Swapping tab_* for {gtsummary}

[aspina7]

May be worth considering to use {gtsummary } for descriptive tables.

Would mean swapping to {flextable } rather than kable. Which would also play nicely if we swapped to officedown as in #188

Would then mean that we could retire tab_linelist and would significantly lighten {epibuffet}.

Thoughts @zkamvar @pbkeating ?

[zkamvar]

I fully support this idea. I don't know if it would necessarily lighten epibuffet since much of the weight is coming from {surveyr}, but I like the approach of {gt} and {gtsummary} and think that it has had a lot more thought an effort put into it than {epibuffet}.

[aspina7]

also has functions for survey weighted tables
as well as for inline text

[zkamvar]

I am 100% for this (assuming it works for our use-cases). We may even consider just making {gtsummary} a backend for {epibuffet}

[aspina7]

turns out is possible to replicate the results of our tab_univariate (example below) - so actually the only wrapper that needs writing is to produce stratified estimates (mantel haenszel)
@pbkeating this shaves off a bit of time!

output <- linelist %>% 
  select(died_covid, gender, age_group) %>%    # keep variables of interest
  tbl_uvregression(                         ## produce univariate table
    method = glm,                           ## define regression want to run (generalised linear model)
    y = died_covid,                            ## define outcome variable
    method.args = list(family = binomial),  ## define what type of glm want to run (logistic)
    exponentiate = TRUE,                    ## exponentiate to produce odds ratios (rather than log odds)
    hide_n = TRUE                               ## dont include overall counts in regression table
  ) 

## produce counts for each of the variables of interest
cross_tab <- output$inputs$data %>% 
  tbl_summary(by = died_covid)

## combine for a full table 
tbl_merge(list(cross_tab, output))

[aspina7]

in progress for surveys in #275