data-raw/std_mctq.R
In gipsousp/mctq: Tools to Process the Munich ChronoType Questionnaire (MCTQ)
# # Notes
#
# * Source the file before running the functions.
# * Don't forget to uncomment the 'library' functions below.
# library(checkmate)
# library(cli)
# library(dplyr)
# library(gutils) # https://github.com/giperbio/gutils
# library(hms)
# library(lubridate)
# library(mctq)
# library(rlang)
# library(usethis)
# library(utils)
# library(validate)
#' Build a fictional standard MCTQ raw dataset
#'
#' @description
#'
#' `build_std_mctq()` builds a fictional raw dataset, __for testing and learning
#' purposes__, composed of basic/measurable variables of the Munich ChronoType
#' Questionnaire (MCTQ) standard version. See [`?std_mctq`][mctq::std_mctq] to
#' learn more.
#'
#' @param write (optional) a [`logical`][base::logical()] value indicating if
#' the function must write a `std_mctq.csv` file to `"./inst/extdata/"`
#' (default: `FALSE`).
#' @param random_cases (optional) a [`logical`][base::logical()]` value
#' indicating if the function must add random MCTQ cases besides the core
#' ones.
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a raw standard MCTQ
#' dataset.
#'
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(build_std_mctq())
#' }
#' }
build_std_mctq <- function(write = FALSE, random_cases = TRUE) {
# Check arguments -----
checkmate::assert_flag(write)
checkmate::assert_flag(random_cases)
cli::cli_progress_step("Building MCTQ data")
# Set IDs -----
set.seed(1)
reserved_id <- sample(50, 15)
id <- seq(50)[!(seq(50) %in% reserved_id)]
# Create cases -----
## Base respondent: sleeps less than the recommended for an adult on
## workdays and stretches during work-free days.
std_mctq <- dplyr::tibble(
`ID` = as.character(reserved_id[1]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "00:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "01:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "06:30", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "02:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "02:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "12:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "04:00" # Duration | [H]MS, [H]M, [H]
)
## Random cases
format_logical <- function(x) {
dplyr::case_when(
x == TRUE ~ "Yes",
x == FALSE ~ "No"
)
}
format_hms <- function(x) {
format <- c(1, 5)
x <- hms::hms(mctq:::extract_seconds(x))
substr(as.character(x), format[1], format[2])
}
format_duration <- function(x) {
as.character(as.numeric(x) / 60)
}
if (isTRUE(random_cases)) {
for (i in id) {
random_case <-
mctq::random_mctq(model = "standard") |>
dplyr::as_tibble() %>% # Don't change the pipe.
dplyr::transmute(
`ID` = as.character(i),
`WORK REGULAR` = format_logical(.data$work),
`WORK DAYS` = as.character(.data$wd),
`W BEDTIME` = format_hms(.data$bt_w),
`W SLEEP PREP` = format_hms(.data$sprep_w),
`W SLEEP LAT` = format_duration(.data$slat_w),
`W SLEEP END` = format_hms(.data$se_w),
`W SLEEP INERTIA` = format_duration(.data$si_w),
`W ALARM` = format_logical(.data$alarm_w),
`W WAKE BEFORE ALARM` = format_logical(.data$wake_before_w),
`W LIGHT EXPOSURE` = format_hms(.data$le_w),
`F BEDTIME` = format_hms(.data$bt_f),
`F SLEEP PREP` = format_hms(.data$sprep_f),
`F SLEEP LAT` = format_duration(.data$slat_f),
`F SLEEP END` = format_hms(.data$se_f),
`F SLEEP INERTIA` = format_duration(.data$si_f),
`F ALARM` = format_logical(.data$alarm_f),
`F REASONS` = format_logical(.data$reasons_f),
`F REASONS WHY` = .data$reasons_why_f,
`F LIGHT EXPOSURE` = format_hms(.data$le_f)
)
std_mctq <- dplyr::bind_rows(std_mctq, random_case)
}
}
## Inverted values for bedtime and sleep preparing on workdays
std_mctq <-
std_mctq |>
dplyr::add_row(
`ID` = as.character(reserved_id[2]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "4", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h] # INVERSION
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h] # INVERSION
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "05:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "04:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "01:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "11:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Child(ren)/pet(s)", # character
`F LIGHT EXPOSURE` = "06:00" # Duration | [H]MS, [H]M, [H]
) |>
## Inverted values for bedtime and sleep preparing on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[3]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "30", # Duration | M
`W SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Yes", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "23:00", # hms | HMS, HM, H [0-24h] # INVERSION
`F SLEEP PREP` = "22:30", # hms | HMS, HM, H [0-24h] # INVERSION
`F SLEEP LAT` = "45", # Duration | M
`F SLEEP END` = "08:30", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "00:00" # Duration | [H]MS, [H]M, [H]
) |>
## Presence of invalid values
dplyr::add_row(
`ID` = as.character(reserved_id[4]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "10", # integer | [0-7] # INVALID
`W BEDTIME` = "27:00", # hms | HMS, HM, H [0-24h] # INVALID
`W SLEEP PREP` = "02:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "30", # Duration | M
`W SLEEP END` = "12:15", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "20", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Sim", # logical | Yes/No # INVALID
`W LIGHT EXPOSURE` = "02:15", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "34:00", # hms | HMS, HM, H [0-24h] # INVALID
`F SLEEP PREP` = "04:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "14:12", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "-01:30" # Duration | [H]MS, [H]M, [H] # INV.
) |>
## Sleeps more on workdays than on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[5]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "2", # integer | [0-7]
`W BEDTIME` = "21:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "2130", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "09:15", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "0500", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "5", # Duration | M
`F SLEEP END` = "06:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "07:00" # Duration | [H]MS, [H]M, [H]
) |>
## Uses an alarm clock on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[6]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:55", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "30", # Duration | M
`F SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "0", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No # Alarm == "Yes"
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Child(ren)/pet(s)", # character
`F LIGHT EXPOSURE` = "04:45" # Duration | [H]MS, [H]M, [H]
) |>
## Null MCTQ
dplyr::add_row(
`ID` = as.character(reserved_id[7]), # integer | [auto-increment]
`WORK REGULAR` = "", # logical | Yes/No
`WORK DAYS` = "", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "", # Duration | M
`F SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "", # Duration | M
`F ALARM` = "", # logical | Yes/No
`F REASONS` = "", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "" # Duration | [H]MS, [H]M, [H]
) |>
## Did not answer workdays questions
dplyr::add_row(
`ID` = as.character(reserved_id[8]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "03:30", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "04:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "90", # Duration | M
`F SLEEP END` = "15:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "00:30" # Duration | [H]MS, [H]M, [H]
) |>
## All, or almost all, basic variables have the same values
dplyr::add_row(
`ID` = as.character(reserved_id[9]), # integer | [auto-increment]
`WORK REGULAR` = "0", # logical | Yes/No
`WORK DAYS` = "0", # integer | [0-7]
`W BEDTIME` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "0", # Duration | M
`W SLEEP END` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "0", # Duration | M
`W ALARM` = "0", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "0", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "0", # Duration | M
`F SLEEP END` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "0", # Duration | M
`F ALARM` = "0", # logical | Yes/No
`F REASONS` = "0", # logical | Yes/No
`F REASONS WHY` = "0", # character
`F LIGHT EXPOSURE` = "0" # Duration | [H]MS, [H]M, [H]
) |>
## Works 7 days a week and didn't answer the work-free days section
dplyr::add_row(
`ID` = as.character(reserved_id[10]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "7", # integer | [0-7]
`W BEDTIME` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "06:30", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "02:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "", # Duration | M
`F SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "", # Duration | M
`F ALARM` = "", # logical | Yes/No
`F REASONS` = "", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "" # Duration | [H]MS, [H]M, [H]
) |>
## Suspicious values
dplyr::add_row(
`ID` = as.character(reserved_id[11]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "6", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h] # SUSPICIOUS
`W SLEEP LAT` = "120", # Duration | M # SUSPICIOUS
`W SLEEP END` = "04:00", # hms | HMS, HM, H [0-24h] # SUSPICIOUS
`W SLEEP INERTIA` = "0", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Yes", # logical | Yes/No
`W LIGHT EXPOSURE` = "18:00", # Duration | [H]MS, [H]M, [H] # SUSP.
