## Top-level fitting functions

Set of functions to fit variants of the Poisson lognormal model

PLNmodels

PLNmodels

PLN()

Poisson lognormal model

PLNLDA()

Poisson lognormal model towards Linear Discriminant Analysis

PLNPCA()

Poisson lognormal model towards Principal Component Analysis

PLNnetwork()

Poisson lognormal model towards sparse network inference

PLNmixture()

Poisson lognormal mixture model

## Poisson lognormal fit

Description of the PLNfit object and methods for its manipulation. Any PLN variant in the package inherits from this class (PLNPCAfit, PLNnetworkfit, PLNLDAfit).

PLNfit

An R6 Class to represent a PLNfit in a standard, general framework

PLNfit_diagonal PLNLDAfit_spherical

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

PLN_param()

Control of a PLN fit

coef(<PLNfit>)

Extract model coefficients

vcov(<PLNfit>)

Calculate Variance-Covariance Matrix for a fitted PLN() model object

sigma(<PLNfit>)

Extract variance-covariance of residuals 'Sigma'

predict(<PLNfit>)

Predict counts of a new sample

predict_cond()

Predict counts conditionally

fitted(<PLNfit>)

Extracts model fitted values from objects returned by PLN() and its variants

standard_error()

Component-wise standard errors of B

## Linear discriminant analysis via a Poisson lognormal fit

Description of the PLNLDAfit object and methods for its manipulation.

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

PLNfit_diagonal 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

plot(<PLNLDAfit>)

LDA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

predict(<PLNLDAfit>)

Predict group of new samples

coef(<PLNLDAfit>)

Extracts model coefficients from objects returned by PLNLDA()

## Poisson Lognormal PCA fit

Description of the PLNPCAfit and PLNPCAfamily objects and methods for their manipulation.

PLNPCAfit

An R6 Class to represent a PLNfit in a PCA framework

PLNPCA_param()

Control of PLNPCA fit

plot(<PLNPCAfit>)

PCA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

PLNPCAfamily

An R6 Class to represent a collection of PLNPCAfit

plot(<PLNPCAfamily>)

Display the criteria associated with a collection of PLNPCA fits (a PLNPCAfamily)

getBestModel()

Best model extraction from a collection of models

getModel()

Model extraction from a collection of models

## Mixture of Poisson Lognormal fits

Description of the PLNmixturefit and PLNmixturefamily objects and methods for their manipulation.

PLNmixturefit

An R6 Class to represent a PLNfit in a mixture framework

PLNmixture_param()

Control of a PLNmixture fit

plot(<PLNmixturefit>)

Mixture visualization of a PLNmixturefit object

PLNmixturefamily

An R6 Class to represent a collection of PLNmixturefit

plot(<PLNmixturefamily>)

Display the criteria associated with a collection of PLNmixture fits (a PLNmixturefamily)

coef(<PLNmixturefit>)

Extract model coefficients

predict(<PLNmixturefit>)

Prediction for a PLNmixturefit object

sigma(<PLNmixturefit>)

Extract variance-covariance of residuals 'Sigma'

fitted(<PLNmixturefit>)

Extracts model fitted values from objects returned by PLNmixture() and its variants

getBestModel()

Best model extraction from a collection of models

getModel()

Model extraction from a collection of models

## Sparse Poisson lognormal fit and network

Description of the PLNnetworkfit and PLNnetworkfamily objects and methods for their manipulation.

PLNnetworkfit

An R6 Class to represent a PLNfit in a sparse inverse covariance framework

PLNnetwork_param()

Control of PLNnetwork fit

plot(<PLNnetworkfit>)

Extract and plot the network (partial correlation, support or inverse covariance) from a PLNnetworkfit object

PLNnetworkfamily

An R6 Class to represent a collection of PLNnetworkfit

plot(<PLNnetworkfamily>)

Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of PLNnetwork fits (a PLNnetworkfamily)

getBestModel()

Best model extraction from a collection of models

getModel()

Model extraction from a collection of models

coefficient_path()

Extract the regularization path of a PLNnetwork fit

stability_selection()

Compute the stability path by stability selection

extract_probs()

Extract edge selection frequency in bootstrap subsamples

## Other functions and objects

prepare_data()

Prepare data for use in PLN models

compute_offset()

Compute offsets from a count data using one of several normalization schemes

PLNfamily

An R6 Class to represent a collection of PLNfit

plot(<PLNfamily>)

Display the criteria associated with a collection of PLN fits (a PLNfamily)

rPLN()

PLN RNG

## Data sets

trichoptera

Trichoptera data set

oaks

Oaks amplicon data set

barents

Barents fish data set

mollusk

Mollusk data set