Add Mantel-Fleiss criterion function mantel_fleiss_crit().

[wwojciech]

Fixes #1512

[wwojciech]

@danielinteractive - I was wondering whether I should introduce an na.rm = FALSE parameter and allow missing values. Currently, I want to be consistent with the other tern prop_*() functions, which expect no missing values.

Do you think having an na.rm argument and allowing missing values would be useful?

[danielinteractive]

Thanks @wwojciech , please see few comments below - otherwise looks nice.
I don't think we need na.rm argument when the other functions which are used together with this don't have it.

[wwojciech]

@danielinteractive - I am now thinking that it would probably be better to change the UI to tbl (contingency table), instead of grp, rsp, and strata, and introduce a separate helper to reliably build tbl from these three vectors.

Most (if not all) of the prop_* test functions (prop_cmh(), prop_fisher(), ...) already require tbl, so I would need to create such a table anyway, since after checking the MF criterion I need to run the test.

[danielinteractive]

@wwojciech yeah starting from the table is probably a good idea

[wwojciech]

Thank you @danielinteractive for your review. I’ve updated the code to address all of your suggestions and changed the UI as discussed. Please review the PR again when you have a chance. Thanks!

[wwojciech]

@danielinteractive - do you think this below little helper should go to {tern} or to {junco}? I would probably say {tern}...

#' @param rsp (`logical`)\cr
#'   A logical vector indicating whether each observation is a responder.
#' @param grp (`factor`)\cr
#'   A factor assigning observations to one of two groups (e.g., reference
#'   and treatment). It must have exactly two levels.
#' @param strata (`factor`)\cr
#'   Factor defining the stratification variable. Each unique
#'   stratum defines a separate 2 x 2 contingency table.
safe_2x2_strat_table <- function(rsp, grp, strata) {
  checkmate::assert_logical(rsp, any.missing = FALSE)
  checkmate::assert_factor(grp, len = length(rsp), any.missing = FALSE, n.levels = 2)
  checkmate::assert_factor(strata, len = length(rsp), any.missing = FALSE)

  # Make rsp a factor to handle cases with only TRUE or only FALSE.
  rsp <- factor(rsp, levels = c("TRUE", "FALSE"))

  table(grp, rsp, strata)
}

[danielinteractive]

Thanks @wwojciech yeah to tern because there it can be used in multiple places