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Set the Value of Admiral Options

Source: R/admiral_options.R
set_admiral_options.Rd

Set the Values of Admiral Options That Can Be Modified for Advanced Users.

Usage

set_admiral_options(subject_keys, signif_digits)

Arguments

subject_keys

Variables to uniquely identify a subject, defaults to exprs(STUDYID, USUBJID). This option is used as default value for the subject_keys argument in all admiral functions.

signif_digits

Holds number of significant digits when comparing to numeric variables, defaults to 15. This option is used as default value for the signif_dig argument in admiral functions derive_var_atoxgr_dir() and derive_var_anrind().

Value

No return value, called for side effects.

Details

Modify an admiral option, e.g subject_keys, such that it automatically affects downstream function inputs where get_admiral_option() is called such as derive_param_exist_flag().

See also

get_admiral_option(), derive_param_exist_flag(),derive_param_tte(), derive_var_dthcaus(), derive_var_extreme_dtm(), derive_vars_period(), create_period_dataset(), derive_var_atoxgr_dir(), derive_var_anrind()

Other admiral_options: get_admiral_option()

Examples

library(lubridate)
library(dplyr, warn.conflicts = FALSE)
library(tibble)
set_admiral_options(subject_keys = exprs(STUDYID, USUBJID2))

# Derive a new parameter for measurable disease at baseline
adsl <- tribble(
  ~USUBJID2,
  "1",
  "2",
  "3"
) %>%
  mutate(STUDYID = "XX1234")

tu <- tribble(
  ~USUBJID2,      ~VISIT,    ~TUSTRESC,
  "1",       "SCREENING",     "TARGET",
  "1",          "WEEK 1",     "TARGET",
  "1",          "WEEK 5",     "TARGET",
  "1",          "WEEK 9", "NON-TARGET",
  "2",       "SCREENING", "NON-TARGET",
  "2",       "SCREENING", "NON-TARGET"
) %>%
  mutate(
    STUDYID = "XX1234",
    TUTESTCD = "TUMIDENT"
  )

derive_param_exist_flag(
  dataset_ref = adsl,
  dataset_add = tu,
  filter_add = TUTESTCD == "TUMIDENT" & VISIT == "SCREENING",
  condition = TUSTRESC == "TARGET",
  false_value = "N",
  missing_value = "N",
  set_values_to = exprs(
    PARAMCD = "MDIS",
    PARAM = "Measurable Disease at Baseline"
  )
)
#> # A tibble: 3 × 5
#>   USUBJID2 STUDYID AVALC PARAMCD PARAM                         
#>   <chr>    <chr>   <chr> <chr>   <chr>                         
#> 1 1        XX1234  Y     MDIS    Measurable Disease at Baseline
#> 2 2        XX1234  N     MDIS    Measurable Disease at Baseline
#> 3 3        XX1234  N     MDIS    Measurable Disease at Baseline

set_admiral_options(signif_digits = 14)

# Derive ANRIND for ADVS
advs <- tribble(
  ~PARAMCD, ~AVAL, ~ANRLO, ~ANRHI,
  "DIABP",     59,     60,     80,
  "SYSBP",    120,     90,    130,
  "RESP",      21,      8,     20,
)

derive_var_anrind(advs)
#> # A tibble: 3 × 5
#>   PARAMCD  AVAL ANRLO ANRHI ANRIND
#>   <chr>   <dbl> <dbl> <dbl> <chr> 
#> 1 DIABP      59    60    80 LOW   
#> 2 SYSBP     120    90   130 NORMAL
#> 3 RESP       21     8    20 HIGH