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Create dataset of single doses

Source: R/create_single_dose_dataset.R
create_single_dose_dataset.Rd

Derives dataset of single dose from aggregate dose information. This may be necessary when e.g. calculating last dose before an adverse event in ADAE or deriving a total dose parameter in ADEX when EXDOSFRQ != ONCE.

Usage

create_single_dose_dataset(
  dataset,
  dose_freq = EXDOSFRQ,
  start_date = ASTDT,
  start_datetime = NULL,
  end_date = AENDT,
  end_datetime = NULL,
  lookup_table = dose_freq_lookup,
  lookup_column = CDISC_VALUE,
  keep_source_vars = quo_c(vars(USUBJID), dose_freq, start_date, start_datetime,
    end_date, end_datetime)
)

Arguments

dataset

Input dataset

The columns specified by dose_freq, start_date and the end_date parameters are expected.

dose_freq

The dose frequency

The aggregate dosing frequency used for multiple doses in a row.

Permitted Values: defined by lookup table.

start_date

The start date

A date object is expected. This object cannot contain NA values.

Refer to derive_vars_dt() to impute and derive a date from a date character vector to a date object.

start_datetime

The start date-time

A date-time object is expected. This object cannot contain NA values.

Refer to derive_vars_dtm() to impute and derive a date-time from a date character vector to a date object.

If the input dataset contains frequencies which refer to DOSE_WINDOW equals "HOUR" or "MINUTE", the parameter must be specified.

end_date

The end date

A date or date-time object is expected. This object cannot contain NA values.

Refer to derive_vars_dt() to impute and derive a date from a date character vector to a date object.

end_datetime

The end date-time

A date-time object is expected. This object cannot contain NA values.

Refer to derive_vars_dtm() to impute and derive a date-time from a date character vector to a date object.

If the input dataset contains frequencies which refer to DOSE_WINDOW equals "HOUR" or "MINUTE", the parameter must be specified.

lookup_table

The dose frequency value lookup table

The table used to look up dose_freq values and determine the appropriate multiplier to be used for row generation. If a lookup table other than the default is used, it must have columns DOSE_WINDOW, DOSE_COUNT, and CONVERSION_FACTOR. The default table dose_freq_lookup is described in detail here.

Permitted Values for DOSE_WINDOW: "MINUTE", "HOUR", "DAY", "WEEK", "MONTH", "YEAR"

lookup_column

The dose frequency value column in the lookup table

The column of lookup_table.

keep_source_vars

List of variables to be retained from source dataset

This parameter can be specified if additional information is required in the output dataset. For example EXTRT for studies with more than one drug.

Value

The input dataset with a single dose per row.

Details

Each aggregate dose row is split into multiple rows which each represent a single dose.The number of completed dose periods between start_date or start_datetime and end_date or end_datetime is calculated with compute_duration and multiplied by DOSE_COUNT. For DOSE_WINDOW values of "WEEK", "MONTH", and "YEAR", CONVERSION_FACTOR is used to convert into days the time object to be added to start_date.

Observations with dose frequency "ONCE" are copied to the output dataset unchanged.

See also

Creating auxiliary datasets: create_period_dataset(), create_query_data()

Author

Michael Thorpe, Andrew Smith

Examples

# Example with default lookup

library(lubridate)
library(stringr)
library(tibble)

data <- tribble(
  ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
  "P01", "Q2D", ymd("2021-01-01"), ymd_hms("2021-01-01 10:30:00"),
  ymd("2021-01-07"), ymd_hms("2021-01-07 11:30:00"),
  "P01", "Q3D", ymd("2021-01-08"), ymd_hms("2021-01-08 12:00:00"),
  ymd("2021-01-14"), ymd_hms("2021-01-14 14:00:00"),
  "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd_hms("2021-01-15 09:57:00"),
  ymd("2021-01-29"), ymd_hms("2021-01-29 10:57:00")
)

create_single_dose_dataset(data)
#> # A tibble: 9 x 4
#>   USUBJID EXDOSFRQ ASTDT      AENDT     
#>   <chr>   <chr>    <date>     <date>    
#> 1 P01     ONCE     2021-01-01 2021-01-01
#> 2 P01     ONCE     2021-01-03 2021-01-03
#> 3 P01     ONCE     2021-01-05 2021-01-05
#> 4 P01     ONCE     2021-01-07 2021-01-07
#> 5 P01     ONCE     2021-01-08 2021-01-08
#> 6 P01     ONCE     2021-01-11 2021-01-11
#> 7 P01     ONCE     2021-01-14 2021-01-14
#> 8 P01     ONCE     2021-01-15 2021-01-15
#> 9 P01     ONCE     2021-01-29 2021-01-29


# Example with custom lookup

custom_lookup <- tribble(
  ~Value,   ~DOSE_COUNT, ~DOSE_WINDOW, ~CONVERSION_FACTOR,
  "Q30MIN", (1 / 30),    "MINUTE",                      1,
  "Q90MIN", (1 / 90),    "MINUTE",                      1
)

data <- tribble(
  ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~ASTDTM, ~AENDT, ~AENDTM,
  "P01", "Q30MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
  ymd("2021-01-01"), ymd_hms("2021-01-01T07:00:00"),
  "P02", "Q90MIN", ymd("2021-01-01"), ymd_hms("2021-01-01T06:00:00"),
  ymd("2021-01-01"), ymd_hms("2021-01-01T09:00:00")
)

create_single_dose_dataset(data,
  lookup_table = custom_lookup,
  lookup_column = Value,
  start_datetime = ASTDTM,
  end_datetime = AENDTM
)
#> # A tibble: 6 x 6
#>   USUBJID EXDOSFRQ ASTDT      ASTDTM              AENDT      AENDTM             
#>   <chr>   <chr>    <date>     <dttm>              <date>     <dttm>             
#> 1 P01     ONCE     2021-01-01 2021-01-01 06:00:00 2021-01-01 2021-01-01 06:00:00
#> 2 P01     ONCE     2021-01-01 2021-01-01 06:30:00 2021-01-01 2021-01-01 06:30:00
#> 3 P01     ONCE     2021-01-01 2021-01-01 07:00:00 2021-01-01 2021-01-01 07:00:00
#> 4 P02     ONCE     2021-01-01 2021-01-01 06:00:00 2021-01-01 2021-01-01 06:00:00
#> 5 P02     ONCE     2021-01-01 2021-01-01 07:30:00 2021-01-01 2021-01-01 07:30:00
#> 6 P02     ONCE     2021-01-01 2021-01-01 09:00:00 2021-01-01 2021-01-01 09:00:00