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Derive Criterion Flag Variables CRITy, CRITyFL, and CRITyFN

Source: R/derive_vars_crit_flag.R
derive_vars_crit_flag.Rd

The function derives ADaM compliant criterion flags, e.g., to facilitate subgroup analyses.

If a criterion flag can't be derived with this function, the derivation is not ADaM compliant. It helps to ensure that

  • the condition of the criterion depends only on variables of the same row,

  • the CRITyFL is populated with valid values, i.e, either "Y" and NA or "Y", "N", and NA,

  • the CRITy variable is populated correctly, i.e.,

    • set to a constant value within a parameter if CRITyFL is populated with "Y", "N", and NA and

    • set to a constant value within a parameter if the criterion condition is fulfilled and to NA otherwise if CRITyFL is populated with "Y", and NA

Usage

derive_vars_crit_flag(
  dataset,
  crit_nr = 1,
  condition,
  description,
  values_yn = FALSE,
  create_numeric_flag = FALSE
)

Arguments

dataset

Input dataset

crit_nr

The criterion number, i.e., the y in CRITy

Permitted Values: a positive integer

condition

Condition for flagging records

See description of the values_yn argument for details on how the CRITyFL variable is populated.

Permitted Values: an unquoted expression which evaluates to a logical (in dataset)

description

The description of the criterion

The CRITy variable is set to the specified value.

An expression can be specified to set the value depending on the parameter. Please note that the value must be constant within a parameter.

Permitted Values: an unquoted expression which evaluates to a character (in dataset)

values_yn

Should "Y" and "N" be used for CRITyFL?

If set to TRUE, the CRITyFL variable is set to "Y" if the condition (condition) evaluates to TRUE, it is set to "N" if the condition evaluate to FALSE, and to NA if it evaluates to NA.

Otherwise, the CRITyFL variable is set to "Y" if the condition (condition) evaluates to TRUE, and to NA otherwise.

Permitted Values: TRUE, FALSE

create_numeric_flag

Create a numeric flag?

If set to TRUE, the CRITyFN variable is created. It is set to 1 if CRITyFL == "Y", it set to 0 if CRITyFL == "N", and to NA otherwise.

Permitted Values: TRUE, FALSE

Value

The input dataset with the variables CRITy, CRITyFL, and optionally CRITyFN added.

See also

BDS-Findings Functions that returns variable appended to dataset: derive_basetype_records(), derive_var_analysis_ratio(), derive_var_anrind(), derive_var_atoxgr(), derive_var_atoxgr_dir(), derive_var_base(), derive_var_chg(), derive_var_ontrtfl(), derive_var_pchg(), derive_var_shift()

Examples

library(tibble)
adbds <- tribble(
  ~PARAMCD, ~AVAL,
  "AST",    42,
  "AST",    52,
  "AST",    NA_real_,
  "ALT",    33,
  "ALT",    51
)

# Create a criterion flag with values "Y" and NA
derive_vars_crit_flag(
  adbds,
  condition = AVAL > 50,
  description = "Absolute value > 50"
)
#> # A tibble: 5 × 4
#>   PARAMCD  AVAL CRIT1FL CRIT1              
#>   <chr>   <dbl> <chr>   <chr>              
#> 1 AST        42 NA      NA                 
#> 2 AST        52 Y       Absolute value > 50
#> 3 AST        NA NA      NA                 
#> 4 ALT        33 NA      NA                 
#> 5 ALT        51 Y       Absolute value > 50

# Create criterion flag with values "Y", "N", and NA and parameter dependent
# criterion description
derive_vars_crit_flag(
  adbds,
  crit_nr = 2,
  condition = AVAL > 50,
  description = paste(PARAMCD, "> 50"),
  values_yn = TRUE,
  create_numeric_flag = TRUE
)
#> # A tibble: 5 × 5
#>   PARAMCD  AVAL CRIT2FL CRIT2    CRIT2FN
#>   <chr>   <dbl> <chr>   <chr>      <int>
#> 1 AST        42 N       AST > 50       0
#> 2 AST        52 Y       AST > 50       1
#> 3 AST        NA NA      AST > 50      NA
#> 4 ALT        33 N       ALT > 50       0
#> 5 ALT        51 Y       ALT > 50       1