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Calculate fatal pathogen distribution (P_{Lk})

Source: R/burden.R
calculate_P_Lk_fatal.Rd

Computes the fatal pathogen distribution for a given infectious syndrome (L) using facility-level microbiology data. This quantity represents the fractional contribution of each pathogen (k) to fatal infection cases, and is used in YLL / mortality burden estimation.

Usage

calculate_P_Lk_fatal(
  data,
  syndrome_col,
  syndrome_name,
  specimen_col = NULL,
  specimen_name = NULL,
  polymicrobial_col,
  patient_col,
  pathogen_col,
  outcome_col,
  death_value = "Death",
  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 or NULL. Column containing specimen type. If NULL, no specimen filter is applied.

specimen_name

Character or NULL. Specimen to restrict to (e.g., "Blood"). Required when specimen_col is provided.

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 a fatal outcome. Default "Death".

glass_ref

Character vector of valid pathogen names, or a data frame with columns specimen and pathogen. Applied to polymicrobial patients only. When specimen_name is NULL and glass_ref is a data frame, all pathogens in the reference are used regardless of specimen. NULL skips GLASS filtering.

facility_col

Character or NULL. Facility identifier column. When provided without facility_name, returns both facility-level and pooled P_LK.

facility_name

Character or NULL. Restricts to a single facility.

pathogen_name

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

Value

A list:

P_Lk_fatal

Pooled P_LK data frame: pathogen_col, N_F_LK, N_F_L, P_Lk_fatal.

facility_level

Per-facility P_LK (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. For a patient with \(m_r\) valid pathogens, each pathogen receives weight \(1/m_r\).

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.

The pooled formula across facilities is: $$P_{LK}^{\text{pooled}} = \frac{\sum_f N^{F}_{f,L,K}}{\sum_f N^{F}_{f,L}}$$