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Map ICD Codes to Infectious Syndromes

Source: R/prep_diagnosis.R
prep_map_icd_to_syndrome.Rd

Joins an ICD-to-syndrome reference table onto the data. The reference must have at minimum two columns: an ICD code/description column and a syndrome column. Typically this is a manually curated mapping CSV.

Usage

prep_map_icd_to_syndrome(
  data,
  icd_col = "icd_code",
  icd_to_syndrome_ref,
  ref_icd_col = "icd_code",
  ref_syndrome_col = "infectious_syndrome",
  output_col = "syndrome",
  unmatched_label = NA_character_
)

Arguments

data

Data frame (output of prep_map_diagnosis_to_icd() or any data frame with an ICD column).

icd_col

Character. Column in data holding ICD codes or descriptions to match on. Default "icd_code".

icd_to_syndrome_ref

Data frame. Reference table with at minimum icd_col values and a syndrome column.

ref_icd_col

Character. The ICD column name in icd_to_syndrome_ref. Default "icd_code".

ref_syndrome_col

Character. The syndrome column name in the reference. Default "infectious_syndrome".

output_col

Character. Name for the syndrome column added to data. Default "syndrome".

unmatched_label

Character. Label for rows with no syndrome match. Default NA_character_.

Value

Data frame with output_col added.