# Poisson Lognormal Models

## Documentation for package ‘PLNmodels’ version 1.2.0

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

## Help Pages

barents | Barents fish data set
coef.PLNfit | Extract model coefficients
coef.PLNLDAfit | Extracts model coefficients from objects returned by 'PLNLDA()'
coef.PLNmixturefit | Extract model coefficients
coef.ZIPLNfit | 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
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()' and its variants
fitted.PLNmixturefit | Extracts model fitted values from objects returned by 'PLNmixture()' and its variants
fitted.ZIPLNfit | Extracts model fitted values from objects returned by 'ZIPLN()' and its variants
getBestModel | Best model extraction from a collection of models
getBestModel.Networkfamily | 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
getBestModel.ZIPLNnetworkfamily | Best model extraction from a collection of models
getModel | Model extraction from a collection of models
getModel.Networkfamily | 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
getModel.ZIPLNnetworkfamily | Model extraction from a collection of models
mollusk | Mollusk data set
Networkfamily | An R6 Class to virtually represent a collection of network fits
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
PLNfit_diagonal | An R6 Class to represent a PLNfit in a standard, general framework, with diagonal residual covariance
PLNfit_fixedcov | An R6 Class to represent a PLNfit in a standard, general framework, with fixed (inverse) residual covariance
PLNfit_spherical | An R6 Class to represent a PLNfit in a standard, general framework, with spherical residual covariance
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 diagonal covariance
PLNLDAfit_spherical | An R6 Class to represent a PLNfit in a standard, general framework, with diagonal residual covariance
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
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 covariance framework
PLNnetwork_param | Control of PLNnetwork 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
PLN_param | Control of a PLN fit
plot.Networkfamily | Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
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 network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
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
plot.ZIPLNfit_sparse | Extract and plot the network (partial correlation, support or inverse covariance) from a 'ZIPLNfit_sparse' object
plot.ZIPLNnetworkfamily | Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
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
predict_cond | Predict counts conditionally
predict_cond.PLNfit | Predict counts conditionally
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
standard_error.PLNfit | Component-wise standard errors of B
standard_error.PLNfit_fixedcov | Component-wise standard errors of B
standard_error.PLNmixturefit | Component-wise standard errors of B
standard_error.PLNnetworkfit | Component-wise standard errors of B
standard_error.PLNPCAfit | Component-wise standard errors of B
trichoptera | Trichoptera data set
vcov.PLNfit | Calculate Variance-Covariance Matrix for a fitted 'PLN()' model object
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 framework, with diagonal residual covariance
ZIPLNfit_fixed | An R6 Class to represent a ZIPLNfit in a standard, general framework, with fixed (inverse) residual covariance
ZIPLNfit_sparse | An R6 Class to represent a ZIPLNfit in a standard, general framework, with sparse inverse residual covariance
ZIPLNfit_spherical | An R6 Class to represent a ZIPLNfit in a standard, general framework, with spherical residual covariance
ZIPLNnetwork | Zero Inflated Sparse Poisson lognormal model for network inference
ZIPLNnetworkfamily | An R6 Class to represent a collection of ZIPLNnetwork
ZIPLNnetwork_param | Control of ZIPLNnetwork fit
ZIPLN_param | Control of a ZIPLN fit