check_model() does not produce Uniformity of Residuals plot for binomial models

[mz555]

I was playing with a glm() to check how various packages check for assumptions, and I saw that for binomial models it does not produce the QQ plot (although the documentation says it should).

Reproducible example

data(mtcars)

library(performance)
model <- glm(am ~ wt + cyl, data = mtcars, family = binomial)

check_model(model)
check_residuals(model)

check_models() produces this:

The function for it seems to work, as if you call check_residuals() directly it says:
> check_residuals(model) OK: Simulated residuals appear as uniformly distributed (p = 0.912).

Not sure why there is no plot. Maybe I am making a mistake somewhere.

[strengejacke]

I think the problem is that the lower left panel is empty.

[strengejacke]

See https://easystats.github.io/see/articles/performance.html#logistic-regression-model

[Ecosantos]

Same here but with poisson glm and negative binomial glm. However, after having installed qqplotr package it worked!

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

[strengejacke]

Can you post your session info?

[Ecosantos]

Hi @strengejacke.

here is the current session info, which is after I have installed qqplotr_0.0.6

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default

oocale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.utf8

time zone: America/Sao_Paulo
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] performance_0.12.2

loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 robustbase_0.99-3
[4] qqconf_1.3.2 bitops_1.0-8 lattice_0.22-6
[7] pracma_2.4.4 lme4_1.1-35.5 magrittr_2.0.3
[10] caTools_1.18.2 grid_4.4.1 iterators_1.0.14
[13] foreach_1.5.2 doParallel_1.0.17 Matrix_1.7-0
[16] opdisDownsampling_1.0.1 ggrepel_0.9.5 mgcv_1.9-1
[19] fansi_1.0.6 scales_1.3.0 codetools_0.2-20
[22] cli_3.6.3 rlang_1.1.4 pbmcapply_1.5.1
[25] munsell_0.5.1 splines_4.4.1 withr_3.0.1
[28] tools_4.4.1 datawizard_0.12.2 parallel_4.4.1
[31] nloptr_2.1.1 see_0.8.5 minqa_1.2.7
[34] dplyr_1.1.4 colorspace_2.1-1 ggplot2_3.5.1
[37] bayestestR_0.14.0 boot_1.3-30 vctrs_0.6.5
[40] R6_2.5.1 lifecycle_1.0.4 MASS_7.3-61
[43] insight_0.20.2 pkgconfig_2.0.3 pillar_1.9.0
[46] gtable_0.3.5 glue_1.7.0 Rcpp_1.0.13
[49] DEoptimR_1.1-3 tibble_3.2.1 tidyselect_1.2.1
[52] farver_2.1.2 patchwork_1.2.0 nlme_3.1-165
[55] labeling_0.4.3 qqplotr_0.0.6 compiler_4.4.1
[58] twosamples_2.0.1

[Issengard83]

I discovered this bug yesterday when several of my students were unable to generate a QQ plot for logistic regression models. After replicating the issue myself, I confirmed the problem. I attempted to adjust the options in check_model() and updated both the performance package and all other installed packages, but the issue persisted:

The weird part was that the code didn't produce any warning or error messages, unlike when other dependencies are missing. However, after running simulate_residuals() %>% plot(), the warning message finally appeared:

> simulate_residuals(fit1) %>% plot()
For confidence bands, please install `qqplotr`.
Warning messages:
1: Computation failed in `stat_qq()`.
Caused by error in `distribution()`:
! could not find function "distribution" 
2: Computation failed in `stat_qq_line()`.
Caused by error in `distribution()`:
! could not find function "distribution" 

And here´s the plot:

Below you can find my session info. However, we tried in several computers at work and get the same problem.

