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Prepare Diagnosis Text

Source: R/prep_diagnosis.R
prep_diagnosis_text.Rd

Combines a primary diagnosis column with an optional fallback column, trims whitespace, and collapses repeated separators. Optionally appends the organism name to the text (as the notebook does for context-aware embedding).

Usage

prep_diagnosis_text(
  data,
  diagnosis_col,
  fallback_col = NULL,
  output_col = "diagnosis_text",
  include_organism = FALSE,
  organism_col = "organism_normalized",
  keep_original = TRUE
)

Arguments

data

Data frame.

diagnosis_col

Character. Primary diagnosis column.

fallback_col

Character or NULL. Used when diagnosis_col is NA. Default NULL.

output_col

Character. Name for the output text column. Default "diagnosis_text".

include_organism

Logical. Append organism name to the text. Default FALSE.

organism_col

Character. Organism column. Used only when include_organism = TRUE. Default "organism_normalized".

keep_original

Logical. Keep the original diagnosis columns. Default TRUE.

Value

Data frame with output_col added.