PLNmixturefamily {PLNmodels} | R Documentation |
An R6 Class to represent a collection of PLNmixturefit
Description
The function PLNmixture()
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
-> PLNmixturefamily
Active bindings
clusters
vector indicating the number of clusters considered is the successively fitted models
Methods
Public methods
Inherited methods
Method new()
helper function for forward smoothing: split a group
Initialize all models in the collection.
Usage
PLNmixturefamily$new( clusters, responses, covariates, offsets, formula, control )
Arguments
clusters
the dimensions of the successively fitted models
responses
the matrix of responses common to every models
covariates
the matrix of covariates common to every models
offsets
the matrix of offsets common to every models
formula
model formula used for fitting, extracted from the formula in the upper-level call
control
a list for controlling the optimization. See details.
control
a list for controlling the optimization. See details.
Method optimize()
Call to the optimizer on all models of the collection
Usage
PLNmixturefamily$optimize(config)
Arguments
config
a list for controlling the optimization
Method smooth()
function to restart clustering to avoid local minima by smoothing the loglikelihood values as a function of the number of clusters
Usage
PLNmixturefamily$smooth(control)
Arguments
control
a list to control the smoothing process
Method plot()
Lineplot of selected criteria for all models in the collection
Usage
PLNmixturefamily$plot(criteria = c("loglik", "BIC", "ICL"), reverse = FALSE)
Arguments
criteria
A valid model selection criteria for the collection of models. Any of "loglik", "BIC" or "ICL" (all).
reverse
A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood..
Returns
A ggplot2
object
Method plot_objective()
Plot objective value of the optimization problem along the penalty path
Usage
PLNmixturefamily$plot_objective()
Returns
a ggplot
graph
Method getBestModel()
Extract best model in the collection
Usage
PLNmixturefamily$getBestModel(crit = c("BIC", "ICL", "loglik"))
Arguments
crit
a character for the criterion used to performed the selection. Either "BIC", "ICL" or "loglik". Default is
ICL
Returns
a PLNmixturefit
object
Method show()
User friendly print method
Usage
PLNmixturefamily$show()
Method print()
User friendly print method
Usage
PLNmixturefamily$print()
Method clone()
The objects of this class are cloneable with this method.
Usage
PLNmixturefamily$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.
See Also
The function PLNmixture
, the class PLNmixturefit