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "30", # Duration | M
`F SLEEP END` = "09:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "17:00" # Duration | [H]MS, [H]M, [H] # SUSP.
) |>
## Different formats
dplyr::add_row(
`ID` = as.character(reserved_id[12]), # integer | [auto-increment]
`WORK REGULAR` = "true", # logical | Yes/No # AMBIGUOUS
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "11:00 PM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP PREP` = "0000", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP LAT` = "00:15", # Duration | M #AMBIGUOUS
`W SLEEP END` = "07:15 AM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP INERTIA` = "30", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "3", # Duration | [H]MS, [H]M, [H] # AMBIGUOUS
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "0130 AM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`F SLEEP LAT` = "60", # Duration | M
`F SLEEP END` = "10:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "15", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "04:30" # Duration | [H]MS, [H]M, [H]
) |>
## Possible filling error
dplyr::add_row(
`ID` = as.character(reserved_id[13]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "6", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "22:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "06:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "3", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "01:30" # Duration | [H]MS, [H]M, [H]
) |>
## Repeated workdays and work-free days values (possible carryover
## effect)
dplyr::add_row(
`ID` = as.character(reserved_id[14]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "22:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "22:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "10", # Duration | M
`F SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "No", # character
`F LIGHT EXPOSURE` = "01:00" # Duration | [H]MS, [H]M, [H]
) |>
## Sleep onset is equal or greater than sleep end
## [(s_prep + s_lat) >= se]
dplyr::add_row(
`ID` = as.character(reserved_id[15]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "2", # integer | [0-7]
`W BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "60", # Duration | M
`W SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:20", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "02:00", # hms | HMS, HM, H [0-24h] # ERROR
`F SLEEP LAT` = "120", # Duration | M # ERROR
`F SLEEP END` = "04:00", # hms | HMS, HM, H [0-24h] # ERROR
`F SLEEP INERTIA` = "15", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "04:00" # Duration | [H]MS, [H]M, [H]
)
std_mctq <-
std_mctq %>% # Don't change the pipe.
dplyr::arrange(as.integer(.data$`ID`))
# Write and return output -----
if (isTRUE(write)) {
if (!(dir.exists("./inst/extdata/"))) dir.create("./inst/extdata/")
std_mctq |>
utils::write.csv(
paste0("./inst/extdata/", "std_mctq", ".csv"),
row.names = FALSE,
quote = FALSE
)
}
invisible(std_mctq)
}
#' Tidy `build_std_mctq()` output
#'
#' @description
#'
#' `tidy_std_mctq` tidy the output of `build_std_mctq()`. See
#' [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Here, the process of _tiding_ a dataset is understood as transforming it in
#' input data, like described in Loo and Jonge (2018). It's a very similar
#' process of tiding data described in the workflow proposed by Wickham and
#' Grolemund (n.d.).
#'
#' Please note that input data is not the same as valid data. To get a valid
#' `std_mctq` data, run `validate_std_mctq()`.
#'
#' To learn more about the concept of tidy data, see Wickham (2014) and
#' Wickham and Grolemund (n.d.).
#'
#' @param write (optional) a [`logical`][base::logical()] value indicating if
#' the function must write a `std_mctq.rda` file to `"./data/"` (default:
#' `FALSE`).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a tidied, but not
#' validated, standard MCTQ dataset.
#'
#' @template references_e
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(tidy_std_mctq())
#' }
#' }
tidy_std_mctq <- function(write = FALSE) {
# Check arguments -----
checkmate::assert_flag(write)
cli::cli_progress_step("Tyding MCTQ data")
# Set values -----
std_mctq <- build_std_mctq()
# Clean NULL cases -----
fix_character <- function(x) {
x <- trimws(x)
for (i in c("", "NA")) {
x <- dplyr::na_if(x, i)
}
x
}
std_mctq <-
std_mctq |>
dplyr::mutate(dplyr::across(.fns = fix_character)) |>
dplyr::rowwise() %>% # Don't change the pipe.
dplyr::mutate(
length = dplyr::n_distinct(dplyr::c_across(-.data$ID))
) %>% # Don't change the pipe.
dplyr::mutate(
dplyr::across(
-.data$ID,
.fns = ~ ifelse(length <= 2, NA, .x)
)
) |>
dplyr::ungroup() |>
dplyr::select(-length)
# Convert columns -----
pattern_1 <- "^\\d{1,3}$"
pattern_2 <- "^([-+])?(2[4-9]|[3-9]\\d|\\d{3,})(:)?[0-5]\\d((:)?[0-5]\\d)?"
pattern_3 <- "^\\-"
std_mctq <-
std_mctq %>% # Don't change the pipe.
