larmarange
commented
1 year ago 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
ddsjoberg
codecov[bot]
First draft of support of margin effects (with
effects::allEffects()), average margin effects (frommargins::margins()) and conditional effects (withggeffects::ggpredict()).Need to mature and to be tested. Requires proper documentation, unit tests and examples.