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"),
      reverse = FALSE,
      log.x = TRUE,
      stability = 0.9,
      ...
    )

### 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"`.
`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

### 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`.

### 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).

### Examples

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

    ## End(Not run)

[Package PLNmodels version 0.11.4 Index]