FR: an option to automatic adding reference row for factors

[iago-pssjd]

I know it is possible doing that by hand: https://stackoverflow.com/questions/64989689/how-to-add-a-text-line-to-your-regression-table-above-one-coefficient-using-the

But it would be great if it was possible through something like reference = TRUE

[vincentarelbundock]

This is already possible by using include_reference=TRUE if you are using the latest version of the parameters package.

[iago-pssjd]

Thanks @vincentarelbundock However, doing this, coef_rename =TRUE has no effect

[vincentarelbundock]

On my computer, this seems to work:

library(modelsummary)
mod <- lm(mpg ~ hp + factor(cyl), mtcars)
modelsummary(mod, coef_rename = TRUE, include_reference = TRUE)

+-------------+---------+
|             | (1)     |
+=============+=========+
| (Intercept) | 28.650  |
+-------------+---------+
|             | (1.588) |
+-------------+---------+
| hp          | -0.024  |
+-------------+---------+
|             | (0.015) |
+-------------+---------+
| cyl [4]     | -       |
+-------------+---------+
| cyl [6]     | -5.968  |
+-------------+---------+
|             | (1.639) |
+-------------+---------+
| cyl [8]     | -8.521  |
+-------------+---------+
|             | (2.326) |
+-------------+---------+
| Num.Obs.    | 32      |
+-------------+---------+
| R2          | 0.754   |
+-------------+---------+
| R2 Adj.     | 0.727   |
+-------------+---------+
| AIC         | 169.9   |
+-------------+---------+
| BIC         | 177.2   |
+-------------+---------+
| Log.Lik.    | -79.948 |
+-------------+---------+
| F           | 28.585  |
+-------------+---------+
| RMSE        | 2.94    |
+-------------+---------+ 

[iago-pssjd]

Not in any of both I use (yesterday, Windows 10 computer at job, now Linux at home): I would expect in next modelsummary table appear Gross horsepower instead of hp

> mtcars2 <- mtcars
> attr(mtcars2$hp, "label") <- "Gross horsepower"
> library(modelsummary)
`modelsummary` 2.0.0 now uses `tinytable` as its default table-drawing backend. Learn more
  at: https://vincentarelbundock.github.io/tinytable/

Revert to `kableExtra` for one session:

  options(modelsummary_factory_default = 'kableExtra')

Change the default backend persistently:

  config_modelsummary(factory_default = 'gt')

Silence this message forever:

  config_modelsummary(startup_message = FALSE)
> mod <- lm(mpg ~ hp + factor(cyl), mtcars2)
> modelsummary(mod, coef_rename = TRUE, include_reference = TRUE)

+-------------+---------+
|             | (1)     |
+=============+=========+
| (Intercept) | 28.650  |
+-------------+---------+
|             | (1.588) |
+-------------+---------+
| hp          | -0.024  |
+-------------+---------+
|             | (0.015) |
+-------------+---------+
| cyl [4]     | -       |
+-------------+---------+
| cyl [6]     | -5.968  |
+-------------+---------+
|             | (1.639) |
+-------------+---------+
| cyl [8]     | -8.521  |
+-------------+---------+
|             | (2.326) |
+-------------+---------+
| Num.Obs.    | 32      |
+-------------+---------+
| R2          | 0.754   |
+-------------+---------+
| R2 Adj.     | 0.727   |
+-------------+---------+
| AIC         | 169.9   |
+-------------+---------+
| BIC         | 177.2   |
+-------------+---------+
| Log.Lik.    | -79.948 |
+-------------+---------+
| F           | 28.585  |
+-------------+---------+
| RMSE        | 2.94    |
+-------------+---------+ 
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

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

other attached packages:
[1] modelsummary_2.0.0

loaded via a namespace (and not attached):
 [1] Matrix_1.6-5        future.apply_1.11.2 compiler_4.3.3      tinytable_0.2.1    
 [5] parallel_4.3.3      globals_0.16.3      splines_4.3.3       fastmap_1.1.1      
 [9] lattice_0.22-5      coda_0.19-4.1       TH.data_1.1-2       tables_0.9.17      
[13] generics_0.1.3      lmtest_0.9-40       knitr_1.46          MASS_7.3-60.0.1    
[17] backports_1.4.1     checkmate_2.3.1     future_1.33.2       insight_0.19.10    
[21] rlang_1.1.3         multcomp_1.4-25     performance_0.11.0  xfun_0.43          
[25] parameters_0.21.6   datawizard_0.10.0   estimability_1.5    cli_3.6.2          
[29] emmeans_1.10.1      digest_0.6.35       grid_4.3.3          rstudioapi_0.16.0  
[33] xtable_1.8-4        mvtnorm_1.2-4       sandwich_3.1-0      effectsize_0.8.7   
[37] glue_1.7.0          data.table_1.15.4   listenv_0.9.1       codetools_0.2-19   
[41] zoo_1.8-12          survival_3.5-8      fansi_1.0.6         parallelly_1.37.1  
[45] bayestestR_0.13.2   tools_4.3.3         htmltools_0.5.8.1  
> 

(There is also no effect if the labelled variable is cyl)

[vincentarelbundock]

thanks, I see that now (you had not mentioned attribute labels before).

I traced it to a problem in an upstream package. Once it is fixed there, modelsummary shoudl be fixed automatically. I opened an issue here: https://github.com/easystats/parameters/issues/961

[iago-pssjd]

Thanks!

[iago-pssjd]

Dear @vincentarelbundock ,

I only tested now this functionality (since https://github.com/easystats/parameters/issues/961 seemed to be solved). And I get that the pretty_names are not applied to the reference row. For example, see the rows 1 and 6 in the next screenshot:

[vincentarelbundock]

still seems like a parameters problem. Maybe you can come up with a minimal working example with just parameters and report it there.