sdtm.oak (version 0.1.0)

assign_no_ct: Derive an SDTM variable

Description

• assign_no_ct() maps a variable in a raw dataset to a target SDTM variable that has no terminology restrictions.

• assign_ct() maps a variable in a raw dataset to a target SDTM variable following controlled terminology recoding.

Usage

assign_no_ct(
  tgt_dat = NULL,
  tgt_var,
  raw_dat,
  raw_var,
  id_vars = oak_id_vars()
)
assign_ct(
  tgt_dat = NULL,
  tgt_var,
  raw_dat,
  raw_var,
  ct_spec,
  ct_clst,
  id_vars = oak_id_vars()
)

Value

The returned data set depends on the value of tgt_dat:

• If no target dataset is supplied, meaning that tgt_dat defaults to NULL, then the returned data set is raw_dat, selected for the variables indicated in id_vars, and a new extra column: the derived variable, as indicated in tgt_var.

• If the target dataset is provided, then it is merged with the raw data set raw_dat by the variables indicated in id_vars, with a new column: the derived variable, as indicated in tgt_var.

Arguments

tgt_dat

Target dataset: a data frame to be merged against raw_dat by the variables indicated in id_vars. This parameter is optional, see section Value for how the output changes depending on this argument value.

tgt_var

The target SDTM variable: a single string indicating the name of variable to be derived.

raw_dat

The raw dataset (dataframe); must include the variables passed in id_vars and raw_var.

raw_var

The raw variable: a single string indicating the name of the raw variable in raw_dat.

id_vars

Key variables to be used in the join between the raw dataset (raw_dat) and the target data set (raw_dat).

ct_spec

Study controlled terminology specification: a dataframe with a minimal set of columns, see ct_spec_vars() for details.

ct_clst

A codelist code indicating which subset of the controlled terminology to apply in the derivation.

Examples

md1 <-
  tibble::tibble(
    oak_id = 1:14,
    raw_source = "MD1",
    patient_number = 101:114,
    MDIND = c(
      "NAUSEA", "NAUSEA", "ANEMIA", "NAUSEA", "PYREXIA",
      "VOMITINGS", "DIARHHEA", "COLD",
      "FEVER", "LEG PAIN", "FEVER", "COLD", "COLD", "PAIN"
    )
  )

assign_no_ct(
  tgt_var = "CMINDC",
  raw_dat = md1,
  raw_var = "MDIND"
)

cm_inter <-
  tibble::tibble(
    oak_id = 1:14,
    raw_source = "MD1",
    patient_number = 101:114,
    CMTRT = c(
      "BABY ASPIRIN",
      "CORTISPORIN",
      "ASPIRIN",
      "DIPHENHYDRAMINE HCL",
      "PARCETEMOL",
      "VOMIKIND",
      "ZENFLOX OZ",
      "AMITRYPTYLINE",
      "BENADRYL",
      "DIPHENHYDRAMINE HYDROCHLORIDE",
      "TETRACYCLINE",
      "BENADRYL",
      "SOMINEX",
      "ZQUILL"
    ),
    CMROUTE = c(
      "ORAL",
      "ORAL",
      NA,
      "ORAL",
      "ORAL",
      "ORAL",
      "INTRAMUSCULAR",
      "INTRA-ARTERIAL",
      NA,
      "NON-STANDARD",
      "RANDOM_VALUE",
      "INTRA-ARTICULAR",
      "TRANSDERMAL",
      "OPHTHALMIC"
    )
  )

# Controlled terminology specification
(ct_spec <- read_ct_spec_example("ct-01-cm"))

assign_ct(
  tgt_dat = cm_inter,
  tgt_var = "CMINDC",
  raw_dat = md1,
  raw_var = "MDIND",
  ct_spec = ct_spec,
  ct_clst = "C66729"
)