PLNmodels (version 1.2.2)

plot.Networkfamily: Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either PLNnetworkfamily or ZIPLNnetworkfamily)

Description

Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either PLNnetworkfamily or ZIPLNnetworkfamily)

Usage

# S3 method for Networkfamily
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)
# S3 method for PLNnetworkfamily
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)
# S3 method for ZIPLNnetworkfamily
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)

Value

Produces either a diagnostic plot (with type = 'diagnostic'), a stability plot (with type = 'stability') or the evolution of the criteria of the different models considered (with type = 'criteria', the default).

Arguments

x

an R6 object with class PLNnetworkfamily or ZIPLNnetworkfamily

type

a character, either "criteria", "stability" or "diagnostic" for the type of plot.

criteria

Vector of criteria to plot, to be selected among "loglik" (log-likelihood), "BIC", "ICL", "R_squared", "EBIC" and "pen_loglik" (penalized log-likelihood). Default is c("loglik", "pen_loglik", "BIC", "EBIC"). Only used when type = "criteria".

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.

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.

...

additional parameters for S3 compatibility. Not used

Functions

• plot(PLNnetworkfamily): Display various outputs associated with a collection of network fits

• plot(ZIPLNnetworkfamily): Display various outputs associated with a collection of network fits

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)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
if (FALSE) {
plot(fits)
}