Variable names for models with no model.frame method

[ddsjoberg]

When there is no model.frame() method, the user sees a very informative message. (super helpful!)

The resulting table has column for variable, but the columns are NA. Can we add the term as the variable for these models? In gtsummary, we use the variable name to do further manipulation (and in broom.helpers too), but with no name these variables cannot be selected.

I know the term is not the proper variable name, but I think the printed message is enough of a cue to users that the original variable names are not available.

library(broom.helpers)
library(gtsummary)

# 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
    )
  )

# 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
}

# fit the interval-censored survival model with icenReg::ic_sp()
icenReg::ic_sp(
  survival::Surv(lint, rint, type = "interval2") ~ trt,
  model = "ph",
  bs_samples = 3,
  data = trial2
) %>%
  # tidy up with broom.helpers
  tidy_and_attach(tidy_fun = tidy_ic_sp) %>%
  tidy_identify_variables() %>%
  tidy_add_variable_labels() %>%
  tidy_add_header_rows() %>%
  select(term, variable, var_label, label, estimate)
#> x Unable to identify the list of variables.
#>   
#>   This is usually due to an error calling `stats::model.frame(x)`or `stats::model.matrix(x)`.
#>   It could be the case if that type of model does not implement these methods.
#>   Rarely, this error may occur if the model object was created within
#>   a functional programming framework (e.g. using `lappy()`, `purrr::map()`, etc.).
#> # A tibble: 1 x 5
#>   term      variable var_label label     estimate
#>   <chr>     <chr>    <chr>     <chr>        <dbl>
#> 1 trtDrug B <NA>     trtDrug B trtDrug B    0.160

^{Created on 2020-10-19 by the reprex package (v0.3.0)}

[larmarange]

This is a good point. Maybe in that case var_type needs to be populated with "unknown" or something similar.

I need to check that out will not break other functions and to do some tests.

[ddsjoberg]

The type for these variables is already indicated as unknown! You're already ahead :)

[larmarange]

Fixed now :-)

[ddsjoberg]

YAY! You're so fast!