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Compute Patient-Level Post-Infection LOS

Source: R/burden.R
compute_patient_los.Rd

Computes LOS with infection-type-specific clock start:

  • CAI: LOS = date_discharge - date_admission

  • HAI: LOS = date_discharge - date_culture

  • Unknown / Not known: LOS = date_discharge - date_culture (if culture date present), else date_discharge - date_admission. If neither reference date is available the patient is excluded.

Only discharged patients are retained. A checkpoint reports how many are missing a discharge date; those patients fall back to los_col when provided, otherwise they are excluded. Rows with LOS <= 0 or LOS > max_los are dropped. Returns one row per patient.

Usage

compute_patient_los(
  data,
  patient_id_col = "PatientInformation_id",
  facility_col = "center_name",
  facility_name = NULL,
  organism_col = "organism_name",
  syndrome_col = "syndrome",
  syndrome_name = NULL,
  date_admission_col = "date_of_admission",
  date_discharge_col = "final_outcome_date",
  date_culture_col = "date_of_first_positive_culture",
  final_outcome_col = "final_outcome",
  final_outcome_value = "Discharged",
  infection_type_derived_col = "infection_type_derived",
  los_col = NULL,
  max_los = 200
)

Arguments

data

Data frame (after derive_infection_type() has been run).

patient_id_col

Character. Default "PatientInformation_id".

facility_col

Character. Default "center_name".

facility_name

Character or NULL. If provided, filters data to the specified facility before computing LOS. Default NULL.

organism_col

Character. Column containing organism/pathogen names. Used for episode grouping: a new episode is only created when the culture date gap exceeds 14 days AND the organism differs from the episode's first organism. Default "organism_name".

syndrome_col

Character. Syndrome column name. Only used when syndrome_name is not NULL. Default "syndrome".

syndrome_name

Character or NULL. If provided, only patients with this syndrome are retained before LOS computation. Default NULL.

date_admission_col

Character. Default "date_of_admission".

date_discharge_col

Character. Default "final_outcome_date".

date_culture_col

Character. Default "date_of_first_positive_culture".

final_outcome_col

Character. Default "final_outcome".

final_outcome_value

Character. Default "Discharged".

infection_type_derived_col

Character. Column from derive_infection_type(). Default "infection_type_derived".

los_col

Character or NULL. Optional name of a pre-computed LOS column (e.g. recorded directly in the data). Used only for patients whose discharge date is missing. Values that are NA, zero, or negative are treated as invalid and those patients are excluded. Default NULL.

max_los

Numeric. Upper cap on LOS in days; patients exceeding this are excluded. Default 200.

Value

Data frame: one row per patient with patient_id_col, facility_col, infection_type_derived_col, LOS_days.