# Poisson Lognormal Models

## Documentation for package ‘PLNmodels’ version 1.3.0

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

## Help Pages

A B C E F G I L M N O P R S T V Z

## -- A --

AIC.PLNfit | Akaike Information Criterion for a fitted PLN model
AIC.ZIPLNfit | Akaike Information Criterion for a fitted ZIPLN model

## -- B --

barents | Barents fish data set
BIC.PLNfit | Bayesian Information Criterion for a fitted PLN model
BIC.ZIPLNfit | Bayesian Information Criterion for a fitted ZIPLN model

## -- C --

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.
compute_ZIPLN_starting_point | Helper function for ZIPLN initialization.

## -- E --

extract_probs | Extract edge selection frequency in bootstrap subsamples

## -- F --

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

## -- G --

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

## -- I --

ICL | Integrated Classification Likelihood
ICL.PLNfit | Integrated Classification Likelihood
ICL.ZIPLNfit | Integrated Classification Likelihood

## -- L --

logLik.PLNfit | Extract log-likelihood of a fitted PLN model
logLik.ZIPLNfit | Extract log-likelihood of a fitted ZIPLN model

## -- M --

microcosm | Cow microbiome data set
mollusk | Mollusk data set

## -- N --

Networkfamily | An R6 Class to virtually represent a collection of network fits

## -- O --

oaks | Oaks amplicon data set

## -- P --

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_genpop | An R6 Class to represent a PLNfit with a residual covariance structured by a fixed correlation matrix (e.g. a genetic relationship matrix), motivated by population genetics
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

## -- R --

rPLN | PLN RNG

## -- S --

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

## -- T --

trichoptera | Trichoptera data set

## -- V --

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

## -- Z --

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