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Assign Syndrome from Wide-Format Syndrome Flags

Source: R/prep_diagnosis.R
infer_patient_syndrome_wide.Rd

Converts a wide-format data frame (one column per syndrome, values indicating presence) to long format and assigns the highest-priority syndrome per patient using the infectious syndrome hierarchy.

Usage

infer_patient_syndrome_wide(
  data,
  patient_col = "patient_id",
  syndrome_cols = NULL,
  positive_values = c(1, "1", TRUE, "TRUE", "True", "true", "Yes", "YES", "yes"),
  collapse_unspecified_respiratory = TRUE,
  keep_only_burden_syndromes = FALSE
)

Arguments

data

Data frame in wide format where syndrome columns contain presence indicators (1/TRUE/"Yes" etc.).

patient_col

Character. Patient ID column. Default "patient_id".

syndrome_cols

Character vector. Columns to treat as syndrome flags. If NULL, all columns except patient_col are used. Default NULL.

positive_values

Character/logical/numeric vector. Values treated as "syndrome present". Default covers common representations of TRUE/1/Yes.

collapse_unspecified_respiratory

Logical. Passed to prep_assign_patient_syndrome(). Default TRUE.

keep_only_burden_syndromes

Logical. Passed to prep_assign_patient_syndrome(). Default FALSE.

Value

Data frame with one row per patient and the selected syndrome.

Details

This is a convenience wrapper around prep_assign_patient_syndrome(). All syndrome-selection logic and parameters (hierarchy, burden filter, respiratory collapsing) are handled there.