PLNmodels (version 1.2.2)

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

Description

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

Usage

# S3 method for PLNPCAfamily
plot(x, criteria = c("loglik", "BIC", "ICL"), reverse = FALSE, ...)

Value

Produces a plot representing the evolution of the criteria of the different models considered, highlighting the best model in terms of BIC and ICL (see details).

Arguments

x

an R6 object with class PLNPCAfamily

criteria

vector of characters. The criteria to plot in c("loglik", "BIC", "ICL"). Default is c("loglik", "BIC", "ICL").

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.

...

additional parameters for S3 compatibility. Not used

Details

The BIC and ICL criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model log-likelihood. You can change this direction and use the alternate form '-2*loglik + penalty', as some authors do, by setting reverse = TRUE.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
if (FALSE) {
plot(myPCAs)
}