dplyr::transmute(
id = as.integer(.data$`ID`),
work = dplyr::case_when(
tolower(.data$`WORK REGULAR`) == "yes" ~ TRUE,
tolower(.data$`WORK REGULAR`) == "true" ~ TRUE,
tolower(.data$`WORK REGULAR`) == "no" ~ FALSE
),
wd = as.integer(.data$`WORK DAYS`),
bt_w = dplyr::case_when(
grepl(pattern_2, .data$`W BEDTIME`, perl = TRUE) ~
mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W BEDTIME`, "HM")
)),
TRUE ~ mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W BEDTIME`, c("HM", "IMp"))
))
),
sprep_w = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`W SLEEP PREP`, c("HMS", "HM", "H")
))),
slat_w = dplyr::case_when(
grepl(pattern_1, .data$`W SLEEP LAT`, perl = TRUE) ~
mctq:::shush(lubridate::dminutes(as.numeric(
.data$`W SLEEP LAT`
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`W SLEEP LAT`, c("HMS", "HM", "H"))
)))
),
se_w = mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W SLEEP END`, c("HMS", "HM", "H"))
)),
si_w = mctq:::shush(lubridate::dminutes(as.numeric(
.data$`W SLEEP INERTIA`
))),
alarm_w = dplyr::case_when(
tolower(.data$`W ALARM`) == "yes" ~ TRUE,
tolower(.data$`W ALARM`) == "no" ~ FALSE
),
wake_before_w = dplyr::case_when(
tolower(.data$`W WAKE BEFORE ALARM`) == "yes" ~ TRUE,
tolower(.data$`W WAKE BEFORE ALARM`) == "no" ~ FALSE
),
le_w = mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(
.data$`W LIGHT EXPOSURE`, c("HMS", "HM", "H")
)
))),
bt_f = dplyr::case_when(
grepl(pattern_2, .data$`F BEDTIME`, perl = TRUE) ~
mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F BEDTIME`, "HM"
))),
TRUE ~ mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F BEDTIME`, c("HMS", "HM", "H")
)))
),
sprep_f = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F SLEEP PREP`, c("HMS", "HM", "H")
))),
slat_f = mctq:::shush(lubridate::dminutes(as.numeric(
.data$`F SLEEP LAT`
))),
se_f = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F SLEEP END`, c("HMS", "HM", "H")
))),
si_f = dplyr::case_when(
grepl(pattern_1, .data$`F SLEEP INERTIA`) ~
mctq:::shush(lubridate::dminutes(as.numeric(
.data$`F SLEEP INERTIA`
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(
.data$`F SLEEP INERTIA`, c("HMS", "HM", "H")
)
)))
),
alarm_f = dplyr::case_when(
tolower(.data$`F ALARM`) == "yes" ~ TRUE,
tolower(.data$`F ALARM`) == "no" ~ FALSE
),
reasons_f = dplyr::case_when(
tolower(.data$`F REASONS`) == "yes" ~ TRUE,
tolower(.data$`F REASONS`) == "no" ~ FALSE
),
reasons_why_f = .data$`F REASONS WHY`,
le_f = dplyr::case_when(
grepl(pattern_3, .data$`F LIGHT EXPOSURE`) ~
mctq:::shush(- lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`F LIGHT EXPOSURE`, "HM")
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`F LIGHT EXPOSURE`, "HM")
)))
)
)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
#' Validate `tidy_std_mctq()` output
#'
#' @description
#'
#' `validate_std_mctq()` validates the output of `tidy_std_mctq()`.
#' See [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Here, the process of _validating_ a dataset is understood as detecting
#' invalid data, by checking whether data satisfies certain assumptions from
#' domain knowledge, to them, removing or, if possible, fixing them. You can
#' find more about data validation and error location in Loo and Jonge (2018).
#'
#' This process can be considered as part of the process of transforming data,
#' described in the workflow proposed by Wickham and Grolemund (n.d.).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a validated standard
#' MCTQ dataset.
#'
#' @inheritParams tidy_std_mctq
#' @template references_d
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data := !!
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(validate_std_mctq())
#' }
#' }
validate_std_mctq <- function(write = FALSE) {
# To do -----
#
# * Adapt this process by using `errorlocate` package with `validate`.
# Check arguments -----
checkmate::assert_flag(write)
cli::cli_progress_step("Validating MCTQ data")
# Set values -----
set.seed(1)
reserved_id <- sample(50, 15)
std_mctq <- tidy_std_mctq()
# Do univariate validation -----
std_mctq <-
std_mctq |>
dplyr::mutate(
wd = dplyr::case_when(
validate::in_range(wd, min = 0, max = 7) ~ wd
)
) |>
dplyr::mutate(dplyr::across(
dplyr::matches("^bt_|^sprep_|^se_"),
~ dplyr::case_when(
.x == hms::parse_hm("24:00") ~ hms::parse_hm("00:00"),
.x >= hms::parse_hm("00:00") &
.x < hms::parse_hm("24:00") ~ .x
)
),
dplyr::across(
dplyr::matches("^slat_|^si_"),
~ dplyr::case_when(
validate::in_range(
.x,
min = lubridate::dhours(0),
max = lubridate::dhours(6)
) ~ .x
)
),
dplyr::across(
dplyr::matches("^le_"),
~ dplyr::case_when(
validate::in_range(
.x,
min = lubridate::dhours(0),
max = lubridate::dhours(24)
) ~ .x
)
)
)
# Do multivariate validation -----
for (i in c("_w", "_f")) {
bt_i <- paste0("bt", i)
sprep_i <- paste0("sprep", i)
std_mctq <-
std_mctq |>
dplyr::mutate(
dummy = dplyr::case_when(
mctq::assign_date(!!as.symbol(bt_i), !!as.symbol(sprep_i)) >
lubridate::dhours(12) ~ TRUE,
TRUE ~ FALSE
),
bkp = !!as.symbol(bt_i),
!!as.symbol(bt_i) := dplyr::if_else(
dummy, !!as.symbol(sprep_i), !!as.symbol(bt_i)
),
!!as.symbol(sprep_i) := dplyr::if_else(
dummy, bkp, !!as.symbol(sprep_i)
)
) |>
dplyr::select(-dummy, -bkp)
}
for (i in c("_w", "_f")) {
sprep_i <- paste0("sprep", i)
slat_i <- paste0("slat", i)
se_i <- paste0("se", i)
test <-
std_mctq |>
dplyr::mutate(
so_i = mctq::so(!!as.symbol(sprep_i), !!as.symbol(slat_i)),
sd_i = mctq::sdu(so_i, !!as.symbol(se_i)),
dummy = dplyr::case_when(
sd_i < lubridate::dhours(2) |
sd_i > lubridate::dhours(18) ~ TRUE,
TRUE ~ FALSE
)
) |>
dplyr::select(dummy)
std_mctq <-
std_mctq |>
dplyr::bind_cols(test) |>
dplyr::mutate(dplyr::across(
dplyr::ends_with(i),
~ dplyr::if_else(dummy, gutils:::na_as(.x), .x)
)) |>
dplyr::select(-dummy)
}
# Clean invalid cases -----
## Cases: "Suspicious values"
invalid <- c(reserved_id[11])
std_mctq <-
std_mctq |>
dplyr::rowwise() %>% # Don't change the pipe.
dplyr::mutate(dplyr::across(
-.data$id,
.fns = ~ dplyr::if_else(
.data$id %in% invalid, gutils:::na_as(.x), .x
)
)
) |>
dplyr::ungroup()
# Fix/impute linked data -----
std_mctq <-
std_mctq |>
dplyr::mutate(
wd = dplyr::case_when(
work == FALSE & is.na(wd) ~ as.integer(0),
TRUE ~ wd
),
work = dplyr::case_when(
work == FALSE & wd > 0 ~ TRUE,
TRUE ~ work
),
wake_before_w = dplyr::case_when(
alarm_w == FALSE ~ as.logical(NA),
TRUE ~ wake_before_w
),
reasons_why_f = dplyr::case_when(
tolower(reasons_why_f) == "no" ~ as.character(NA),
TRUE ~ reasons_why_f
),
reasons_f = dplyr::case_when(
!is.na(reasons_why_f) ~ TRUE,
TRUE ~ reasons_f
)
)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
#' Analyze `validate_std_mctq()` output
#'
#' @description
#'
#' `analyse_std_mctq()` computes and creates the non-measured MCTQ variables
#' based on the output of `validate_std_mctq()`. See
#' [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Computing and creating new variables is part of the process of producing
#' statistics, like described in Loo and Jonge (2018). It's also a part of the
#' process of transforming data, described in the workflow proposed by Wickham
#' and Grolemund (n.d.).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with all the variables
#' proposed for a standard MCTQ dataset.
