coef.PLNfit | Extract model coefficients |
coef.PLNLDAfit | Extracts model coefficients from objects returned by 'PLNLDA()' |
coef.PLNmixturefit | Extract model coefficients |
coefficient_path | Extract the regularization path of a PLNnetwork fit |
compute_offset | Compute offsets from a count data using one of several normalization schemes |
extract_probs | Extract edge selection frequency in bootstrap subsamples |
fisher | Fisher information matrix for Theta |
fisher.PLNfit | Fisher information matrix for Theta |
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 |
getBestModel | Best model extraction from a collection of models |
getBestModel.PLNmixturefamily | Best model extraction from a collection of models |
getBestModel.PLNnetworkfamily | Best model extraction from a collection of models |
getBestModel.PLNPCAfamily | Best model extraction from a collection of models |
getModel | Model extraction from a collection of models |
getModel.PLNmixturefamily | Model extraction from a collection of models |
getModel.PLNnetworkfamily | Model extraction from a collection of models |
getModel.PLNPCAfamily | Model extraction from a collection of models |
mollusk | Mollusk data set |
oaks | Oaks amplicon data set |
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 framework |
PLNLDA | Poisson lognormal model towards Linear Discriminant Analysis |
PLNLDAfit | An R6 Class to represent a PLNfit in a LDA framework |
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 |
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 covariance framework |
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.PLNfamily | Display the criteria associated with a collection of PLN fits (a PLNfamily) |
plot.PLNLDAfit | LDA visualization (individual and/or variable factor map(s)) for a 'PLNPCAfit' object |
plot.PLNmixturefamily | Display the criteria associated with a collection of PLNmixture fits (a PLNmixturefamily) |
plot.PLNmixturefit | Mixture visualization of a 'PLNmixturefit' object |
plot.PLNnetworkfamily | Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of PLNnetwork fits (a 'PLNnetworkfamily') |
plot.PLNnetworkfit | Extract and plot the network (partial correlation, support or inverse covariance) from a 'PLNnetworkfit' 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 |
predict.PLNfit | Predict counts of a new sample |
predict.PLNLDAfit | Predict group of new samples |
predict.PLNmixturefit | Prediction for a 'PLNmixturefit' object |
prepare_data | Prepare data for use in PLN models |
rPLN | PLN RNG |
sigma.PLNfit | Extract variance-covariance of residuals 'Sigma' |
sigma.PLNmixturefit | Extract variance-covariance of residuals 'Sigma' |
stability_selection | Compute the stability path by stability selection |
standard_error | Component-wise standard errors of Theta |
standard_error.PLNfit | Component-wise standard errors of Theta |
trichoptera | Trichoptera data set |
vcov.PLNfit | Calculate Variance-Covariance Matrix for a fitted 'PLN()' model object |