# Poisson Lognormal Models

## Documentation for package ‘PLNmodels’ version 0.9.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

coef.PLNfit | Extract model coefficients
coef.PLNLDAfit | Extracts model coefficients from objects returned by 'PLNLDA'
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
getBestModel | 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.PLNnetworkfamily | Model extraction from a collection of models
getModel.PLNPCAfamily | Model extraction from a collection of models
mollusk | Mollusk 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 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 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.PLNLDAfit | LDA vizualiation (individual and/or variable factor map(s)) for a 'PLNPCAfit' object
plot.PLNnetworkfamily | Display various ouputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of PLNnetwork fits (a PLNnetworkfamily)
plot.PLNnetworkfit | Extract and plot the network (aprtial 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 vizualiation (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
prepare_data | Prepare data for use in PLN models
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
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