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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

Permitted values

a dataset, i.e., a data.frame or tibble

Default value

none

crit_nr

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

Permitted values

a positive integer, e.g. 2 or 5

Default value

1

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 condition, e.g., AVISIT == "BASELINE"

Default value

none

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)

Default value

none

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"

Default value

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"

Default value

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

Data setup

The following examples use the BDS dataset below as a basis.

library(tibble, warn.conflicts = FALSE)

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

Creating a simple criterion flag with values "Y" and NA (condition, description)

The following call is a simple application of derive_vars_crit_flag() to derive a criterion flag/variable pair in a BDS dataset.

  • The new variables are named CRIT1/CRIT1FL because the argument crit_nr has not been passed.

  • Since the argument values_yn has also not been passed and thus is set to its default of FALSE, CRIT1FL is set to Y only if condition evaluates to TRUE. For example, in both the first and third records, where condition is respectively FALSE and NA, we set CRIT1FL = NA_character_. The fourth record also exhibits this behavior. Also, as per CDISC standards, in this case CRIT1 is populated only for records where condition evaluates to TRUE.

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

The description argument also accepts expressions which depend on other variables in the input dataset. This can be useful to dynamically populate CRITx, for instance in the case below where we improve the CRIT1 text because the same flag/variable pair is actually being used for multiple parameters.

derive_vars_crit_flag(
  adbds,
  condition = AVAL > 50,
  description = paste(PARAMCD, "> 50"),
)
#> # A tibble: 5 × 4
#>   PARAMCD  AVAL CRIT1FL CRIT1
#>   <chr>   <dbl> <chr>   <chr>
#> 1 AST        42 <NA>    <NA>
#> 2 AST        52 Y       AST > 50
#> 3 AST        NA <NA>    <NA>
#> 4 ALT        33 <NA>    <NA>
#> 5 ALT        51 Y       ALT > 50

Creating a criterion flag with values "Y", "N" and NA (values_yn)

The next call builds on the previous example by using value_yn = TRUE to distinguish between the cases where condition is FALSE and those where it is not evaluable at all.

  • As compared to the previous example, for the first record condition evaluates to FALSE and so we set CRIT1FL = "N", whereas for the third record, condition evaluates to NA because AVAL is missing and so we set CRIT1FL to NA.

  • Note also that because we are using the values "Y", "N" and NA for the flag, as per CDISC standards CRIT1 is now populated for all records rather than just for the "Y" records.

derive_vars_crit_flag(
  adbds,
  condition = AVAL > 50,
  description = paste(PARAMCD, "> 50"),
  values_yn = TRUE
)
#> # A tibble: 5 × 4
#>   PARAMCD  AVAL CRIT1FL CRIT1
#>   <chr>   <dbl> <chr>   <chr>
#> 1 AST        42 N       AST > 50
#> 2 AST        52 Y       AST > 50
#> 3 AST        NA <NA>    AST > 50
#> 4 ALT        33 N       ALT > 50
#> 5 ALT        51 Y       ALT > 50

If the user wishes to set the criterion flag to "N" whenever the condition is not fulfilled, condition can be updated using an if_else call, where the third argument determines the behavior when the condition is not evaluable.

derive_vars_crit_flag(
  adbds,
  condition = if_else(AVAL > 50, TRUE, FALSE, FALSE),
  description = paste(PARAMCD, "> 50"),
  values_yn = TRUE
)
#> # A tibble: 5 × 4
#>   PARAMCD  AVAL CRIT1FL CRIT1
#>   <chr>   <dbl> <chr>   <chr>
#> 1 AST        42 N       AST > 50
#> 2 AST        52 Y       AST > 50
#> 3 AST        NA N       AST > 50
#> 4 ALT        33 N       ALT > 50
#> 5 ALT        51 Y       ALT > 50

Specifying the criterion variable/flag number and creating a numeric flag (crit_nr, create_numeric_flag).

The user can manually specify the criterion variable/flag number to use to name CRITy/CRITyFL by passing the crit_nr argument. This may be necessary if, for instance, other criterion flags already exist in the input dataset.

The user can also choose to create an additional, equivalent numeric flag CRITyFN by setting create_numeric_flag to TRUE.

derive_vars_crit_flag(
  adbds,
  condition = AVAL > 50,
  description = paste(PARAMCD, "> 50"),
  values_yn = TRUE,
  crit_nr = 2,
  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