Allow tbl_regression() when no model frame method

[ddsjoberg]

What changes are proposed in this pull request?
Update allows a user to utilize tbl_regression() when there is no model.frame() method for the model type. This means that no reference rows can be added. If the underlying data were labelled, the labels cannot be retrieved.

library(gtsummary)
#> #Uighur

# make up some interval censored data 
trial2 <-
  trial %>% 
  dplyr::mutate(
    lint = dplyr::case_when(
      death == 1 ~ runif(200) + 2,
      death == 0 ~ ttdeath
    ),
    rint = dplyr::case_when(
      death == 1 ~ ttdeath,
      death == 0 ~ Inf
    )
  )

# fit the interval-censored survival model with icenReg::ic_sp()
mod1 <-
  icenReg::ic_sp(
    survival::Surv(lint, rint, type = "interval2") ~ trt,
    model = "ph",
    bs_samples = 3,
    data = trial2
  ) 

# Write a custom tidier
tidy_ic_sp <- function(x, exponentiate =  FALSE, conf.level = 0.95, ...) {
  tidy <-
    tibble::tibble(
      term = names(x[["coefficients"]]),
      estimate = x[["coefficients"]],
      std.error = sqrt(diag(x[["var"]])),
      statistic = summary(x)$summaryParameters[, "z-value"],
      p.value = summary(x)$summaryParameters[, "p"],
      conf.low = confint(x, level = conf.level)[, 1],
      conf.high = confint(x, level = conf.level)[, 2]
    )
  
  if (exponentiate == TRUE)
    tidy <- dplyr::mutate_at(tidy, vars(estimate, conf.low, conf.high), exp)
  
  tidy
}

# check that the custom tidier works
tidy_ic_sp(mod1, exponentiate = TRUE)
#> # A tibble: 1 x 7
#>   term      estimate std.error statistic p.value conf.low conf.high
#>   <chr>        <dbl>     <dbl>     <dbl>   <dbl>    <dbl>     <dbl>
#> 1 trtDrug B     1.17     0.148      1.08   0.281    0.878      1.57


tbl_regression(
  mod1,
  exponentiate = TRUE,
  tidy_fun = tidy_ic_sp,
  label = list("trtDrug B" = "Drug B (Drug A is Ref.)")
) %>% 
  modify_header(estimate ~ "**HR**") %>%
  modify_footnote(estimate ~ "HR = Hazard Ratio", abbreviation = TRUE) %>%
  as_kable() # convert to kable to render properly on GH
#> x Unable to identify the list of variables.
#>   
#>   This is usually due to an error calling `stats::model.frame(x)`.
#>   It could be the case if that type of model does not implement this method.
#>   Rarely, this error may occur if the model object was created within
#>   a functional programming framework (e.g. using `lappy()`, `purrr::map()`, etc.).
#> x Unable to identify the list of variables.
#>   
#>   This is usually due to an error calling `stats::model.frame(x)`.
#>   It could be the case if that type of model does not implement this method.
#>   Rarely, this error may occur if the model object was created within
#>   a functional programming framework (e.g. using `lappy()`, `purrr::map()`, etc.).
#> x `trtDrug B` terms have not been found in `x`.
#> x There was an error calling `stats::model.frame(x)`.
#>   
#>   Most likely, this is because the argument passed in `x =` was
#>   misspelled, does not exist, or is not a regression model.
#>   
#>   Rarely, this error may occur if the model object was created within
#>   a functional programming framework (e.g. using `lappy()`, `purrr::map()`, etc.).
#>   Review the GitHub issue linked below for a possible solution.
#>   The model N will not be available in the output.
#>   https://github.com/ddsjoberg/gtsummary/issues/231

Characteristic	HR	95% CI	p-value
Drug B (Drug A is Ref.)	1.17	0.88, 1.57	0.3

^{Created on 2020-10-06 by the reprex package (v0.3.0)}

---

Checklist for PR reviewer

• PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
• If an update was made to tbl_summary(), was the same change implemented for tbl_svysummary()?
• If a new function was added, function included in _pkgdown.yml
• If a bug was fixed, a unit test was added for the bug check
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• R CMD Check runs without errors, warnings, and notes
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• When the branch is ready to be merged into master, increment the version number using usethis::use_version(which = "dev"), run codemetar::write_codemeta(), approve, and merge the PR.

[ddsjoberg]

@zabore can you review this one? we'll need this to allow for summarizing models with no model.frame() method.

[ddsjoberg]

this will now be incorporated into broom.helpers, so we don't need to make the update any longer
larmarange/broom.helpers#63