#'
#' @inheritParams tidy_std_mctq
#' @inheritParams pretty_mctq
#' @template references_d
#' @family data functions
#' @importFrom magrittr %>%
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(analyze_std_mctq())
#' }
#' }
analyze_std_mctq <- function(write = FALSE, round = TRUE, hms = FALSE) {
# Check arguments -----
checkmate::assert_flag(write)
checkmate::assert_flag(round)
checkmate::assert_flag(hms)
cli::cli_progress_step("Analyzing MCTQ data")
# Compute variables -----
std_mctq <-
validate_std_mctq() |>
dplyr::mutate(
fd = mctq::fd(wd),
so_w = mctq::so(sprep_w, slat_w),
gu_w = mctq::gu(se_w, si_w),
sd_w = mctq::sdu(so_w, se_w),
tbt_w = mctq::tbt(bt_w, gu_w),
msw = mctq::msl(so_w, sd_w),
so_f = mctq::so(sprep_f, slat_f),
gu_f = mctq::gu(se_f, si_f),
sd_f = mctq::sdu(so_f, se_f),
tbt_f = mctq::tbt(bt_f, gu_f),
msf = mctq::msl(so_f, sd_f),
sd_week = mctq::sd_week(sd_w, sd_f, wd),
msf_sc = mctq::msf_sc(msf, sd_w, sd_f, sd_week, alarm_f),
sloss_week = mctq::sloss_week(sd_w, sd_f, wd),
le_week = mctq::le_week(le_w, le_f, wd),
sjl_rel = mctq::sjl_rel(msw, msf),
sjl = abs(sjl_rel),
sjl_sc_rel = mctq::sjl_sc_rel(so_w, se_w, so_f, se_f),
sjl_sc = abs(sjl_sc_rel)
) |>
dplyr::relocate(
id, work, wd, fd,
bt_w, sprep_w, slat_w, so_w, se_w, si_w, gu_w, alarm_w,
wake_before_w, sd_w, tbt_w, le_w, msw,
bt_f, sprep_f, slat_f, so_f, se_f, si_f, gu_f, alarm_f,
reasons_f, reasons_why_f, sd_f, tbt_f, le_f, msf,
sd_week, sloss_week, le_week, msf_sc, sjl_rel, sjl, sjl_sc_rel,
sjl_sc
)
# Fix missing sections -----
## See `vignette("missing-sections", pakckage = "mctq")` to learn more.
count_w <- length(names(std_mctq)[grepl("_w$", names(std_mctq))])
count_f <- length(names(std_mctq)[grepl("_f$", names(std_mctq))])
count_w <- count_w * (2 / 3)
count_f <- count_f * (2 / 3)
count_na <- function(x) {
checkmate::assert_atomic(x)
length(which(is.na(x)))
}
test <-
std_mctq |>
dplyr::mutate(dplyr::across(.fns = as.character)) |>
dplyr::rowwise() |>
dplyr::mutate(
dummy_0_a = as.integer(wd) == 0,
dummy_0_b = count_na(dplyr::c_across(dplyr::ends_with("_w"))) >= count_w,
dummy_0_c = alarm_f == FALSE,
dummy_7_a = as.integer(wd) == 7,
dummy_7_b = count_na(dplyr::c_across(dplyr::ends_with("_f"))) >= count_f,
dummy_0 = dummy_0_a & dummy_0_b & dummy_0_c & dummy_7_b == FALSE,
dummy_7 = dummy_7_a & dummy_7_b & dummy_0_b == FALSE
) |>
dplyr::ungroup() |>
dplyr::select(dummy_0, dummy_7)
std_mctq <-
dplyr::bind_cols(std_mctq, test) |>
dplyr::mutate(
sd_week = dplyr::case_when(
dummy_0 == TRUE ~ sd_f,
dummy_7 == TRUE ~ sd_w,
TRUE ~ sd_week
),
msf_sc = dplyr::if_else(dummy_0, msf, msf_sc),
sloss_week = dplyr::if_else(
dummy_0, lubridate::dhours(0), sloss_week
),
le_week = dplyr::case_when(
dummy_0 == TRUE ~ le_f,
dummy_7 == TRUE ~ le_w,
TRUE ~ le_week
),
sjl_rel = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl_rel),
sjl = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl),
sjl_sc_rel = dplyr::if_else(
dummy_0, lubridate::dhours(0), sjl_sc_rel
),
sjl_sc = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl_sc)
) |>
dplyr::select(-dummy_0, -dummy_7)
# Make MCTQ pretty -----
std_mctq <-
std_mctq |>
pretty_mctq(round = round, hms = hms)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
# raw <- build_std_mctq()
# tidy <- tidy_std_mctq()
# valid <- validate_std_mctq()
# analysis <- analyze_std_mctq()
gipsousp/mctq documentation built on Dec. 3, 2023, 7:11 p.m.
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# # Notes
#
# * Source the file before running the functions.
# * Don't forget to uncomment the 'library' functions below.
# library(checkmate)
# library(cli)
# library(dplyr)
# library(gutils) # https://github.com/giperbio/gutils
# library(hms)
# library(lubridate)
# library(mctq)
# library(rlang)
# library(usethis)
# library(utils)
# library(validate)
#' Build a fictional standard MCTQ raw dataset
#'
#' @description
#'
#' `build_std_mctq()` builds a fictional raw dataset, __for testing and learning
#' purposes__, composed of basic/measurable variables of the Munich ChronoType
#' Questionnaire (MCTQ) standard version. See [`?std_mctq`][mctq::std_mctq] to
#' learn more.
#'
#' @param write (optional) a [`logical`][base::logical()] value indicating if
#' the function must write a `std_mctq.csv` file to `"./inst/extdata/"`
#' (default: `FALSE`).
#' @param random_cases (optional) a [`logical`][base::logical()]` value
#' indicating if the function must add random MCTQ cases besides the core
#' ones.
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a raw standard MCTQ
#' dataset.
