Add AE observation — add_ae_observation • nif

Usage

add_ae_observation(
  nif,
  sdtm,
  ae_term,
  ae_field = "AEDECOD",
  analyte = NULL,
  parent = NULL,
  cmt = NULL,
  subject_filter = "!ACTARMCD %in% c('SCRNFAIL', 'NOTTRT')",
  observation_filter = "TRUE",
  coding_table = NULL,
  keep = NULL,
  debug = FALSE,
  silent = NULL
)

Arguments

nif

A nif object.

sdtm

A sdtm object.

ae_term

The AE term as character.

ae_field

The field in which the AE term is specified in. Can be:

AEDECOD: Dictionary-derived term
AELLT: Lowest-level term
AEHLT: High-level term
AEHLGT: High-level group term
AESOC: System organ class
AEBODSYS: Body system or organ class

or any other field from the 'AE' domain

analyte

The name for the AE observation, defaults to 'AE_xx' with xx the ae_term.

parent

The parent compound as character.

cmt

The compartment as numeric.

subject_filter

A subject filter term.

observation_filter

An observation filter term.

coding_table

A DV coding table as data frame. The coding table translates columns included in the AE domain into a DV field.

keep

Columns to keep, as character.

debug

Include debug fields, as logical.

silent

Suppress messages, defaults to nif_option setting, if NULL.

Value

A nif object.

Details

This function adds AE events as observations with the time of the AE onset as the observation time point and the severity grade as the dependent variable if the field AETOXGR is included. If AETOXGR is not included in the AE domain, a coding table must be provided to translate any other field into a numeric DV column, e.g., coding_table = data.frame( AESEV = c("MILD", "MODERATE", "SEVERE"), DV = c(1, 2, 3)