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Create a Reference Dataset for Subperiods, Periods, or Phases

Source: R/period_dataset.R
create_period_dataset.Rd

The function creates a reference dataset for subperiods, periods, or phases from the ADSL dataset. The reference dataset can be used to derive subperiod, period, or phase variables like ASPER, ASPRSDT, ASPREDT, APERIOD, APERSDT, APEREDT, TRTA, APHASEN, PHSDTM, PHEDTM, ... in OCCDS and BDS datasets.

Usage

create_period_dataset(
  dataset,
  new_vars,
  subject_keys = get_admiral_option("subject_keys")
)

Arguments

dataset

Input dataset

The variables specified by the new_vars and subject_keys arguments are expected to be in the dataset. For each element of new_vars at least one variable of the form of the right hand side value must be available in the dataset.

new_vars

New variables

A named list of variables like exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw) is expected. The left hand side of the elements defines a variable of the output dataset, the right hand side defines the source variables from the ADSL dataset in CDISC notation.

If the lower case letter "w" is used it refers to a phase variable, if the lower case letters "xx" are used it refers to a period variable, and if both "xx" and "w" are used it refers to a subperiod variable.

Only one type must be used, e.g., all right hand side values must refer to period variables. It is not allowed to mix for example period and subperiod variables. If period and subperiod variables are required, separate reference datasets must be created.

subject_keys

Variables to uniquely identify a subject

A list of expressions where the expressions are symbols as returned by exprs() is expected.

Value

A period reference dataset (see "Details" section)

Details

For each subject and each subperiod/period/phase where at least one of the source variable is not NA an observation is added to the output dataset.

Depending on the type of the source variable (subperiod, period, or phase) the variable ASPER, APERIOD, or APHASEN is added and set to the number of the subperiod, period, or phase.

The variables specified for new_vars (left hand side) are added to the output dataset and set to the value of the source variable (right hand side).

See also

derive_vars_period()

Creating auxiliary datasets: consolidate_metadata(), create_query_data(), create_single_dose_dataset()

Examples

library(tibble)
library(dplyr, warn.conflicts = FALSE)
library(lubridate)

# Create reference dataset for periods
adsl <- tribble(
  ~USUBJID, ~AP01SDT,     ~AP01EDT,     ~AP02SDT,     ~AP02EDT,     ~TRT01A, ~TRT02A,
  "1",      "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "A",     "B",
  "2",      "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01", "B",     "A",
) %>%
  mutate(
    across(matches("AP\\d\\d[ES]DT"), ymd)
  ) %>%
  mutate(
    STUDYID = "xyz"
  )

create_period_dataset(
  adsl,
  new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT, TRTA = TRTxxA)
)
#> # A tibble: 4 × 6
#>   STUDYID USUBJID APERIOD APERSDT    APEREDT    TRTA 
#>   <chr>   <chr>     <int> <date>     <date>     <chr>
#> 1 xyz     1             1 2021-01-04 2021-02-06 A    
#> 2 xyz     1             2 2021-02-07 2021-03-07 B    
#> 3 xyz     2             1 2021-02-02 2021-03-02 B    
#> 4 xyz     2             2 2021-03-03 2021-04-01 A    

# Create reference dataset for phases
adsl <- tribble(
  ~USUBJID, ~PH1SDT,      ~PH1EDT,      ~PH2SDT,      ~PH2EDT,      ~APHASE1,    ~APHASE2,
  "1",      "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
  "2",      "2021-02-02", "2021-03-02", NA,           NA,           "TREATMENT", NA
) %>%
  mutate(
    across(matches("PH\\d[ES]DT"), ymd)
  ) %>%
  mutate(
    STUDYID = "xyz"
  )

create_period_dataset(
  adsl,
  new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw)
)
#> # A tibble: 3 × 6
#>   STUDYID USUBJID APHASEN PHSDT      PHEDT      APHASE   
#>   <chr>   <chr>     <int> <date>     <date>     <chr>    
#> 1 xyz     1             1 2021-01-04 2021-02-06 TREATMENT
#> 2 xyz     1             2 2021-02-07 2021-03-07 FUP      
#> 3 xyz     2             1 2021-02-02 2021-03-02 TREATMENT

# Create reference datasets for subperiods
adsl <- tribble(
  ~USUBJID, ~P01S1SDT,    ~P01S1EDT,    ~P01S2SDT,    ~P01S2EDT,    ~P02S1SDT,    ~P02S1EDT,
  "1",      "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
  "2",      "2021-02-02", "2021-03-02", NA,           NA,           "2021-03-03", "2021-04-01"
) %>%
  mutate(
    across(matches("P\\d\\dS\\d[ES]DT"), ymd)
  ) %>%
  mutate(
    STUDYID = "xyz"
  )

create_period_dataset(
  adsl,
  new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT)
)
#> # A tibble: 5 × 6
#>   STUDYID USUBJID APERIOD ASPER ASPRSDT    ASPREDT   
#>   <chr>   <chr>     <int> <int> <date>     <date>    
#> 1 xyz     1             1     1 2021-01-04 2021-01-19
#> 2 xyz     1             1     2 2021-01-20 2021-02-06
#> 3 xyz     1             2     1 2021-02-07 2021-03-07
#> 4 xyz     2             1     1 2021-02-02 2021-03-02
#> 5 xyz     2             2     1 2021-03-03 2021-04-01