Support GAMs

[ddsjoberg]

Making this issue so I don't forget about it. I can work on this at some point in the future

library(gtsummary)

tidy_gam <- function(x, conf.int = FALSE, exponentiate = FALSE, ...) {
  broom::tidy(x, 
                    conf.int = conf.int, 
                    exponentiate = exponentiate, 
                    parametric = TRUE,  ...) %>%
    dplyr::mutate(parametric = TRUE) %>%
    dplyr::bind_rows(
      broom::tidy(x, parametric = FALSE, ...) %>%
        dplyr::mutate(parametric = FALSE)
    ) %>%
    dplyr::relocate(.data$parametric, .after = dplyr::last_col())
}

tidy <-
  mgcv::gam(age ~ s(marker, ttdeath) + grade, data = trial) %>%
  tidy_gam(conf.int = TRUE)
tidy
#> # A tibble: 4 x 10
#>   term  estimate std.error statistic  p.value conf.low conf.high   edf ref.df
#>   <chr>    <dbl>     <dbl>     <dbl>    <dbl>    <dbl>     <dbl> <dbl>  <dbl>
#> 1 (Int~   46.2        1.85    24.9   2.37e-59    42.5      49.8    NA     NA 
#> 2 grad~    0.467      2.72     0.172 8.64e- 1    -4.86      5.79   NA     NA 
#> 3 grad~    2.13       2.69     0.792 4.30e- 1    -3.14      7.40   NA     NA 
#> 4 s(ma~   NA         NA        0.163 8.49e- 1    NA        NA       2.     2.
#> # ... with 1 more variable: parametric <lgl>

# parametric terms are tidied just like a regular model
# the smooth non-parametric terms are taken as is
# this is what I would like to see
tibble::tribble(
  ~variable, ~term, ~label, 
  "(Intercept)", "(Intercept)", "(Intercept)",
  "grade", "gradeI", "I",
  "grade", "gradeII", "II",
  "grade", "gradeIII", "III",
  "s(marker,ttdeath)", "s(marker,ttdeath)", "s(marker,ttdeath)"
) %>%
  dplyr::left_join(tidy, by = "term")
#> # A tibble: 5 x 12
#>   variable term  label estimate std.error statistic   p.value conf.low conf.high
#>   <chr>    <chr> <chr>    <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>
#> 1 (Interc~ (Int~ (Int~   46.2        1.85    24.9    2.37e-59    42.5      49.8 
#> 2 grade    grad~ I       NA         NA       NA     NA           NA        NA   
#> 3 grade    grad~ II       0.467      2.72     0.172  8.64e- 1    -4.86      5.79
#> 4 grade    grad~ III      2.13       2.69     0.792  4.30e- 1    -3.14      7.40
#> 5 s(marke~ s(ma~ s(ma~   NA         NA        0.163  8.49e- 1    NA        NA   
#> # ... with 3 more variables: edf <dbl>, ref.df <dbl>, parametric <lgl>

^{Created on 2021-01-08 by the reprex package (v0.3.0)}