PLNPCAfamily {PLNmodels}R Documentation

An R6 Class to represent a collection of PLNPCAfit

Description

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

This class comes with a set of methods, some of them being useful for the user: See the documentation for getBestModel(), getModel() and plot().

Super class

PLNmodels::PLNfamily -> PLNPCAfamily

Active bindings

ranks

the dimensions of the successively fitted models

Methods

Public methods

Inherited methods

Method new()

Initialize all models in the collection.

Usage
PLNPCAfamily$new(
  ranks,
  responses,
  covariates,
  offsets,
  weights,
  model,
  xlevels,
  control
)
Arguments
ranks

the dimensions of the successively fitted models

responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

weights

the vector of observation weights

model

model used for fitting, extracted from the formula in the upper-level call

xlevels

named listed of factor levels included in the models, extracted from the formula in the upper-level call and used for predictions.

control

a list for controlling the optimization. See details.

Method optimize()

Call to the C++ optimizer on all models of the collection

Usage
PLNPCAfamily$optimize(control)
Arguments
control

a list for controlling the optimization. See details.

Method getBestModel()

Extract best model in the collection

Usage
PLNPCAfamily$getBestModel(crit = c("BIC", "ICL", "R_squared"))
Arguments
crit

a character for the criterion used to performed the selection. Either "BIC", "ICL", or "R_squared". Default is BIC

Returns

a PLNPCAfit object

Method plot()

Lineplot of selected criteria for all models in the collection

Usage
PLNPCAfamily$plot(criteria = c("loglik", "BIC", "ICL"), annotate = TRUE)
Arguments
criteria

A valid model selection criteria for the collection of models. Any of "loglik", "BIC" or "ICL" (all).

annotate

Logical. Should R2 be added to the plot (defaults to TRUE)

Returns

A ggplot2 object

Method show()

User friendly print method

Usage
PLNPCAfamily$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNPCAfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNPCA(), the class PLNPCAfit()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
class(myPCAs)
[Package PLNmodels version 0.10.6 Index]