#'
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(build_std_mctq())
#' }
#' }
build_std_mctq <- function(write = FALSE, random_cases = TRUE) {
# Check arguments -----
checkmate::assert_flag(write)
checkmate::assert_flag(random_cases)
cli::cli_progress_step("Building MCTQ data")
# Set IDs -----
set.seed(1)
reserved_id <- sample(50, 15)
id <- seq(50)[!(seq(50) %in% reserved_id)]
# Create cases -----
## Base respondent: sleeps less than the recommended for an adult on
## workdays and stretches during work-free days.
std_mctq <- dplyr::tibble(
`ID` = as.character(reserved_id[1]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "00:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "01:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "06:30", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "02:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "02:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "12:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "04:00" # Duration | [H]MS, [H]M, [H]
)
## Random cases
format_logical <- function(x) {
dplyr::case_when(
x == TRUE ~ "Yes",
x == FALSE ~ "No"
)
}
format_hms <- function(x) {
format <- c(1, 5)
x <- hms::hms(mctq:::extract_seconds(x))
substr(as.character(x), format[1], format[2])
}
format_duration <- function(x) {
as.character(as.numeric(x) / 60)
}
if (isTRUE(random_cases)) {
for (i in id) {
random_case <-
mctq::random_mctq(model = "standard") |>
dplyr::as_tibble() %>% # Don't change the pipe.
dplyr::transmute(
`ID` = as.character(i),
`WORK REGULAR` = format_logical(.data$work),
`WORK DAYS` = as.character(.data$wd),
`W BEDTIME` = format_hms(.data$bt_w),
`W SLEEP PREP` = format_hms(.data$sprep_w),
`W SLEEP LAT` = format_duration(.data$slat_w),
`W SLEEP END` = format_hms(.data$se_w),
`W SLEEP INERTIA` = format_duration(.data$si_w),
`W ALARM` = format_logical(.data$alarm_w),
`W WAKE BEFORE ALARM` = format_logical(.data$wake_before_w),
`W LIGHT EXPOSURE` = format_hms(.data$le_w),
`F BEDTIME` = format_hms(.data$bt_f),
`F SLEEP PREP` = format_hms(.data$sprep_f),
`F SLEEP LAT` = format_duration(.data$slat_f),
`F SLEEP END` = format_hms(.data$se_f),
`F SLEEP INERTIA` = format_duration(.data$si_f),
`F ALARM` = format_logical(.data$alarm_f),
`F REASONS` = format_logical(.data$reasons_f),
`F REASONS WHY` = .data$reasons_why_f,
`F LIGHT EXPOSURE` = format_hms(.data$le_f)
)
std_mctq <- dplyr::bind_rows(std_mctq, random_case)
}
}
## Inverted values for bedtime and sleep preparing on workdays
std_mctq <-
std_mctq |>
dplyr::add_row(
`ID` = as.character(reserved_id[2]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "4", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h] # INVERSION
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h] # INVERSION
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "05:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "04:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "01:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "11:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Child(ren)/pet(s)", # character
`F LIGHT EXPOSURE` = "06:00" # Duration | [H]MS, [H]M, [H]
) |>
## Inverted values for bedtime and sleep preparing on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[3]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "30", # Duration | M
`W SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Yes", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "23:00", # hms | HMS, HM, H [0-24h] # INVERSION
`F SLEEP PREP` = "22:30", # hms | HMS, HM, H [0-24h] # INVERSION
`F SLEEP LAT` = "45", # Duration | M
`F SLEEP END` = "08:30", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "00:00" # Duration | [H]MS, [H]M, [H]
) |>
## Presence of invalid values
dplyr::add_row(
`ID` = as.character(reserved_id[4]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "10", # integer | [0-7] # INVALID
`W BEDTIME` = "27:00", # hms | HMS, HM, H [0-24h] # INVALID
`W SLEEP PREP` = "02:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "30", # Duration | M
`W SLEEP END` = "12:15", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "20", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Sim", # logical | Yes/No # INVALID
`W LIGHT EXPOSURE` = "02:15", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "34:00", # hms | HMS, HM, H [0-24h] # INVALID
`F SLEEP PREP` = "04:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "14:12", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "-01:30" # Duration | [H]MS, [H]M, [H] # INV.
) |>
## Sleeps more on workdays than on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[5]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "2", # integer | [0-7]
`W BEDTIME` = "21:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "2130", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "09:15", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "0500", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "5", # Duration | M
`F SLEEP END` = "06:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "07:00" # Duration | [H]MS, [H]M, [H]
) |>
## Uses an alarm clock on work-free days
dplyr::add_row(
`ID` = as.character(reserved_id[6]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "15", # Duration | M
`W SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:55", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "30", # Duration | M
`F SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "0", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No # Alarm == "Yes"
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Child(ren)/pet(s)", # character
`F LIGHT EXPOSURE` = "04:45" # Duration | [H]MS, [H]M, [H]
) |>
## Null MCTQ
dplyr::add_row(
`ID` = as.character(reserved_id[7]), # integer | [auto-increment]
`WORK REGULAR` = "", # logical | Yes/No
`WORK DAYS` = "", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "", # Duration | M
`F SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "", # Duration | M
`F ALARM` = "", # logical | Yes/No
`F REASONS` = "", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "" # Duration | [H]MS, [H]M, [H]
) |>
## Did not answer workdays questions
dplyr::add_row(
`ID` = as.character(reserved_id[8]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "03:30", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "04:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "90", # Duration | M
`F SLEEP END` = "15:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "30", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "00:30" # Duration | [H]MS, [H]M, [H]
) |>
## All, or almost all, basic variables have the same values
dplyr::add_row(
`ID` = as.character(reserved_id[9]), # integer | [auto-increment]
`WORK REGULAR` = "0", # logical | Yes/No
`WORK DAYS` = "0", # integer | [0-7]
`W BEDTIME` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "0", # Duration | M
`W SLEEP END` = "0", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "0", # Duration | M
`W ALARM` = "0", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "0", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "0", # Duration | M
`F SLEEP END` = "0", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "0", # Duration | M
`F ALARM` = "0", # logical | Yes/No
`F REASONS` = "0", # logical | Yes/No
`F REASONS WHY` = "0", # character
`F LIGHT EXPOSURE` = "0" # Duration | [H]MS, [H]M, [H]
) |>
## Works 7 days a week and didn't answer the work-free days section
dplyr::add_row(
`ID` = as.character(reserved_id[10]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "7", # integer | [0-7]
`W BEDTIME` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:30", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "06:30", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "02:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "", # Duration | M
`F SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "", # Duration | M
`F ALARM` = "", # logical | Yes/No
`F REASONS` = "", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "" # Duration | [H]MS, [H]M, [H]
) |>
## Suspicious values
dplyr::add_row(
`ID` = as.character(reserved_id[11]), # integer | [auto-increment]
`WORK REGULAR` = "No", # logical | Yes/No
`WORK DAYS` = "6", # integer | [0-7]
`W BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h] # SUSPICIOUS
`W SLEEP LAT` = "120", # Duration | M # SUSPICIOUS
`W SLEEP END` = "04:00", # hms | HMS, HM, H [0-24h] # SUSPICIOUS
`W SLEEP INERTIA` = "0", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "Yes", # logical | Yes/No
`W LIGHT EXPOSURE` = "18:00", # Duration | [H]MS, [H]M, [H] # SUSP.
