sdtm.oak (version 0.1.0)

harcode: Derive an SDTM variable with a hardcoded value

Description

• hardcode_no_ct() maps a hardcoded value to a target SDTM variable that has no terminology restrictions.

• hardcode_ct() maps a hardcoded value to a target SDTM variable with controlled terminology recoding.

Usage

hardcode_no_ct(
  tgt_dat = NULL,
  tgt_val,
  raw_dat,
  raw_var,
  tgt_var,
  id_vars = oak_id_vars()
)
hardcode_ct(
  tgt_dat = NULL,
  tgt_val,
  raw_dat,
  raw_var,
  tgt_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_val

The target SDTM value to be hardcoded into the variable indicated in tgt_var.

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.

tgt_var

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

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. This parameter is optional, if left as NULL no controlled terminology recoding is applied.

ct_clst

A codelist code indicating which subset of the controlled terminology to apply in the derivation. This parameter is optional, if left as NULL, all possible recodings in ct_spec are attempted.

Examples

md1 <-
  tibble::tribble(
    ~oak_id, ~raw_source, ~patient_number, ~MDRAW,
    1L,      "MD1",       101L,            "BABY ASPIRIN",
    2L,      "MD1",       102L,            "CORTISPORIN",
    3L,      "MD1",       103L,            NA_character_,
    4L,      "MD1",       104L,            "DIPHENHYDRAMINE HCL"
  )

# Derive a new variable `CMCAT` by overwriting `MDRAW` with the
# hardcoded value "GENERAL CONCOMITANT MEDICATIONS".
hardcode_no_ct(
  tgt_val = "GENERAL CONCOMITANT MEDICATIONS",
  raw_dat = md1,
  raw_var = "MDRAW",
  tgt_var = "CMCAT"
)

cm_inter <-
  tibble::tribble(
    ~oak_id, ~raw_source, ~patient_number, ~CMTRT,                ~CMINDC,
    1L,      "MD1",       101L,            "BABY ASPIRIN",        NA,
    2L,      "MD1",       102L,            "CORTISPORIN",         "NAUSEA",
    3L,      "MD1",       103L,            "ASPIRIN",             "ANEMIA",
    4L,      "MD1",       104L,            "DIPHENHYDRAMINE HCL", "NAUSEA",
    5L,      "MD1",       105L,            "PARACETAMOL",         "PYREXIA"
  )

# Derive a new variable `CMCAT` by overwriting `MDRAW` with the
# hardcoded value "GENERAL CONCOMITANT MEDICATIONS" with a prior join to
# `target_dataset`.
hardcode_no_ct(
  tgt_dat = cm_inter,
  tgt_val = "GENERAL CONCOMITANT MEDICATIONS",
  raw_dat = md1,
  raw_var = "MDRAW",
  tgt_var = "CMCAT"
)

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

# Hardcoding of `CMCAT` with the value `"GENERAL CONCOMITANT MEDICATIONS"`
# involving terminology recoding. `NA` values in `MDRAW` are preserved in
# `CMCAT`.
hardcode_ct(
  tgt_dat = cm_inter,
  tgt_var = "CMCAT",
  raw_dat = md1,
  raw_var = "MDRAW",
  tgt_val = "GENERAL CONCOMITANT MEDICATIONS",
  ct_spec = ct_spec,
  ct_clst = "C66729"
)