| barents | Barents fish data set |
| coefficient_path | Extract the regularization path of a PLNnetwork fit |
| coef.PLNfit | Extract model coefficients |
| coef.PLNLDAfit | Extracts model coefficients from objects returned by... |
| coef.PLNmixturefit | Extract model coefficients |
| coef.ZIPLNfit | Extract model coefficients |
| compute_offset | Compute offsets from a count data using one of several... |
| compute_PLN_starting_point | Helper function for PLN initialization. |
| extract_probs | Extract edge selection frequency in bootstrap subsamples |
| fitted.PLNfit | Extracts model fitted values from objects returned by 'PLN()'... |
| fitted.PLNmixturefit | Extracts model fitted values from objects returned by... |
| fitted.ZIPLNfit | Extracts model fitted values from objects returned by... |
| getBestModel | Best model extraction from a collection of models |
| getModel | Model extraction from a collection of models |
| mollusk | Mollusk data set |
| Networkfamily | An R6 Class to virtually represent a collection of network... |
| oaks | Oaks amplicon data set |
| pipe | Pipe operator |
| PLN | Poisson lognormal model |
| PLNfamily | An R6 Class to represent a collection of PLNfit |
| PLNfit | An R6 Class to represent a PLNfit in a standard, general... |
| PLNfit_diagonal | An R6 Class to represent a PLNfit in a standard, general... |
| PLNfit_fixedcov | An R6 Class to represent a PLNfit in a standard, general... |
| PLNfit_spherical | An R6 Class to represent a PLNfit in a standard, general... |
| PLNLDA | Poisson lognormal model towards Linear Discriminant Analysis |
| 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... |
| PLNLDA_param | Control of a PLNLDA fit |
| PLNmixture | Poisson lognormal mixture model |
| PLNmixturefamily | An R6 Class to represent a collection of PLNmixturefit |
| PLNmixturefit | An R6 Class to represent a PLNfit in a mixture framework |
| PLNmixture_param | Control of a PLNmixture fit |
| PLNmodels-package | PLNmodels: Poisson Lognormal Models |
| PLNnetwork | Sparse Poisson lognormal model for network inference |
| PLNnetworkfamily | An R6 Class to represent a collection of 'PLNnetworkfit's |
| PLNnetworkfit | An R6 Class to represent a PLNfit in a sparse inverse... |
| PLNnetwork_param | Control of PLNnetwork fit |
| PLN_param | Control of a PLN fit |
| PLNPCA | Poisson lognormal model towards Principal Component Analysis |
| PLNPCAfamily | An R6 Class to represent a collection of PLNPCAfit |
| PLNPCAfit | An R6 Class to represent a PLNfit in a PCA framework |
| PLNPCA_param | Control of PLNPCA fit |
| plot.Networkfamily | Display various outputs (goodness-of-fit criteria,... |
| plot.PLNfamily | Display the criteria associated with a collection of PLN fits... |
| plot.PLNLDAfit | LDA visualization (individual and/or variable factor map(s))... |
| plot.PLNmixturefamily | Display the criteria associated with a collection of... |
| plot.PLNmixturefit | Mixture visualization of a 'PLNmixturefit' object |
| plot.PLNnetworkfit | Extract and plot the network (partial correlation, support or... |
| plot.PLNPCAfamily | Display the criteria associated with a collection of PLNPCA... |
| plot.PLNPCAfit | PCA visualization (individual and/or variable factor map(s))... |
| plot.ZIPLNfit_sparse | Extract and plot the network (partial correlation, support or... |
| predict_cond | Predict counts conditionally |
| predict.PLNfit | Predict counts of a new sample |
| predict.PLNLDAfit | Predict group of new samples |
| predict.PLNmixturefit | Prediction for a 'PLNmixturefit' object |
| predict.ZIPLNfit | Predict counts of a new sample |
| 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 | Component-wise standard errors of B |
| trichoptera | Trichoptera data set |
| vcov.PLNfit | Calculate Variance-Covariance Matrix for a fitted 'PLN()'... |
| ZIPLN | Zero Inflated Poisson lognormal model |
| ZIPLNfit | An R6 Class to represent a ZIPLNfit |
| ZIPLNfit_diagonal | An R6 Class to represent a ZIPLNfit in a standard, general... |
| ZIPLNfit_fixed | An R6 Class to represent a ZIPLNfit in a standard, general... |
| ZIPLNfit_sparse | An R6 Class to represent a ZIPLNfit in a standard, general... |
| ZIPLNfit_spherical | An R6 Class to represent a ZIPLNfit in a standard, general... |
| ZIPLNnetwork | Zero Inflated Sparse Poisson lognormal model for network... |
| ZIPLNnetworkfamily | An R6 Class to represent a collection of ZIPLNnetwork |
| ZIPLNnetwork_param | Control of ZIPLNnetwork fit |
| ZIPLN_param | Control of a ZIPLN fit |
