R/postprocess.R

In tsostarics/anrlab: What the Package Does (One Line, Title Case)

#' Postprocess instrument data
#'
#' After pivoting an instrument, some postprocessing needs to be done. Usually
#' this means converting datatypes from character to numeric.
#'
#' @param inst_data One instrument's data
#' @param inst_prefix Character, instrument's prefix
#' @param verbose Logical, defaults to True, inherits from split_instruments
#'
#' @return A dataframe with some cleaned up names and datatypes
.postprocess <- function(inst_data, inst_prefix, verbose = T) {
  # Common .postprocessing that should be done on all instruments
  # Change item number and accuracy scores to integers
  if ("number" %in% colnames(inst_data)) {
    inst_data[["number"]] <- as.integer(inst_data[["number"]])
  }
  if ("acc" %in% colnames(inst_data)) {
    inst_data[["acc"]] <- as.integer(inst_data[["acc"]])
  }

  # Remove instrument prefix from column names for readability
  colnames(inst_data) <- gsub(
    paste0(inst_prefix, "_"),
    "",
    colnames(inst_data)
  )

  # Compose a function call of the form .postprocess_[prefix]()
  # this may need to come after the type conversion? maybe not though
  # need to actually implement this for the non repeatable instruments
  fx_name <- paste0('.postprocess_',inst_prefix)
  if(methods::existsFunction(fx_name)){
    inst_data <- do.call(fx_name, args = list(inst_data))
  }

  # Turns out readr CAN operate on existing data with type_convert so it can
  # generalize a whole lot better than hard coding everything
  if (verbose) {
    readr::type_convert(inst_data)
  } else {
    suppressWarnings(suppressMessages(readr::type_convert(inst_data)))
  }
}

.postprocess_navs <- function(inst_data) {
  dplyr::relocate(inst_data, "z", .before = "A")
}

.postprocess_demo <- function(inst_data) {
  dplyr::select(inst_data, -tidyselect::starts_with("redcap")) |>
    dplyr::mutate(sex        = dplyr::case_when(sex == 1 ~ 'Male',
                                                sex == 2 ~ 'Female',
                                                TRUE ~ 'Other'),
                  handedness = dplyr::case_when(handedness == 1 ~ 'Left',
                                                handedness == 2 ~ 'Right',
                                                TRUE ~ 'Ambidextrous'))
}

.postprocess_med <- function(inst_data) {
  # TODO: rename checkboxes
  inst_data
}

.postprocess_nat <- function(inst_data) {
  dplyr::select(inst_data, -subtest)
}


.postprocess_hand <- function(inst_data) {
  dplyr::transmute(inst_data,
                   record_id,
                   redcap_repeat_instrument,
                   redcap_repeat_instance,
                   number,
                   left = as.numeric(choice1) + as.numeric(choice2),
                   right = as.numeric(choice3) + as.numeric(choice4))
}