R/stats.R

In Tplyr: A Traceability Focused Grammar of Clinical Data Summary

#' Process a tplyr_statistic object
#'
#' This is an internal function that is not meant for use externally, but must be exported.
#' Use with caution.
#'
#' @param x A tplyr_statistic environment
#' @param ... Additional pass through parameters
#'
#' @return Numeric statistc data from a tplyr statistc
#' @export
#' @keywords internal
process_statistic_data <- function(x, ...) {
  UseMethod('process_statistic_data')
}

#' Risk difference numeric processing
#'
#' @param x a tplyr_statistic object
#' @param ... pass through parameters
#'
#' @return numeric risk difference data
#' @noRd
#' @export
process_statistic_data.tplyr_riskdiff <- function(x, ...) {

  evalq({

    comp_numeric_data <- vector('list', length(comparisons))
    trans_numeric_data <- vector('list', length(comparisons))

    # Execute over each set of comparisons
    for (i in seq_along(comparisons)) {
      comp <- comparisons[[i]]
      # Prep the two-way data
      comp_numeric_data[[i]] <- prep_two_way() %>%
        # Calculate the risk-difference and form the data frame
        pmap_dfr(riskdiff, args=args)

      # Put in the group name
      names(comp_numeric_data)[[i]] <- paste0(comp, collapse="_")

      # Create a numeric copy of the data in long form
      trans_numeric_data[[i]] <- comp_numeric_data[[i]] %>%
        # Pivot all of the measures into long form, rename group to the value column name
        pivot_longer(cols = tail(names(comp_numeric_data[[i]]), 5),
                     names_to='measure',
                     values_to=paste0(comp, collapse="_"))

    }

    # Join each of the comparisons together
    stats_numeric_data <- reduce(trans_numeric_data,
                                 full_join,
                                 by=c(match_exact(c(by, cols)),'summary_var', 'measure'))

    stats_numeric_data

  }, envir=x)
}

#' Process string formatting on a tplyr_statistic object
#'
#' This is an internal function that is not meant for use externally, but must be exported.
#' Use with caution.
#'
#' @param x A tplyr_statistic environment
#' @param ... Additional pass through parameters
#'
#' @return Formatted tplyr_statistic data
#' @export
#' @keywords internal
process_statistic_formatting <- function(x, ...) {
  UseMethod('process_statistic_formatting')
}

#' Risk difference string formatting
#'
#' @param x A tplyr_statistc object
#' @param ... Pass through paramters
#'
#' @return Formatted risk difference data
#' @noRd
#' @export
process_statistic_formatting.tplyr_riskdiff <- function(x, ...) {

  evalq({

    # Grab the default format string
    if (!"riskdiff" %in% names(format_strings)) {
      format_strings[['riskdiff']] <- gather_defaults(env_parent())[['riskdiff']]
    }

    # Grab the format string object
    fmt <- format_strings$riskdiff

    # Prepare the formatted datasets
    formatted_statistic_data <- comp_numeric_data

    for (name in names(comp_numeric_data)) {

      # Construct the display string from the numeric variables
      display_string <- comp_numeric_data[[name]] %>%
        pmap_chr(construct_riskdiff_string, .fmt_str = fmt)

      # Pick off all the labels
      formatted_statistic_data[[name]] <- formatted_statistic_data[[name]] %>%
        select(summary_var, !!!head(target_var, -1), map_chr(by, as_label) , !!!cols)

      # Put the display string in
      formatted_statistic_data[[name]][paste0('rdiff_', name)] <- display_string

    }

    # Join the rdiff columns together
    formatted_statistic_data <- reduce(formatted_statistic_data,
                                       full_join,
                                       by=c(match_exact(c(by, cols, head(target_var, -1))),  'summary_var'))

    if (length(cols) > 0) {

      # If only one comparison was made, the columns won't prefix with the transposed variable name
      # So trick it by introducing a column I can drop later. Not great, but functional
      formatted_statistic_data['rdiffx'] <- ''

      # Pivot by column
      formatted_statistic_data <- formatted_statistic_data %>%
        pivot_wider(id_cols=c(match_exact(c(by, head(target_var, -1))),  'summary_var'),
                    names_from = match_exact(cols),
                    names_sep = "_",
                    values_from=starts_with('rdiff'))

      # Drop the dummied columns
      formatted_statistic_data <- formatted_statistic_data %>% select(-starts_with('rdiffx'))

    }

    formatted_statistic_data

  }, envir=x)
}