Revising check_model()

[strengejacke]

Fixes #697

TODO or to check

• wonky plot from check_model() on a glmmTMB example  #654
• Unnecessary checks in check_model for NB models #500
• check_overdispersion underestimates dispersion in mixed models #464
• Improving check_model() for GLMs #376
• check_autocorrelation of residuals #274
• detrend in Q-Q plots (DHARMa implementation for new check_residuals() function #643 (comment))
• plot() for check_overdispersion()

[strengejacke]

@bwiernik and @mccarthy-m-g - I think the implementation works quite well now for the first methods. The plot() method works fine for the Q-Q plots (easystats/see#329). Things we should consider:

• We would have to update the plot for overdispersion/zero-inflation checks (see DHARMa implementation for new check_residuals() function #643 (comment)). This is still based on the classical residuals, not the simulated ones. I have played around with revising the current code, copying the function .diag_overdispersion into a new .new_diag_overdispersion (see

  performance/R/check_model_diagnostics.R

  Line 296 in ad60db1

  .new_diag_overdispersion <- function(model, ...) {

  ). This did not really work - do you have any ideas how we can have new plots for overdispersion/zero-inflation? I found these plots quite informative and would like to keep them, beside the Q-Q plot. See also discussion here.

• check_zeroinflation() and check_overdispersion() now rely on simulate_residuals() for zero-inflated or negative binomial models etc., so only the really "simple" models that returned identical results to DHARMa-tests still use the old code. Only Poisson mixed models also use the "old" code, which still could be inaccurate (see check_overdispersion underestimates dispersion in mixed models #464) - do we want to use simulate_residuals() in general for mixed models when calling check_zeroinflation() and check_overdispersion()?

• How do we want to deal with y axis limits when detrend = TRUE in Q-Q plots? (see DHARMa implementation for new check_residuals() function #643 (comment))

• A method for check_autocorrelation() is not yet implemented. Since the DHARMa tests require additional information, I'm not sure about how to best implement such methods.

[codecov]

Codecov Report

Attention: Patch coverage is 12.50000% with 7 lines in your changes missing coverage. Please review.

Project coverage is 57.73%. Comparing base (6e1eb60) to head (2be53b8).
Report is 3 commits behind head on main.

Files	Patch %	Lines
R/check_model_diagnostics.R	12.50%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #698      +/-   ##
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+ Coverage   57.69%   57.73%   +0.03%     
==========================================
  Files          87       87              
  Lines        6444     6464      +20     
==========================================
+ Hits         3718     3732      +14     
- Misses       2726     2732       +6     

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