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "00:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "30", # Duration | M
`F SLEEP END` = "09:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "17:00" # Duration | [H]MS, [H]M, [H] # SUSP.
) |>
## Different formats
dplyr::add_row(
`ID` = as.character(reserved_id[12]), # integer | [auto-increment]
`WORK REGULAR` = "true", # logical | Yes/No # AMBIGUOUS
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "11:00 PM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP PREP` = "0000", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP LAT` = "00:15", # Duration | M #AMBIGUOUS
`W SLEEP END` = "07:15 AM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`W SLEEP INERTIA` = "30", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "3", # Duration | [H]MS, [H]M, [H] # AMBIGUOUS
`F BEDTIME` = "01:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "0130 AM", # hms | HMS, HM, H [0-24h] # AMBIGUOUS
`F SLEEP LAT` = "60", # Duration | M
`F SLEEP END` = "10:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "15", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "04:30" # Duration | [H]MS, [H]M, [H]
) |>
## Possible filling error
dplyr::add_row(
`ID` = as.character(reserved_id[13]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "6", # integer | [0-7]
`W BEDTIME` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "", # Duration | M
`W SLEEP END` = "", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "", # Duration | M
`W ALARM` = "", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "22:30", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "15", # Duration | M
`F SLEEP END` = "06:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "3", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No
`F REASONS` = "Yes", # logical | Yes/No
`F REASONS WHY` = "Hobbies", # character
`F LIGHT EXPOSURE` = "01:30" # Duration | [H]MS, [H]M, [H]
) |>
## Repeated workdays and work-free days values (possible carryover
## effect)
dplyr::add_row(
`ID` = as.character(reserved_id[14]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "5", # integer | [0-7]
`W BEDTIME` = "22:00", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "10", # Duration | M
`W SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "5", # Duration | M
`W ALARM` = "Yes", # logical | Yes/No
`W WAKE BEFORE ALARM` = "No", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:00", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "22:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "23:00", # hms | HMS, HM, H [0-24h]
`F SLEEP LAT` = "10", # Duration | M
`F SLEEP END` = "07:00", # hms | HMS, HM, H [0-24h]
`F SLEEP INERTIA` = "5", # Duration | M
`F ALARM` = "Yes", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "No", # character
`F LIGHT EXPOSURE` = "01:00" # Duration | [H]MS, [H]M, [H]
) |>
## Sleep onset is equal or greater than sleep end
## [(s_prep + s_lat) >= se]
dplyr::add_row(
`ID` = as.character(reserved_id[15]), # integer | [auto-increment]
`WORK REGULAR` = "Yes", # logical | Yes/No
`WORK DAYS` = "2", # integer | [0-7]
`W BEDTIME` = "22:30", # hms | HMS, HM, H [0-24h]
`W SLEEP PREP` = "00:00", # hms | HMS, HM, H [0-24h]
`W SLEEP LAT` = "60", # Duration | M
`W SLEEP END` = "08:00", # hms | HMS, HM, H [0-24h]
`W SLEEP INERTIA` = "10", # Duration | M
`W ALARM` = "No", # logical | Yes/No
`W WAKE BEFORE ALARM` = "", # logical | Yes/No
`W LIGHT EXPOSURE` = "01:20", # Duration | [H]MS, [H]M, [H]
`F BEDTIME` = "00:00", # hms | HMS, HM, H [0-24h]
`F SLEEP PREP` = "02:00", # hms | HMS, HM, H [0-24h] # ERROR
`F SLEEP LAT` = "120", # Duration | M # ERROR
`F SLEEP END` = "04:00", # hms | HMS, HM, H [0-24h] # ERROR
`F SLEEP INERTIA` = "15", # Duration | M
`F ALARM` = "No", # logical | Yes/No
`F REASONS` = "No", # logical | Yes/No
`F REASONS WHY` = "", # character
`F LIGHT EXPOSURE` = "04:00" # Duration | [H]MS, [H]M, [H]
)
std_mctq <-
std_mctq %>% # Don't change the pipe.
dplyr::arrange(as.integer(.data$`ID`))
# Write and return output -----
if (isTRUE(write)) {
if (!(dir.exists("./inst/extdata/"))) dir.create("./inst/extdata/")
std_mctq |>
utils::write.csv(
paste0("./inst/extdata/", "std_mctq", ".csv"),
row.names = FALSE,
quote = FALSE
)
}
invisible(std_mctq)
}
#' Tidy `build_std_mctq()` output
#'
#' @description
#'
#' `tidy_std_mctq` tidy the output of `build_std_mctq()`. See
#' [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Here, the process of _tiding_ a dataset is understood as transforming it in
#' input data, like described in Loo and Jonge (2018). It's a very similar
#' process of tiding data described in the workflow proposed by Wickham and
#' Grolemund (n.d.).
#'
#' Please note that input data is not the same as valid data. To get a valid
#' `std_mctq` data, run `validate_std_mctq()`.
#'
#' To learn more about the concept of tidy data, see Wickham (2014) and
#' Wickham and Grolemund (n.d.).
#'
#' @param write (optional) a [`logical`][base::logical()] value indicating if
#' the function must write a `std_mctq.rda` file to `"./data/"` (default:
#' `FALSE`).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a tidied, but not
#' validated, standard MCTQ dataset.
#'
#' @template references_e
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(tidy_std_mctq())
#' }
#' }
tidy_std_mctq <- function(write = FALSE) {
# Check arguments -----
checkmate::assert_flag(write)
cli::cli_progress_step("Tyding MCTQ data")
# Set values -----
std_mctq <- build_std_mctq()
# Clean NULL cases -----
fix_character <- function(x) {
x <- trimws(x)
for (i in c("", "NA")) {
x <- dplyr::na_if(x, i)
}
x
}
std_mctq <-
std_mctq |>
dplyr::mutate(dplyr::across(.fns = fix_character)) |>
dplyr::rowwise() %>% # Don't change the pipe.
dplyr::mutate(
length = dplyr::n_distinct(dplyr::c_across(-.data$ID))
) %>% # Don't change the pipe.
dplyr::mutate(
dplyr::across(
-.data$ID,
.fns = ~ ifelse(length <= 2, NA, .x)
)
) |>
dplyr::ungroup() |>
dplyr::select(-length)
# Convert columns -----
pattern_1 <- "^\\d{1,3}$"
pattern_2 <- "^([-+])?(2[4-9]|[3-9]\\d|\\d{3,})(:)?[0-5]\\d((:)?[0-5]\\d)?"
pattern_3 <- "^\\-"
std_mctq <-
std_mctq %>% # Don't change the pipe.
