PLNmodels (version 0.9.5)

plot.PLNnetworkfamily: Display various ouputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of PLNnetwork fits (a PLNnetworkfamily)

Description

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

Usage

# S3 method for 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 PLNfamily

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 equals "criteria".

log.x

logical: should the x-axis be repsented 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

# NOT RUN {
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
# }
# NOT RUN {
plot(fits)
# }