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Assign One Syndrome Per Patient or Event

Source: R/prep_diagnosis.R
prep_assign_patient_syndrome.Rd

Selects the highest-priority syndrome per patient using the infectious syndrome hierarchy. Matching is case-insensitive (uses normalized names).

Usage

prep_assign_patient_syndrome(
  data,
  patient_col = "patient_id",
  syndrome_col = "syndrome",
  score_col = "icd_score",
  hierarchy_ref = NULL,
  hierarchy_syndrome_col = "infectious_syndrome",
  hierarchy_rank_col = "rank",
  keep_all_candidates = TRUE,
  collapse_unspecified_respiratory = FALSE,
  keep_only_burden_syndromes = FALSE
)

Arguments

data

Data frame with one row per syndrome candidate.

patient_col

Character. Patient or event ID column. Default "patient_id".

syndrome_col

Character. Syndrome column. Default "syndrome".

score_col

Character or NULL. ICD match score column for secondary priority. Default "icd_score".

hierarchy_ref

Data frame or NULL. Syndrome hierarchy (from load_syndrome_hierarchy()). If NULL, loads automatically.

hierarchy_syndrome_col

Character. Syndrome column in hierarchy. Default "infectious_syndrome".

hierarchy_rank_col

Character. Rank column in hierarchy. Default "rank".

keep_all_candidates

Logical. TRUE -> return all rows with syndrome_selected flag; FALSE -> return one row per patient_col (selected only). Default TRUE.

collapse_unspecified_respiratory

Logical. Map "Other unspecified respiratory site infections" -> "Lower respiratory infections" before selection. Default FALSE.

keep_only_burden_syndromes

Logical. Retain only syndromes where contributes_to_amr_burden == TRUE. Default FALSE.

Value

Data frame. When keep_all_candidates = FALSE, includes contributes_to_amr_burden column from the hierarchy.

Details

Priority order per patient:

  1. Hierarchy rank (lower = higher priority)

  2. ICD match score (higher = higher priority), when score_col present

  3. Alphabetical tie-break

This function absorbs the logic of the former infer_patient_syndrome_long(): use collapse_unspecified_respiratory = TRUE and keep_only_burden_syndromes = TRUE to replicate that behaviour.