dplyr::transmute(
id = as.integer(.data$`ID`),
work = dplyr::case_when(
tolower(.data$`WORK REGULAR`) == "yes" ~ TRUE,
tolower(.data$`WORK REGULAR`) == "true" ~ TRUE,
tolower(.data$`WORK REGULAR`) == "no" ~ FALSE
),
wd = as.integer(.data$`WORK DAYS`),
bt_w = dplyr::case_when(
grepl(pattern_2, .data$`W BEDTIME`, perl = TRUE) ~
mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W BEDTIME`, "HM")
)),
TRUE ~ mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W BEDTIME`, c("HM", "IMp"))
))
),
sprep_w = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`W SLEEP PREP`, c("HMS", "HM", "H")
))),
slat_w = dplyr::case_when(
grepl(pattern_1, .data$`W SLEEP LAT`, perl = TRUE) ~
mctq:::shush(lubridate::dminutes(as.numeric(
.data$`W SLEEP LAT`
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`W SLEEP LAT`, c("HMS", "HM", "H"))
)))
),
se_w = mctq:::shush(hms::as_hms(
lubridate::parse_date_time(.data$`W SLEEP END`, c("HMS", "HM", "H"))
)),
si_w = mctq:::shush(lubridate::dminutes(as.numeric(
.data$`W SLEEP INERTIA`
))),
alarm_w = dplyr::case_when(
tolower(.data$`W ALARM`) == "yes" ~ TRUE,
tolower(.data$`W ALARM`) == "no" ~ FALSE
),
wake_before_w = dplyr::case_when(
tolower(.data$`W WAKE BEFORE ALARM`) == "yes" ~ TRUE,
tolower(.data$`W WAKE BEFORE ALARM`) == "no" ~ FALSE
),
le_w = mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(
.data$`W LIGHT EXPOSURE`, c("HMS", "HM", "H")
)
))),
bt_f = dplyr::case_when(
grepl(pattern_2, .data$`F BEDTIME`, perl = TRUE) ~
mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F BEDTIME`, "HM"
))),
TRUE ~ mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F BEDTIME`, c("HMS", "HM", "H")
)))
),
sprep_f = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F SLEEP PREP`, c("HMS", "HM", "H")
))),
slat_f = mctq:::shush(lubridate::dminutes(as.numeric(
.data$`F SLEEP LAT`
))),
se_f = mctq:::shush(hms::as_hms(lubridate::parse_date_time(
.data$`F SLEEP END`, c("HMS", "HM", "H")
))),
si_f = dplyr::case_when(
grepl(pattern_1, .data$`F SLEEP INERTIA`) ~
mctq:::shush(lubridate::dminutes(as.numeric(
.data$`F SLEEP INERTIA`
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(
.data$`F SLEEP INERTIA`, c("HMS", "HM", "H")
)
)))
),
alarm_f = dplyr::case_when(
tolower(.data$`F ALARM`) == "yes" ~ TRUE,
tolower(.data$`F ALARM`) == "no" ~ FALSE
),
reasons_f = dplyr::case_when(
tolower(.data$`F REASONS`) == "yes" ~ TRUE,
tolower(.data$`F REASONS`) == "no" ~ FALSE
),
reasons_why_f = .data$`F REASONS WHY`,
le_f = dplyr::case_when(
grepl(pattern_3, .data$`F LIGHT EXPOSURE`) ~
mctq:::shush(- lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`F LIGHT EXPOSURE`, "HM")
))),
TRUE ~ mctq:::shush(lubridate::as.duration(hms::as_hms(
lubridate::parse_date_time(.data$`F LIGHT EXPOSURE`, "HM")
)))
)
)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
#' Validate `tidy_std_mctq()` output
#'
#' @description
#'
#' `validate_std_mctq()` validates the output of `tidy_std_mctq()`.
#' See [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Here, the process of _validating_ a dataset is understood as detecting
#' invalid data, by checking whether data satisfies certain assumptions from
#' domain knowledge, to them, removing or, if possible, fixing them. You can
#' find more about data validation and error location in Loo and Jonge (2018).
#'
#' This process can be considered as part of the process of transforming data,
#' described in the workflow proposed by Wickham and Grolemund (n.d.).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with a validated standard
#' MCTQ dataset.
#'
#' @inheritParams tidy_std_mctq
#' @template references_d
#' @family data functions
#' @importFrom magrittr %>%
#' @importFrom rlang .data := !!
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(validate_std_mctq())
#' }
#' }
validate_std_mctq <- function(write = FALSE) {
# To do -----
#
# * Adapt this process by using `errorlocate` package with `validate`.
# Check arguments -----
checkmate::assert_flag(write)
cli::cli_progress_step("Validating MCTQ data")
# Set values -----
set.seed(1)
reserved_id <- sample(50, 15)
std_mctq <- tidy_std_mctq()
# Do univariate validation -----
std_mctq <-
std_mctq |>
dplyr::mutate(
wd = dplyr::case_when(
validate::in_range(wd, min = 0, max = 7) ~ wd
)
) |>
dplyr::mutate(dplyr::across(
dplyr::matches("^bt_|^sprep_|^se_"),
~ dplyr::case_when(
.x == hms::parse_hm("24:00") ~ hms::parse_hm("00:00"),
.x >= hms::parse_hm("00:00") &
.x < hms::parse_hm("24:00") ~ .x
)
),
dplyr::across(
dplyr::matches("^slat_|^si_"),
~ dplyr::case_when(
validate::in_range(
.x,
min = lubridate::dhours(0),
max = lubridate::dhours(6)
) ~ .x
)
),
dplyr::across(
dplyr::matches("^le_"),
~ dplyr::case_when(
validate::in_range(
.x,
min = lubridate::dhours(0),
max = lubridate::dhours(24)
) ~ .x
)
)
)
# Do multivariate validation -----
for (i in c("_w", "_f")) {
bt_i <- paste0("bt", i)
sprep_i <- paste0("sprep", i)
std_mctq <-
std_mctq |>
dplyr::mutate(
dummy = dplyr::case_when(
mctq::assign_date(!!as.symbol(bt_i), !!as.symbol(sprep_i)) >
lubridate::dhours(12) ~ TRUE,
TRUE ~ FALSE
),
bkp = !!as.symbol(bt_i),
!!as.symbol(bt_i) := dplyr::if_else(
dummy, !!as.symbol(sprep_i), !!as.symbol(bt_i)
),
!!as.symbol(sprep_i) := dplyr::if_else(
dummy, bkp, !!as.symbol(sprep_i)
)
) |>
dplyr::select(-dummy, -bkp)
}
for (i in c("_w", "_f")) {
sprep_i <- paste0("sprep", i)
slat_i <- paste0("slat", i)
se_i <- paste0("se", i)
test <-
std_mctq |>
dplyr::mutate(
so_i = mctq::so(!!as.symbol(sprep_i), !!as.symbol(slat_i)),
sd_i = mctq::sdu(so_i, !!as.symbol(se_i)),
dummy = dplyr::case_when(
sd_i < lubridate::dhours(2) |
sd_i > lubridate::dhours(18) ~ TRUE,
TRUE ~ FALSE
)
) |>
dplyr::select(dummy)
std_mctq <-
std_mctq |>
dplyr::bind_cols(test) |>
dplyr::mutate(dplyr::across(
dplyr::ends_with(i),
~ dplyr::if_else(dummy, gutils:::na_as(.x), .x)
)) |>
dplyr::select(-dummy)
}
# Clean invalid cases -----
## Cases: "Suspicious values"
invalid <- c(reserved_id[11])
std_mctq <-
std_mctq |>
dplyr::rowwise() %>% # Don't change the pipe.