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=Spanish_Argentina.utf8  LC_CTYPE=Spanish_Argentina.utf8   
[3] LC_MONETARY=Spanish_Argentina.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Spanish_Argentina.utf8    

time zone: America/Buenos_Aires
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.3    forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4       
 [5] purrr_1.0.2        readr_2.1.5        tidyr_1.3.1        tibble_3.2.1      
 [9] ggplot2_3.5.1      tidyverse_2.0.0    janitor_2.2.0      skimr_2.1.5       
[13] dlookr_0.6.3       gtsummary_1.7.2    performance_0.12.0

loaded via a namespace (and not attached):
 [1] gridExtra_2.3           rlang_1.1.4             magrittr_2.0.3         
 [4] hrbrthemes_0.8.7        snakecase_0.11.1        compiler_4.4.1         
 [7] mgcv_1.9-1              systemfonts_1.1.0       vctrs_0.6.5            
[10] sysfonts_0.8.9          httpcode_0.3.0          pkgconfig_2.0.3        
[13] crayon_1.5.3            fastmap_1.2.0           labeling_0.4.3         
[16] utf8_1.2.4              promises_1.3.0          rmarkdown_2.27         
[19] tzdb_0.4.0              nloptr_2.1.0            bit_4.0.5              
[22] xfun_0.45               showtext_0.9-7          jsonlite_1.8.8         
[25] later_1.3.2             parallel_4.4.1          R6_2.5.1               
[28] stringi_1.8.4           pagedown_0.20           boot_1.3-30            
[31] extrafontdb_1.0         Rcpp_1.0.12             knitr_1.47             
[34] DHARMa_0.4.6            base64enc_0.1-3         extrafont_0.19         
[37] httpuv_1.6.15           Matrix_1.7-0            splines_4.4.1          
[40] timechange_0.3.0        tidyselect_1.2.1        rstudioapi_0.16.0      
[43] curl_5.2.1              lattice_0.22-6          shiny_1.8.1.1          
[46] withr_3.0.0             bayestestR_0.13.2       evaluate_0.24.0        
[49] xml2_1.3.6              pillar_1.9.0            insight_0.20.1         
[52] generics_0.1.3          vroom_1.6.5             hms_1.1.3              
[55] munsell_0.5.1           scales_1.3.0            minqa_1.2.7            
[58] xtable_1.8-4            glue_1.7.0              gdtools_0.3.7          
[61] tools_4.4.1             gfonts_0.2.0            see_0.8.4              
[64] lme4_1.1-35.4           reactable_0.4.4         grid_4.4.1             
[67] Rttf2pt1_1.3.12         datawizard_0.11.0       colorspace_2.1-0       
[70] nlme_3.1-164            patchwork_1.2.0         repr_1.1.7             
[73] showtextdb_3.0          cli_3.6.3               kableExtra_1.4.0       
[76] fontBitstreamVera_0.1.1 fansi_1.0.6             broom.helpers_1.15.0   
[79] viridisLite_0.4.2       svglite_2.1.3           gt_0.10.1              
[82] gtable_0.3.5            digest_0.6.35           fontquiver_0.2.1       
[85] ggrepel_0.9.5           crul_1.4.2              farver_2.1.2           
[88] htmlwidgets_1.6.4       htmltools_0.5.8.1       lifecycle_1.0.4        
[91] mime_0.12               fontLiberation_0.1.0    bit64_4.0.5            
[94] MASS_7.3-60.2

[strengejacke]

Strange. Do you have a traceback()?

[strengejacke]

Short remark: issue is probably somewhere here:

see/R/plot.performance_simres.R

Lines 108 to 128 in b294a18

	} else {
	insight::format_alert("For confidence bands, please install `qqplotr`.")
	qq_stuff <- list(
	ggplot2::geom_qq(
	shape = 16,
	stroke = 0,
	distribution = dfun,
	dparams = dp,
	size = size_point,
	colour = colors[2]
	),
	ggplot2::geom_qq_line(
	linewidth = size_line,
	colour = colors[1],
	na.rm = TRUE,
	distribution = dfun,
	dparams = dp
	)
	)
	y_lab <- "Sample Quantiles"
	}

[strengejacke]

Thanks, should be fixed in #363