derive_vars_duration: Derive Duration

In admiral: ADaM in R Asset Library

Derive Duration

Description

Derives duration between two dates, specified by the variables present in input dataset e.g., duration of adverse events, relative day, age, ...

Usage

derive_vars_duration(
  dataset,
  new_var,
  new_var_unit = NULL,
  start_date,
  end_date,
  in_unit = "days",
  out_unit = "DAYS",
  floor_in = TRUE,
  add_one = TRUE,
  trunc_out = FALSE,
  type = "duration"
)

Arguments

dataset	Input dataset The variables specified by the start_date and end_date arguments are expected to be in the dataset.
new_var	Name of variable to create
new_var_unit	Name of the unit variable If the parameter is not specified, no variable for the unit is created.
start_date	The start date A date or date-time object is expected. Refer to derive_vars_dt() to impute and derive a date from a date character vector to a date object. Refer to convert_dtc_to_dt() to obtain a vector of imputed dates.
end_date	The end date A date or date-time object is expected. Refer to derive_vars_dt() to impute and derive a date from a date character vector to a date object. Refer to convert_dtc_to_dt() to obtain a vector of imputed dates.
in_unit	Input unit See floor_in and add_one parameter for details. Permitted Values (case-insensitive): For years: "year", "years", "yr", "yrs", "y" For months: "month", "months", "mo", "mos" For days: "day", "days", "d" For hours: "hour", "hours", "hr", "hrs", "h" For minutes: "minute", "minutes", "min", "mins" For seconds: "second", "seconds", "sec", "secs", "s"
out_unit	Output unit The duration is derived in the specified unit Permitted Values (case-insensitive): For years: "year", "years", "yr", "yrs", "y" For months: "month", "months", "mo", "mos" For weeks: "week", "weeks", "wk", "wks", "w" For days: "day", "days", "d" For hours: "hour", "hours", "hr", "hrs", "h" For minutes: "minute", "minutes", "min", "mins" For seconds: "second", "seconds", "sec", "secs", "s"
floor_in	Round down input dates? The input dates are round down with respect to the input unit, e.g., if the input unit is 'days', the time of the input dates is ignored. Default: TRUE Permitted Values: TRUE, FALSE
add_one	Add one input unit? If the duration is non-negative, one input unit is added. i.e., the duration can not be zero. Default: TRUE Permitted Values: TRUE, FALSE
trunc_out	Return integer part The fractional part of the duration (in output unit) is removed, i.e., the integer part is returned. Default: FALSE Permitted Values: TRUE, FALSE
type	lubridate duration type. See below for details. Default: "duration" Permitted Values: "duration", "interval"

Details

The duration is derived as time from start to end date in the specified output unit. If the end date is before the start date, the duration is negative. The start and end date variable must be present in the specified input dataset.

The lubridate package calculates two types of spans between two dates: duration and interval. While these calculations are largely the same, when the unit of the time period is month or year the result can be slightly different.

The difference arises from the ambiguity in the length of "1 month" or "1 year". Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years. Durations and intervals help solve the ambiguity in these measures.

The interval between 2000-02-01 and 2000-03-01 is 1 (i.e. one month). The duration between these two dates is 0.95, which accounts for the fact that the year 2000 is a leap year, February has 29 days, and the average month length is 30.4375, i.e. 29 / 30.4375 = 0.95.

For additional details, review the lubridate time span reference page.

Value

The input dataset with the duration and unit variable added

See Also

compute_duration()

Date/Time Derivation Functions that returns variable appended to dataset: derive_var_trtdurd(), derive_vars_dt(), derive_vars_dtm(), derive_vars_dtm_to_dt(), derive_vars_dtm_to_tm(), derive_vars_dy()

Examples

library(lubridate)
library(tibble)

# Derive age in years
data <- tribble(
  ~USUBJID, ~BRTHDT, ~RANDDT,
  "P01", ymd("1984-09-06"), ymd("2020-02-24"),
  "P02", ymd("1985-01-01"), NA,
  "P03", NA, ymd("2021-03-10"),
  "P04", NA, NA
)

derive_vars_duration(data,
  new_var = AAGE,
  new_var_unit = AAGEU,
  start_date = BRTHDT,
  end_date = RANDDT,
  out_unit = "years",
  add_one = FALSE,
  trunc_out = TRUE
)

# Derive adverse event duration in days
data <- tribble(
  ~USUBJID, ~ASTDT, ~AENDT,
  "P01", ymd("2021-03-05"), ymd("2021-03-02"),
  "P02", ymd("2019-09-18"), ymd("2019-09-18"),
  "P03", ymd("1985-01-01"), NA,
  "P04", NA, NA
)

derive_vars_duration(data,
  new_var = ADURN,
  new_var_unit = ADURU,
  start_date = ASTDT,
  end_date = AENDT,
  out_unit = "days"
)

# Derive adverse event duration in minutes
data <- tribble(
  ~USUBJID, ~ADTM, ~TRTSDTM,
  "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-09T05:00:00"),
  "P02", ymd_hms("2019-11-11T10:30:00"), ymd_hms("2019-11-11T11:30:00"),
  "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-11T04:00:00"),
  "P04", NA, ymd_hms("2019-11-11T12:34:56"),
)

derive_vars_duration(data,
  new_var = ADURN,
  new_var_unit = ADURU,
  start_date = ADTM,
  end_date = TRTSDTM,
  in_unit = "minutes",
  out_unit = "minutes",
  add_one = FALSE
)

# Derive adverse event start time since last dose in hours
data <- tribble(
  ~USUBJID, ~ASTDTM, ~LDOSEDTM,
  "P01", ymd_hms("2019-08-09T04:30:56"), ymd_hms("2019-08-08T10:05:00"),
  "P02", ymd_hms("2019-11-11T23:59:59"), ymd_hms("2019-10-11T11:37:00"),
  "P03", ymd_hms("2019-11-11T00:00:00"), ymd_hms("2019-11-10T23:59:59"),
  "P04", ymd_hms("2019-11-11T12:34:56"), NA,
  "P05", NA, ymd_hms("2019-09-28T12:34:56")
)
derive_vars_duration(
  data,
  new_var = LDRELTM,
  new_var_unit = LDRELTMU,
  start_date = LDOSEDTM,
  end_date = ASTDTM,
  in_unit = "hours",
  out_unit = "hours",
  add_one = FALSE
)

admiral documentation built on June 22, 2024, 9:06 a.m.