Poisson Lognormal Models

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 |

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