Computes S_J, the fraction of deaths for underlying cause J that were related to infection. Values range from 0 (no infection involvement) to 1 (all deaths for cause J involved infection).

Usage

calculate_infection_fraction(
  pop_data,
  cause_col = "cause_of_death",
  infection_flag_col = "is_infection_death",
  groupby_cols = NULL
)

Arguments

pop_data: Data frame. Population-level mortality data. Required.
cause_col: Character. Underlying cause of death column (cause J). Default "cause_of_death".
infection_flag_col: Character. Binary column (TRUE/FALSE or 1/0) in pop_data indicating whether the death involved infection. Default "is_infection_death".
groupby_cols: Character vector. Stratification columns present in pop_data. Default NULL.

Value

Data frame with columns: cause_col, any groupby_cols, D_J (total deaths), infection_deaths (infection-related death count), S_J (infection fraction 0-1), S_J_method, S_J_confidence.

Details

This function requires population-level data where each death record carries a binary flag indicating whether infection was involved. If only facility data are available, use calculate_syndrome_deaths() with facility_data instead.

References

Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019. Lancet. 2022.

Examples

if (FALSE) { # \dontrun{
s_j <- calculate_infection_fraction(
  pop_data           = vital_reg,
  cause_col          = "icd10_cause",
  infection_flag_col = "is_infectious",
  groupby_cols       = c("Age_bin", "gender")
)
} # }