Displaying margin effects, average margin effects or conditional effects

[larmarange]

First draft of support of margin effects (with effects::allEffects()), average margin effects (from margins::margins()) and conditional effects (with ggeffects::ggpredict()).

Need to mature and to be tested. Requires proper documentation, unit tests and examples.

• NEWS
• unit tests

[larmarange]

library(broom.helpers)
library(gtsummary)
#> 
#> Attachement du package : 'gtsummary'
#> Les objets suivants sont masqués depuis 'package:broom.helpers':
#> 
#>     all_continuous, all_contrasts
mod <- glm(response ~ stage + grade + age, family = binomial, data = trial)

mod %>%
  tbl_regression(
    tidy_fun = tidy_margins,
    estimate_fun = scales::label_percent(style_positive = "plus")
  ) %>%
  as_kable()

Characteristic	Average Marginal Effects	95% CI	p-value
Age	+0.41%	-0.1%, +0.87%	0.084
Grade
I	—	—
II	-3.59%	-19.9%, +12.72%	0.7
III	+0.95%	-15.5%, +17.37%	>0.9
T Stage
T1	—	—
T2	-11.81%	-29.7%, +6.06%	0.2
T3	-2.17%	-22.3%, +17.97%	0.8
T4	-5.88%	-25.3%, +13.52%	0.6

mod %>%
  tbl_regression(
    tidy_fun = tidy_all_effects,
    estimate_fun = scales::label_percent()
  ) %>%
  as_kable()

Characteristic	Marginal Effects	95% CI
T Stage
T1	36.60%	24.26%, 50.984%
T2	24.65%	14.75%, 38.234%
T3	34.40%	21.17%, 50.582%
T4	30.63%	18.58%, 46.079%
Grade
I	32.07%	21.71%, 44.548%
II	28.42%	18.18%, 41.496%
III	33.04%	22.21%, 46.026%
Age
6	16.97%	6.94%, 35.916%
30	24.54%	16.15%, 35.447%
40	28.30%	21.42%, 36.372%
60	36.76%	27.86%, 46.671%
80	46.13%	28.25%, 65.057%

mod %>%
  tbl_regression(
    tidy_fun = tidy_ggpredict,
    estimate_fun = scales::label_percent()
  ) %>%
  as_kable()
#> Data were 'prettified'. Consider using `terms="age [all]"` to get smooth
#>   plots.

Characteristic	Conditional Effects	95% CI
T Stage
T1	37.54%	22.15%, 55.947%
T2	25.41%	13.58%, 42.493%
T3	35.31%	20.47%, 53.651%
T4	31.50%	17.25%, 50.343%
Grade
I	37.54%	22.15%, 55.947%
II	33.58%	19.93%, 50.660%
III	38.59%	22.59%, 57.495%
Age
0	19.44%	6.24%, 46.657%
10	22.65%	8.78%, 47.103%
20	26.22%	12.00%, 48.074%
30	30.13%	15.75%, 49.864%
40	34.35%	19.62%, 52.867%
50	38.84%	23.04%, 57.396%
60	43.53%	25.59%, 63.336%
70	48.33%	27.24%, 70.034%
80	53.16%	28.19%, 76.648%
90	57.94%	28.67%, 82.524%

^{Created on 2022-12-10 with reprex v2.0.2}

[larmarange]

Relevant documentation:

• https://cran.r-project.org/web/packages/margins/vignettes/Introduction.html
• https://strengejacke.github.io/ggeffects/articles/introduction_marginal_effects.html

[larmarange]

@ddsjoberg I had to prepare a course on marginal effects and I was realising that they were no nicely formatted output for such a thing.

This is exploratory work, but it seems quite easy to implement using customer tieders in broom.helpers (and some other tweaks in other functions).

As you can see, the results are nicely formatted by tbl_regression(), out of the box!

It probably needs to mature a little. Do not hesitate if you have any feedback.

[ddsjoberg]

@larmarange the update looks awesome!

[larmarange]

@ddsjoberg Any comment about the name of the estimate column?

[ddsjoberg]

@ddsjoberg Any comment about the name of the estimate column?

I think estimate is the best name!

[larmarange]

@ddsjoberg Any comment about the name of the estimate column?

I think estimate is the best name!

Currently, I'm using "Average Marginal Effect", "Marginal Effect" and "Conditional Effect". I would prefer to be explicit (as we do with OR for logistic regression).

Does that seem OK? Or would you prefer "AME"? (but less known)

[larmarange]

@ddsjoberg do you want to have a look at this PR before merge?

[codecov]

Codecov Report

Merging #195 (37156c0) into main (9a19921) will decrease coverage by 0.25%.
The diff coverage is 93.33%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #195      +/-   ##
==========================================
- Coverage   97.80%   97.54%   -0.26%     
==========================================
  Files          40       40              
  Lines        1870     1958      +88     
==========================================
+ Hits         1829     1910      +81     
- Misses         41       48       +7     

Impacted Files	Coverage Δ
R/tidy_add_term_labels.R	97.56% <72.72%> (-2.44%)	⬇️
R/tidiers.R	93.75% <91.11%> (-1.78%)	⬇️
R/tidy_add_coefficients_type.R	100.00% <100.00%> (ø)
R/tidy_add_pairwise_contrasts.R	94.73% <100.00%> (+0.98%)	⬆️
R/tidy_add_reference_rows.R	100.00% <100.00%> (ø)
R/tidy_and_attach.R	100.00% <100.00%> (ø)
R/tidy_identify_variables.R	100.00% <100.00%> (ø)