik.PLNfit           Extract log-likelihood of a fitted PLN model
logLik.ZIPLNfit         Extract log-likelihood of a fitted ZIPLN model
microcosm               Cow microbiome data set
mollusk                 Mollusk data set
oaks                    Oaks amplicon data set
plot.Networkfamily      Display various outputs (goodness-of-fit
                        criteria, robustness, diagnostic) associated
                        with a collection of network fits (either
                        'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
plot.PLNLDAfit          LDA visualization (individual and/or variable
                        factor map(s)) for a 'PLNPCAfit' object
plot.PLNPCAfamily       Display the criteria associated with a
                        collection of PLNPCA fits (a PLNPCAfamily)
plot.PLNPCAfit          PCA visualization (individual and/or variable
                        factor map(s)) for a 'PLNPCAfit' object
plot.PLNfamily          Display the criteria associated with a
                        collection of PLN fits (a PLNfamily)
plot.PLNmixturefamily   Display the criteria associated with a
                        collection of PLNmixture fits (a
                        PLNmixturefamily)
plot.PLNmixturefit      Mixture visualization of a 'PLNmixturefit'
                        object
plot.PLNnetworkfit      Extract and plot the network (partial
                        correlation, support or inverse covariance)
                        from a 'PLNnetworkfit' object
plot.ZIPLNfit_sparse    Extract and plot the network (partial
                        correlation, support or inverse covariance)
                        from a 'ZIPLNfit_sparse' object
predict.PLNLDAfit       Predict group of new samples
predict.PLNfit          Predict counts of a new sample
predict.PLNmixturefit   Prediction for a 'PLNmixturefit' object
predict.ZIPLNfit        Predict counts of a new sample
predict_cond            Predict counts conditionally
prepare_data            Prepare data for use in PLN models
rPLN                    PLN RNG
scRNA                   Single cell RNA-seq data
sigma.PLNfit            Extract variance-covariance of residuals
                        'Sigma'
sigma.PLNmixturefit     Extract variance-covariance of residuals
                        'Sigma'
sigma.ZIPLNfit          Extract variance-covariance of residuals
                        'Sigma'
stability_selection     Compute the stability path by stability
                        selection
standard_error.PLNPCAfit
                        Component-wise standard errors of B
trichoptera             Trichoptera data set
vcov.PLNfit             Calculate Variance-Covariance Matrix for a
                        fitted 'PLN()' model object
