Call a Single Derivation Multiple Times

Source: R/call_derivation.R

Call a single derivation multiple times with some parameters/arguments being fixed across iterations and others varying.

call_derivation(dataset = NULL, derivation, variable_params, ...)

Arguments

dataset

Input dataset

Default value

NULL

derivation

The derivation function to call

A function that performs a specific derivation is expected. A derivation adds variables or observations to a dataset. The first argument of a derivation must expect a dataset and the derivation must return a dataset. All expected arguments for the derivation function must be provided through the params() objects passed to the variable_params and ... arguments.

Default value

none

variable_params

A list of function arguments that are different across iterations. Each set of function arguments must be created using params().

Default value

none

...

Any number of named function arguments that stay the same across iterations. If a function argument is specified both inside variable_params and ... then the value in variable_params overwrites the one in ....

@details

It is also possible to pass functions from outside the {admiral} package to call_derivation(), e.g. an extension package function, or dplyr::mutate(). The only requirement for a function being passed to derivation is that it must take a dataset as its first argument and return a dataset.

Default value

none

Value

The input dataset with additional records/variables added depending on which derivation has been used.

See also

params() restrict_derivation() call_derivation()

Higher Order Functions: derivation_slice(), restrict_derivation(), slice_derivation()

Examples

library(dplyr, warn.conflicts = FALSE)
adsl <- tribble(
  ~STUDYID,   ~USUBJID,      ~TRTSDT,      ~TRTEDT,
  "PILOT01", "01-1307",           NA,           NA,
  "PILOT01", "05-1377", "2014-01-04", "2014-01-25",
  "PILOT01", "06-1384", "2012-09-15", "2012-09-24",
  "PILOT01", "15-1085", "2013-02-16", "2013-08-18",
  "PILOT01", "16-1298", "2013-04-08", "2013-06-28"
) %>%
  mutate(
    across(TRTSDT:TRTEDT, as.Date)
  )

ae <- tribble(
  ~STUDYID,  ~DOMAIN,  ~USUBJID,     ~AESTDTC,     ~AEENDTC,
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-23", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-23", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-15", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-23", "2012-09-29",
  "PILOT01",    "AE", "06-1384", "2012-09-23", "2012-09-29",
  "PILOT01",    "AE", "16-1298", "2013-06-08", "2013-07-06",
  "PILOT01",    "AE", "16-1298", "2013-06-08", "2013-07-06",
  "PILOT01",    "AE", "16-1298", "2013-04-22", "2013-07-06",
  "PILOT01",    "AE", "16-1298", "2013-04-22", "2013-07-06",
  "PILOT01",    "AE", "16-1298", "2013-04-22", "2013-07-06",
  "PILOT01",    "AE", "16-1298", "2013-04-22", "2013-07-06"
)

adae <- ae %>%
  derive_vars_merged(
    dataset_add = adsl,
    new_vars = exprs(TRTSDT, TRTEDT),
    by_vars = exprs(USUBJID)
  )

## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()`
## one can add multiple variables in one go
call_derivation(
  dataset = adae,
  derivation = derive_vars_dt,
  variable_params = list(
    params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"),
    params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN")
  ),
  min_dates = exprs(TRTSDT),
  max_dates = exprs(TRTEDT)
)
#> # A tibble: 16 × 9
#>    STUDYID DOMAIN USUBJID AESTDTC    AEENDTC    TRTSDT     TRTEDT     ASTDT     
#>    <chr>   <chr>  <chr>   <chr>      <chr>      <date>     <date>     <date>    
#>  1 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  2 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  3 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#>  4 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#>  5 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  6 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  7 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  8 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  9 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#> 10 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#> 11 PILOT01 AE     16-1298 2013-06-08 2013-07-06 2013-04-08 2013-06-28 2013-06-08
#> 12 PILOT01 AE     16-1298 2013-06-08 2013-07-06 2013-04-08 2013-06-28 2013-06-08
#> 13 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 14 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 15 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 16 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> # ℹ 1 more variable: AENDT <date>

## The above call using `call_derivation()` is equivalent to the following
adae %>%
  derive_vars_dt(
    new_vars_prefix = "AST",
    dtc = AESTDTC,
    date_imputation = "first",
    min_dates = exprs(TRTSDT),
    max_dates = exprs(TRTEDT)
  ) %>%
  derive_vars_dt(
    new_vars_prefix = "AEN",
    dtc = AEENDTC,
    date_imputation = "last",
    min_dates = exprs(TRTSDT),
    max_dates = exprs(TRTEDT)
  )
#> # A tibble: 16 × 9
#>    STUDYID DOMAIN USUBJID AESTDTC    AEENDTC    TRTSDT     TRTEDT     ASTDT     
#>    <chr>   <chr>  <chr>   <chr>      <chr>      <date>     <date>     <date>    
#>  1 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  2 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  3 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#>  4 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#>  5 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  6 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  7 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  8 PILOT01 AE     06-1384 2012-09-15 2012-09-29 2012-09-15 2012-09-24 2012-09-15
#>  9 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#> 10 PILOT01 AE     06-1384 2012-09-23 2012-09-29 2012-09-15 2012-09-24 2012-09-23
#> 11 PILOT01 AE     16-1298 2013-06-08 2013-07-06 2013-04-08 2013-06-28 2013-06-08
#> 12 PILOT01 AE     16-1298 2013-06-08 2013-07-06 2013-04-08 2013-06-28 2013-06-08
#> 13 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 14 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 15 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> 16 PILOT01 AE     16-1298 2013-04-22 2013-07-06 2013-04-08 2013-06-28 2013-04-22
#> # ℹ 1 more variable: AENDT <date>