R: Display various outputs (goodness-of-fit criteria,...

plot.PLNnetworkfamily {PLNmodels}

R Documentation

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

Description

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

Usage

## S3 method for class 'PLNnetworkfamily'
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  log.x = TRUE,
  stability = 0.9,
  annotate = TRUE,
  ...
)

Arguments

`x`	an R6 object with class `PLNnetworkfamily`
`type`	a character, either "criteria", "stability" or "diagnostic" for the type of plot.
`criteria`	vector of characters. The criteria to plot in c("loglik", "BIC", "ICL", "R_squared", "EBIC", "pen_loglik"). Default is c("loglik", "pen_loglik", "BIC", "EBIC"). Only relevant when `type = "criteria"`.
`log.x`	logical: should the x-axis be represented in log-scale? Default is `TRUE`.
`stability`	scalar: the targeted level of stability in stability plot. Default is .9.
`annotate`	logical: should the value of approximated R squared be added to the plot of criteria? Default is `TRUE`.
`...`	additional parameters for S3 compatibility. Not used

Value

Produces a plot representing the evolution of the criteria of the different models considered, highlighting the best model in terms of BIC and EBIC (the greater, the better). These criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model loglikelihood.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
## Not run: 
plot(fits)

## End(Not run)