PLNnetworkfamily {PLNmodels}

An R6 Class to represent a collection of PLNnetworkfits

Description

The function PLNnetwork() produces an instance of this class.

This class comes with a set of methods mostly used to compare network fits (in terms of goodness of fit) or extract one from the family (based on penalty parameter and/or goodness of it). See the documentation for getBestModel(), getModel() and plot() for the user-facing ones.

Super classes

PLNmodels::PLNfamily -> PLNmodels::Networkfamily -> PLNnetworkfamily

Methods

Public methods

• PLNnetworkfamily$new()

• PLNnetworkfamily$stability_selection()

• PLNnetworkfamily$clone()

Inherited methods

• PLNmodels::PLNfamily$getModel()
• PLNmodels::PLNfamily$postTreatment()
• PLNmodels::PLNfamily$print()
• PLNmodels::Networkfamily$coefficient_path()
• PLNmodels::Networkfamily$getBestModel()
• PLNmodels::Networkfamily$optimize()
• PLNmodels::Networkfamily$plot()
• PLNmodels::Networkfamily$plot_objective()
• PLNmodels::Networkfamily$plot_stars()
• PLNmodels::Networkfamily$show()

Method new()

Initialize all models in the collection

Usage

PLNnetworkfamily$new(penalties, data, control)

Arguments

penalties

a vector of positive real number controlling the level of sparsity of the underlying network.

data

a named list used internally to carry the data matrices

control

a list for controlling the optimization.

Returns

Update current PLNnetworkfit with smart starting values

Method stability_selection()

Compute the stability path by stability selection

Usage

PLNnetworkfamily$stability_selection(
  subsamples = NULL,
  control = PLNnetwork_param()
)

Arguments

subsamples

a list of vectors describing the subsamples. The number of vectors (or list length) determines the number of subsamples used in the stability selection. Automatically set to 20 subsamples with size 10*sqrt(n) if n >= 144 and 0.8*n otherwise following Liu et al. (2010) recommendations.

control

a list controlling the main optimization process in each call to PLNnetwork(). See PLNnetwork() and PLN_param() for details.

Method clone()

The objects of this class are cloneable with this method.

Usage

PLNnetworkfamily$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

The function PLNnetwork(), the class PLNnetworkfit

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
class(fits)