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Derive Duration

Source: R/derive_vars_duration.R
derive_vars_duration.Rd

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"

Value

The input dataset with the duration and unit variable added

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.

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
)
#> # A tibble: 4 × 5
#>   USUBJID BRTHDT     RANDDT      AAGE AAGEU
#>   <chr>   <date>     <date>     <dbl> <chr>
#> 1 P01     1984-09-06 2020-02-24    35 years
#> 2 P02     1985-01-01 NA            NA NA   
#> 3 P03     NA         2021-03-10    NA NA   
#> 4 P04     NA         NA            NA NA   

# 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"
)
#> # A tibble: 4 × 5
#>   USUBJID ASTDT      AENDT      ADURN ADURU
#>   <chr>   <date>     <date>     <dbl> <chr>
#> 1 P01     2021-03-05 2021-03-02    -3 days 
#> 2 P02     2019-09-18 2019-09-18     1 days 
#> 3 P03     1985-01-01 NA            NA NA   
#> 4 P04     NA         NA            NA NA   

# 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
)
#> # A tibble: 4 × 5
#>   USUBJID ADTM                TRTSDTM             ADURN ADURU  
#>   <chr>   <dttm>              <dttm>              <dbl> <chr>  
#> 1 P01     2019-08-09 04:30:56 2019-08-09 05:00:00    30 minutes
#> 2 P02     2019-11-11 10:30:00 2019-11-11 11:30:00    60 minutes
#> 3 P03     2019-11-11 00:00:00 2019-11-11 04:00:00   240 minutes
#> 4 P04     NA                  2019-11-11 12:34:56    NA NA     

# 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
)
#> # A tibble: 5 × 5
#>   USUBJID ASTDTM              LDOSEDTM            LDRELTM LDRELTMU
#>   <chr>   <dttm>              <dttm>                <dbl> <chr>   
#> 1 P01     2019-08-09 04:30:56 2019-08-08 10:05:00      18 hours   
#> 2 P02     2019-11-11 23:59:59 2019-10-11 11:37:00     756 hours   
#> 3 P03     2019-11-11 00:00:00 2019-11-10 23:59:59       1 hours   
#> 4 P04     2019-11-11 12:34:56 NA                       NA NA      
#> 5 P05     NA                  2019-09-28 12:34:56      NA NA