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Derive Basetype Variable

Source: R/derive_basetype_records.R
derive_basetype_records.Rd

Baseline Type BASETYPE is needed when there is more than one definition of baseline for a given Analysis Parameter PARAM in the same dataset. For a given parameter, if Baseline Value BASE or BASEC are derived and there is more than one definition of baseline, then BASETYPE must be non-null on all records of any type for that parameter where either BASE or BASEC are also non-null. Each value of BASETYPE refers to a definition of baseline that characterizes the value of BASE on that row. Please see section 4.2.1.6 of the ADaM Implementation Guide, version 1.3 for further background.

Usage 

derive_basetype_records(dataset, basetypes)

Arguments

dataset

Input dataset

The variables specified by the basetypes argument are expected to be in the dataset.

Default value

none

basetypes

A named list of expressions created using the rlang::exprs() function

The names corresponds to the values of the newly created BASETYPE variables and the expressions are used to subset the input dataset.

Default value

none

Value

The input dataset with variable BASETYPE added

Details

Adds the BASETYPE variable to a dataset and duplicates records based upon the provided conditions.

For each element of basetypes the input dataset is subset based upon the provided expression and the BASETYPE variable is set to the name of the expression. Then, all subsets are stacked. Records which do not match any condition are kept and BASETYPE is set to NA.

See also

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_doseint(), derive_param_exist_flag(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples

Add records for different baseline types (basetypes)

The basetypes argument is a named list of expressions where each name becomes a value of BASETYPE and each expression defines which records receive that value. A record can match multiple expressions and will be duplicated once for each matching BASETYPE. In this example, records for subject P01 show the duplication across both baseline types.

Records that do not match any condition in basetypes are kept in the output dataset with BASETYPE set to NA. In this example, SCREENING records do not match any of the basetypes conditions and are therefore retained with BASETYPE = NA.

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

bds <- tribble(
  ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL,
  "P01",    "SCREENING",    "PARAM01",     1,  10.2,
  "P01",    "RUN-IN",       "PARAM01",     2,  10.0,
  "P01",    "RUN-IN",       "PARAM01",     3,   9.8,
  "P01",    "DOUBLE-BLIND", "PARAM01",     4,   9.2,
  "P01",    "DOUBLE-BLIND", "PARAM01",     5,  10.1,
  "P02",    "SCREENING",    "PARAM01",     1,  12.2,
  "P02",    "RUN-IN",       "PARAM01",     2,  12.1,
  "P02",    "DOUBLE-BLIND", "PARAM01",     3,  10.2
)

derive_basetype_records(
  dataset = bds,
  basetypes = exprs(
    "RUN-IN" = EPOCH %in% c("RUN-IN", "DOUBLE-BLIND"),
    "DOUBLE-BLIND" = EPOCH == "DOUBLE-BLIND"
  )
)
#> # A tibble: 11 × 6
#>    USUBJID EPOCH        PARAMCD  ASEQ  AVAL BASETYPE
#>    <chr>   <chr>        <chr>   <dbl> <dbl> <chr>
#>  1 P01     SCREENING    PARAM01     1  10.2 <NA>
#>  2 P02     SCREENING    PARAM01     1  12.2 <NA>
#>  3 P01     RUN-IN       PARAM01     2  10   RUN-IN
#>  4 P01     RUN-IN       PARAM01     3   9.8 RUN-IN
#>  5 P01     DOUBLE-BLIND PARAM01     4   9.2 RUN-IN
#>  6 P01     DOUBLE-BLIND PARAM01     5  10.1 RUN-IN
#>  7 P02     RUN-IN       PARAM01     2  12.1 RUN-IN
#>  8 P02     DOUBLE-BLIND PARAM01     3  10.2 RUN-IN
#>  9 P01     DOUBLE-BLIND PARAM01     4   9.2 DOUBLE-BLIND
#> 10 P01     DOUBLE-BLIND PARAM01     5  10.1 DOUBLE-BLIND
#> 11 P02     DOUBLE-BLIND PARAM01     3  10.2 DOUBLE-BLIND

Include all records for multiple baseline type derivations (basetypes = TRUE)

When all parameter records need to be included for multiple baseline type derivations (such as "LAST" and "WORST"), set each expression in basetypes to TRUE. This duplicates every record once for each named baseline type.

bds <- tribble(
  ~USUBJID, ~EPOCH,         ~PARAMCD,  ~ASEQ, ~AVAL,
  "P01",    "RUN-IN",       "PARAM01",     1,  10.0,
  "P01",    "RUN-IN",       "PARAM01",     2,   9.8,
  "P01",    "DOUBLE-BLIND", "PARAM01",     3,   9.2,
  "P01",    "DOUBLE-BLIND", "PARAM01",     4,  10.1
)

derive_basetype_records(
  dataset = bds,
  basetypes = exprs(
    "LAST" = TRUE,
    "WORST" = TRUE
  )
)
#> # A tibble: 8 × 6
#>   USUBJID EPOCH        PARAMCD  ASEQ  AVAL BASETYPE
#>   <chr>   <chr>        <chr>   <dbl> <dbl> <chr>
#> 1 P01     RUN-IN       PARAM01     1  10   LAST
#> 2 P01     RUN-IN       PARAM01     2   9.8 LAST
#> 3 P01     DOUBLE-BLIND PARAM01     3   9.2 LAST
#> 4 P01     DOUBLE-BLIND PARAM01     4  10.1 LAST
#> 5 P01     RUN-IN       PARAM01     1  10   WORST
#> 6 P01     RUN-IN       PARAM01     2   9.8 WORST
#> 7 P01     DOUBLE-BLIND PARAM01     3   9.2 WORST
#> 8 P01     DOUBLE-BLIND PARAM01     4  10.1 WORST