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Calculate the CFR adjustment factor (CR_L)

Source: R/burden.R
calculate_CR_L.Rd

Computes CR_L, the factor that adjusts a hospital-derived CFR to account for infection cases managed outside the inpatient setting. The adjustment type for each syndrome is looked up from the adjustment_ref table (loaded from inst/extdata/adjustment_for_CFR).

Usage

calculate_CR_L(
  data,
  syndrome_col,
  syndrome_name,
  patient_col,
  visit_type_col,
  inpatient_value = "Inpatient",
  outpatient_value = "Outpatient",
  adjustment_ref,
  facility_col = NULL,
  facility_name = NULL
)

Arguments

data

Data frame of facility-level records.

syndrome_col

Character. Column containing infectious syndrome labels.

syndrome_name

Character. Syndrome to compute CR_L for.

patient_col

Character. Unique patient identifier column.

visit_type_col

Character. Column indicating visit type per record (inpatient / outpatient).

inpatient_value

Character. Value in visit_type_col that denotes an inpatient visit. Default "Inpatient".

outpatient_value

Character. Value in visit_type_col that denotes an outpatient visit. Default "Outpatient".

adjustment_ref

Data frame with columns infectious_syndrome and adjustment_factor_on_CFR. Load from inst/extdata/adjustment_for_CFR.

facility_col

Character or NULL. Facility identifier column. When provided (and facility_name is NULL), CR_L is returned per facility.

facility_name

Character or NULL. If provided, restricts to that facility only.

Value

Data frame with columns syndrome (= syndrome_name), adjustment_type, CR_L, and (when facility_col is supplied) facility_col. Additional columns (n_inpatient, n_total, etc.) give the raw counts used.

Details

Three adjustment types are supported:

None

CR_L = 1. The hospital CFR applies directly (e.g., BSI, Meningitis, hospital-acquired infections).

Inpatient ratio

CR_L = (patients with \(\ge\) 1 inpatient visit) / (all patients). Used when community cases are captured partly in outpatient data (e.g., community-acquired LRI, UTI).

Outpatient to inpatient ratio

CR_L = (patients with \(\ge\) 1 outpatient AND \(\ge\) 1 inpatient visit) / (patients with \(\ge\) 1 outpatient visit). Used for syndromes where OP-to-IP transition captures disease severity (e.g., STI, Skin, Eye, Oral, Bone/joint infections).