Poisson Lognormal Models

coefficient_path | Extract the regularization path of a PLNnetwork fit |

coef.PLNfit | Extract model coefficients |

coef.PLNLDAfit | Extracts model coefficients from objects returned by 'PLNLDA' |

compute_offset | Compute offsets from a count data using one of several... |

extract_probs | Extract edge selection frequency in bootstrap subsamples |

fisher | Fisher information matrix for Theta |

fitted.PLNfit | Extracts model fitted values from objects returned by 'PLN'... |

getBestModel | Best model extraction from a collection of models |

getModel | Model extraction from a collection of models |

mollusk | Mollusk data set |

pipe | Pipe operator |

PLN | Poisson lognormal model |

PLNfit | An R6 Class to represent a PLNfit in a standard, general... |

PLNLDA | Poisson lognormal model towards Linear Disciminant Analysis |

PLNLDAfit | An R6 Class to represent a PLNfit in a LDA framework |

PLNmodels | PLNmodels |

PLNnetwork | Poisson lognormal model towards sparse network inference |

PLNnetworkfamily | An R6 Class to represent a collection of PLNnetworkfit |

PLNnetworkfit | An R6 Class to represent a PLNfit in a sparse inverse... |

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 |

plot.PLNLDAfit | LDA vizualiation (individual and/or variable factor map(s))... |

plot.PLNnetworkfamily | Display various ouputs (goodness-of-fit criteria, robustness,... |

plot.PLNnetworkfit | Extract and plot the network (aprtial correlation, support or... |

plot.PLNPCAfamily | Display the criteria associated with a collection of PLNPCA... |

plot.PLNPCAfit | PCA vizualiation (individual and/or variable factor map(s))... |

predict.PLNfit | Predict counts of a new sample |

predict.PLNLDAfit | Predict group of new samples |

prepare_data | Prepare data for use in PLN models |

prepare_data_from_biom | Prepare data for use in PLN models from a biom object |

prepare_data_from_phyloseq | Prepare data for use in PLN models from a phyloseq object |

rPLN | PLN RNG |

sigma.PLNfit | Extract variance-covariance of residuals 'Sigma' |

stability_selection | Compute the stability path by stability selection |

standard_error | Component-wise standard errors of Theta |

trichoptera | Trichoptera data set |

vcov.PLNfit | Calculate Variance-Covariance Matrix for a fitted 'PLN' model... |

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