metatools (version 0.2.0)

create_var_from_codelist: Create Variable from Codelist

Description

This functions uses code/decode pairs from a metacore object to create new variables in the data

Usage

create_var_from_codelist(
  data,
  metacore,
  input_var,
  out_var,
  codelist = NULL,
  decode_to_code = TRUE,
  strict = TRUE
)

Value

Dataset with a new column added

Arguments

data

Dataset that contains the input variable

metacore

A metacore object to get the codelist from. This should be a subsetted metacore object (of subclass DatasetMeta) created using metacore::select_dataset.

input_var

Name of the variable that will be translated for the new column

out_var

Name of the output variable. Note: Unless a codelist is provided the grouping will always be from the code of the codelist associates with out_var.

codelist

Optional argument to supply a codelist. Must be a data.frame with code and decode columns such as those created by the function metacore::get_control_term. If no codelist is provided the codelist associated with the column supplied to out_var will be used. By default codelist is NULL.

decode_to_code

Direction of the translation. Default value is TRUE, i.e., assumes the input_var is the decode column of the codelist. Set to FALSE if the input_var is the code column of the codelist.

strict

A logical value indicating whether to perform strict checking against the codelist. If TRUE will issue a warning if values in the input_var column are not present in the codelist. If FALSE no warning is issued and values not present in the codelist will likely result in NA results.

Examples

library(metacore)
library(tibble)
data <- tribble(
  ~USUBJID, ~VAR1, ~VAR2,
  1, "M", "Male",
  2, "F", "Female",
  3, "F", "Female",
  4, "U", "Unknown",
  5, "M", "Male",
)
spec <- spec_to_metacore(metacore_example("p21_mock.xlsx"), quiet = TRUE)
dm_spec <- select_dataset(spec, "DM", quiet = TRUE)
create_var_from_codelist(data, dm_spec, VAR2, SEX)
create_var_from_codelist(data, dm_spec, "VAR2", "SEX")
create_var_from_codelist(data, dm_spec, VAR1, SEX, decode_to_code = FALSE)

# Example providing a custom codelist
# This example also reverses the direction of translation
load(metacore_example('pilot_ADaM.rda'))
adlb_spec <- select_dataset(metacore, "ADLBC", quiet = TRUE)
adlb <- tibble(PARAMCD = c("ALB", "ALP", "ALT", "AST", "BILI", "BUN"))
create_var_from_codelist(
   adlb,
   adlb_spec,
   PARAMCD,
   PARAM,
   codelist = get_control_term(adlb_spec, PARAMCD),
   decode_to_code = FALSE,
   strict = FALSE)

if (FALSE) {
# Example expecting warning where `strict` == `TRUE`
adlb <- tibble(PARAMCD = c("ALB", "ALP", "ALT", "AST", "BILI", "BUN", "DUMMY1", "DUMMY2"))
create_var_from_codelist(
   adlb,
   adlb_spec,
   PARAMCD,
   PARAM,
   codelist = get_control_term(adlb_spec, PARAMCD),
   decode_to_code = FALSE,
   strict = TRUE)
}