R/epi_binom.R

In ianhandel/epidemr: Tidy Epidemiology in R

#' Binomial estimates from dataframe column
#'
#' A wrapper for binom::binom.confint  called with a data.frame and
#' unquoted columns or expressions.
#'
#' Given a column of a dataframe (and 'positive' level) generate a
#' binomial proportion estimate and confidence intervals
#'
#' @param x A dataframe or number of sucesses
#' @param y An expression evaluating to TRUE/FALSE or number of trials
#' @param conf_level Probability for confidence interval calculations
#' @param methods Confidence interval method see ?binom::binom.confint
#' @param digits Rounding digits
#' @param ... Additional arguments for binom::binom.confint "bayes" method
#' @return Returns an epi_binom object - this includes a variable for conf_level.
#'
#' \if{html}{
#' \out{
#'  <img src = "https://media.giphy.com/media/IB9foBA4PVkKA/giphy.gif">
#' }}
#'
#'
#' @export
#' @examples
#' head(mtcars)
#' epi_binom(mtcars, cyl==4, conf_level = 0.95, methods = "all")
#' epi_binom(7, 10, conf_level = 0.95, methods = "all")



epi_binom <- function(x,
                      y,
                      conf_level = 0.95,
                      methods = "all",
                      digits,
                      ...) {
  if (length(x) == 1 & !is.list(x)) {
    res <- binom::binom.confint(
      x = x,
      n = y,
      conf.level = conf_level,
      methods = methods,
      ...
    )
  } else {
    var <- rlang::enquo(y)

    x <- dplyr::mutate(x, ..var = !! var)

    var_vec <- x[["..var"]]

    res <- binom::binom.confint(
      x = sum(var_vec),
      n = sum(!is.na(var_vec)),
      conf.level = conf_level,
      methods = methods,
      ...
    )
  }
  # add conf_level as variable
  res <- dplyr::mutate(
    res,
    conf_level = conf_level
  )

  res <- dplyr::rename(res, proportion = mean)

  if (!missing(digits)) {
    res <- tibble::as_tibble(purrr::map_if(
      res,
      purrr::is_bare_numeric,
      round, digits
    ))
  }

  res <- structure(
    tibble::as.tibble(res),
    class = c("epi_binom", "tbl_df", "tbl", "data.frame")
  )
  return(res)
}