ukbwranglr: Exploring UKB Data

# NOTES -------------------------------------------------------------------

# Contains functions under development and some related constants


# CONSTANTS ---------------------------------------------------------------

# ukb special codings -----------------------------------------------------------------

# Used by read_ukb.R
# codings that should, or should not, be converted to NA

CONT_AND_INT_CODINGS_TO_NA <- c(
  # Continuous
  "13",
  "909",
  "1317",
  # Integer
  "100291",
  "100586",
  "37",
  ## **NOTEre 37: also see notes under 'Other notes' in
  ## `ukb_select_codings_to_na.Rmd` re 'polymorphic data fields'
  "513",
  "485",
  "584",
  "100696",
  "170",
  "42",
  "525",
  "100584",
  "218"
)

CONT_AND_INT_CODINGS_NOT_TO_NA <- c(
  # Continuous
  "488",
  # Integer
  "100373", # -10 <- 'Less than one'
  "100329", # -10 <- 'Less than an hour a day'
  "528",
  "100290",
  "100306",
  "100567",
  "100569",
  "100353", # number of cigarettes previously smoked daily
  "487",
  "100298",
  "100300",
  "100307",
  "100355", # number of cigarettes currently smoked daily
  "100504",
  "100537",
  "100582",
  "100585",
  "100595",
  "100598",
  "530",
  "946",
  "957",
  "100698",
  "17",
  "1990",
  "402",
  "511",
  "517",
  "6361"
)

# EXPORTED FUNCTIONS ------------------------------------------------------


# PRIVATE FUNCTIONS -------------------------------------------------------

#' Flag continuous/integer codings as NA
#'
#' Indicate which continuous/integer codings can be converted to \code{NA}
#' (decided through manual inspection)
#'
#' @param data_dict data frame created by \code{make_data_dict}
#'
#' @return data frame
#' @noRd
function(data_dict) {
  # mutate 'cont_int_to_na' column: indicates whether all special codings for a
  # continuous/integer variable can be cleaned to 'NA' (see also
  # `ukb_select_codings_to_na.Rmd`)
  data_dict$cont_int_to_na <- dplyr::case_when(
    # CONVERT TO NA
    data_dict$Coding %in% CONT_AND_INT_CODINGS_TO_NA ~ TRUE,

    # DO *NOT* CONVERT TO NA
    data_dict$Coding %in% CONT_AND_INT_CODINGS_NOT_TO_NA ~ FALSE,
    TRUE ~ FALSE
  )

  return(data_dict)
}