man/examples/as.classcodes.R

In coder: Deterministic Categorization of Items Based on External Code Data

# The Elixhauser comorbidity classification is already a classcodes object
is.classcodes(coder::elixhauser)

# Strip its class attributes to use in examples
df <- as.data.frame(coder::elixhauser)

# Specify which columns store regular expressions and indices
# (assume no hierarchy)
elix <-
  as.classcodes(
    df,
    regex     = c("icd10", "icd10_short", "icd9cm", "icd9cm_ahrqweb", "icd9cm_enhanced"),
    indices   = c("sum_all", "sum_all_ahrq", "walraven",
                "sid29", "sid30", "ahrq_mort", "ahrq_readm"),
    hierarchy = NULL
  )
elix

# Specify hierarchy for patients with different types of cancer and diabetes
# See `?elixhauser` for details
as.classcodes(
  elix,
  hierarchy = list(
    cancer   = c("metastatic cancer", "solid tumor"),
    diabetes = c("diabetes complicated", "diabetes uncomplicated")
  )
)

# Several checks are performed to not allow any erroneous classcodes object
\dontrun{
  as.classcodes(iris)
  as.classcodes(iris, regex = "Species")
}