Conditioned Data Frames
In sdtm.oak: SDTM Data Transformation Engine

knitr::opts_chunk$set(echo = TRUE)
library(sdtm.oak)
library(tibble)

Introduction

Conditioned data frames, or cnd_df, are a powerful tool in the {sdtm.oak} package designed to facilitate conditional transformations on data frames. This article explains how to create and use conditioned data frames, particularly in the context of SDTM domain derivations.

Creating Conditioned Data Frames

A conditioned data frame is a regular data frame extended with a logical vector cnd that marks rows for subsequent conditional transformations. The condition_add() function is used to create these conditioned data frames.

Simple Example

Consider a simple data frame df:

(df <- tibble(x = 1L:3L, y = letters[1L:3L]))

We can create a conditioned data frame where only rows where x > 1 are marked:

(cnd_df <- condition_add(dat = df, x > 1L))

Here, only the second and third rows are marked as TRUE.

Usage in SDTM Domain Derivations

The real power of conditioned data frames manifests when they are used with functions such as assign_no_ct, assign_ct, hardcode_no_ct, and hardcode_ct. These functions perform derivations only for the records that match the pattern of TRUE values in conditioned data frames.

Example with Concomitant Medications (CM) Domain

Consider a simplified dataset of concomitant medications, where we want to derive a new variable CMGRPID (Concomitant Medication Group ID) based on the condition that the medication treatment (CMTRT) is "BENADRYL".

Here is a simplified raw Concomitant Medications data set (cm_raw):

cm_raw <- tibble::tibble(
  oak_id = seq_len(14L),
  raw_source = "ConMed",
  patient_number = c(375L, 375L, 376L, 377L, 377L, 377L, 377L, 378L, 378L, 378L, 378L, 379L, 379L, 379L),
  MDNUM = c(1L, 2L, 1L, 1L, 2L, 3L, 5L, 4L, 1L, 2L, 3L, 1L, 2L, 3L),
  MDRAW = c(
    "BABY ASPIRIN", "CORTISPORIN", "ASPIRIN",
    "DIPHENHYDRAMINE HCL", "PARCETEMOL", "VOMIKIND",
    "ZENFLOX OZ", "AMITRYPTYLINE", "BENADRYL",
    "DIPHENHYDRAMINE HYDROCHLORIDE", "TETRACYCLINE",
    "BENADRYL", "SOMINEX", "ZQUILL"
  )
)
cm_raw

To derive the CMTRT variable we use the assign_no_ct() function to map the MDRAW variable to the CMTRT variable:

tgt_dat <- assign_no_ct(
  tgt_var = "CMTRT",
  raw_dat = cm_raw,
  raw_var = "MDRAW"
)
tgt_dat

Then we create a conditioned data frame from the target data set (tgt_dat), meaning we create a conditioned data frame where only rows with CMTRT equal to "BENADRYL" are marked:

(cnd_tgt_dat <- condition_add(tgt_dat, CMTRT == "BENADRYL"))

Finally, we derive the CMGRPID variable conditionally. Using assign_no_ct(), we derive CMGRPID which indicates the group ID for the medication, based on the conditioned target data set:

derived_tgt_dat <- assign_no_ct(
  tgt_dat = cnd_tgt_dat,
  tgt_var = "CMGRPID",
  raw_dat = cm_raw,
  raw_var = "MDNUM"
)
derived_tgt_dat

Conditioned data frames in the {sdtm.oak} package provide a flexible way to perform conditional transformations on data sets. By marking specific rows for transformation, users can efficiently derive SDTM variables, ensuring that only relevant records are processed.