dplyr::mutate(dplyr::across(
-.data$id,
.fns = ~ dplyr::if_else(
.data$id %in% invalid, gutils:::na_as(.x), .x
)
)
) |>
dplyr::ungroup()
# Fix/impute linked data -----
std_mctq <-
std_mctq |>
dplyr::mutate(
wd = dplyr::case_when(
work == FALSE & is.na(wd) ~ as.integer(0),
TRUE ~ wd
),
work = dplyr::case_when(
work == FALSE & wd > 0 ~ TRUE,
TRUE ~ work
),
wake_before_w = dplyr::case_when(
alarm_w == FALSE ~ as.logical(NA),
TRUE ~ wake_before_w
),
reasons_why_f = dplyr::case_when(
tolower(reasons_why_f) == "no" ~ as.character(NA),
TRUE ~ reasons_why_f
),
reasons_f = dplyr::case_when(
!is.na(reasons_why_f) ~ TRUE,
TRUE ~ reasons_f
)
)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
#' Analyze `validate_std_mctq()` output
#'
#' @description
#'
#' `analyse_std_mctq()` computes and creates the non-measured MCTQ variables
#' based on the output of `validate_std_mctq()`. See
#' [`?std_mctq`][mctq::std_mctq] to learn more.
#'
#' @details
#'
#' Computing and creating new variables is part of the process of producing
#' statistics, like described in Loo and Jonge (2018). It's also a part of the
#' process of transforming data, described in the workflow proposed by Wickham
#' and Grolemund (n.d.).
#'
#' @return An invisible [`tibble`][dplyr::tibble()] with all the variables
#' proposed for a standard MCTQ dataset.
#'
#' @inheritParams tidy_std_mctq
#' @inheritParams pretty_mctq
#' @template references_d
#' @family data functions
#' @importFrom magrittr %>%
#' @noRd
#'
#' @examples
#' \dontrun{
#' if (requireNamespace("utils", quietly = TRUE)) {
#' utils::View(analyze_std_mctq())
#' }
#' }
analyze_std_mctq <- function(write = FALSE, round = TRUE, hms = FALSE) {
# Check arguments -----
checkmate::assert_flag(write)
checkmate::assert_flag(round)
checkmate::assert_flag(hms)
cli::cli_progress_step("Analyzing MCTQ data")
# Compute variables -----
std_mctq <-
validate_std_mctq() |>
dplyr::mutate(
fd = mctq::fd(wd),
so_w = mctq::so(sprep_w, slat_w),
gu_w = mctq::gu(se_w, si_w),
sd_w = mctq::sdu(so_w, se_w),
tbt_w = mctq::tbt(bt_w, gu_w),
msw = mctq::msl(so_w, sd_w),
so_f = mctq::so(sprep_f, slat_f),
gu_f = mctq::gu(se_f, si_f),
sd_f = mctq::sdu(so_f, se_f),
tbt_f = mctq::tbt(bt_f, gu_f),
msf = mctq::msl(so_f, sd_f),
sd_week = mctq::sd_week(sd_w, sd_f, wd),
msf_sc = mctq::msf_sc(msf, sd_w, sd_f, sd_week, alarm_f),
sloss_week = mctq::sloss_week(sd_w, sd_f, wd),
le_week = mctq::le_week(le_w, le_f, wd),
sjl_rel = mctq::sjl_rel(msw, msf),
sjl = abs(sjl_rel),
sjl_sc_rel = mctq::sjl_sc_rel(so_w, se_w, so_f, se_f),
sjl_sc = abs(sjl_sc_rel)
) |>
dplyr::relocate(
id, work, wd, fd,
bt_w, sprep_w, slat_w, so_w, se_w, si_w, gu_w, alarm_w,
wake_before_w, sd_w, tbt_w, le_w, msw,
bt_f, sprep_f, slat_f, so_f, se_f, si_f, gu_f, alarm_f,
reasons_f, reasons_why_f, sd_f, tbt_f, le_f, msf,
sd_week, sloss_week, le_week, msf_sc, sjl_rel, sjl, sjl_sc_rel,
sjl_sc
)
# Fix missing sections -----
## See `vignette("missing-sections", pakckage = "mctq")` to learn more.
count_w <- length(names(std_mctq)[grepl("_w$", names(std_mctq))])
count_f <- length(names(std_mctq)[grepl("_f$", names(std_mctq))])
count_w <- count_w * (2 / 3)
count_f <- count_f * (2 / 3)
count_na <- function(x) {
checkmate::assert_atomic(x)
length(which(is.na(x)))
}
test <-
std_mctq |>
dplyr::mutate(dplyr::across(.fns = as.character)) |>
dplyr::rowwise() |>
dplyr::mutate(
dummy_0_a = as.integer(wd) == 0,
dummy_0_b = count_na(dplyr::c_across(dplyr::ends_with("_w"))) >= count_w,
dummy_0_c = alarm_f == FALSE,
dummy_7_a = as.integer(wd) == 7,
dummy_7_b = count_na(dplyr::c_across(dplyr::ends_with("_f"))) >= count_f,
dummy_0 = dummy_0_a & dummy_0_b & dummy_0_c & dummy_7_b == FALSE,
dummy_7 = dummy_7_a & dummy_7_b & dummy_0_b == FALSE
) |>
dplyr::ungroup() |>
dplyr::select(dummy_0, dummy_7)
std_mctq <-
dplyr::bind_cols(std_mctq, test) |>
dplyr::mutate(
sd_week = dplyr::case_when(
dummy_0 == TRUE ~ sd_f,
dummy_7 == TRUE ~ sd_w,
TRUE ~ sd_week
),
msf_sc = dplyr::if_else(dummy_0, msf, msf_sc),
sloss_week = dplyr::if_else(
dummy_0, lubridate::dhours(0), sloss_week
),
le_week = dplyr::case_when(
dummy_0 == TRUE ~ le_f,
dummy_7 == TRUE ~ le_w,
TRUE ~ le_week
),
sjl_rel = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl_rel),
sjl = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl),
sjl_sc_rel = dplyr::if_else(
dummy_0, lubridate::dhours(0), sjl_sc_rel
),
sjl_sc = dplyr::if_else(dummy_0, lubridate::dhours(0), sjl_sc)
) |>
dplyr::select(-dummy_0, -dummy_7)
# Make MCTQ pretty -----
std_mctq <-
std_mctq |>
pretty_mctq(round = round, hms = hms)
# Write and output dataset -----
if (isTRUE(write)) usethis::use_data(std_mctq, overwrite = TRUE)
invisible(std_mctq)
}
# raw <- build_std_mctq()
# tidy <- tidy_std_mctq()
# valid <- validate_std_mctq()
# analysis <- analyze_std_mctq()
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