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Calculate case fatality ratio by syndrome and pathogen (CFR_{Lk})

Source: R/burden.R
calculate_cfr_lk.Rd

Computes the case fatality ratio (CFR) for each pathogen (k) within a specified infectious syndrome (L) using facility-level microbiology data.

Usage

calculate_cfr_lk(
  data,
  syndrome_col,
  syndrome_name,
  specimen_col,
  specimen_name,
  polymicrobial_col,
  patient_col,
  pathogen_col,
  outcome_col,
  death_value = "Died",
  glass_ref = NULL,
  facility_col = NULL,
  facility_name = NULL,
  pathogen_name = NULL
)

Arguments

data

Data frame of facility-level microbiology records.

syndrome_col

Character. Column containing infectious syndrome labels (L).

syndrome_name

Character. Syndrome to analyse.

specimen_col

Character. Column containing specimen type.

specimen_name

Character. Specimen to restrict to (e.g., "Blood").

polymicrobial_col

Character. Column flagging polymicrobial patients (1 = polymicrobial, 0 = monomicrobial).

patient_col

Character. Unique patient identifier column.

pathogen_col

Character. Pathogen (organism) column (k).

outcome_col

Character. Final patient outcome column.

death_value

Character. Value indicating death. Default "Died".

glass_ref

Character vector of valid pathogen names, or a data frame with columns specimen and pathogen. Applied to polymicrobial patients only. NULL skips GLASS filtering.

facility_col

Character or NULL. Facility identifier column.

facility_name

Character or NULL. Restricts to a single facility.

pathogen_name

Character vector or NULL. Filter to specific pathogen(s).

Value

A list:

cfr_table

Pooled CFR: pathogen_col, weighted_deaths, weighted_total, CFR_LK.

facility_level

Per-facility CFR (only when facility_col is supplied and facility_name is NULL).

Details

The unit of analysis is the patient. Each patient contributes total weight 1, distributed equally across their valid pathogens via a fractional weight \(1/m_r\) (where \(m_r\) is the number of distinct valid pathogens for patient r). This ensures polymicrobial patients are not double-counted.

For polymicrobial patients (polymicrobial_col == 1), only pathogens listed in the GLASS reference (glass_ref) for the given specimen type are retained before weighting. Monomicrobial patients (polymicrobial_col == 0) are never filtered.

When facility_col is supplied and facility_name is NULL, both per-facility and pooled CFR are returned. The pooled CFR sums weighted deaths and totals across facilities before dividing.