Computes M_LJ, the fraction of infection-related deaths for underlying cause J that are attributed to infectious syndrome L. This distributes infection deaths across clinical syndrome categories (e.g., bloodstream infection, pneumonia, urinary tract infection).

Usage

calculate_syndrome_fraction(
  pop_data,
  cause_col = "cause_of_death",
  syndrome_col = "syndrome",
  infection_flag_col = "is_infection_death",
  groupby_cols = NULL
)

Arguments

pop_data: Data frame. Population-level mortality data with cause and syndrome columns. Required.
cause_col: Character. Underlying cause of death column (cause J). Default "cause_of_death".
syndrome_col: Character. Infectious syndrome column (syndrome L), e.g., "infectious_syndrome". Default "syndrome".
infection_flag_col: Character. Binary column (TRUE/FALSE or 1/0) indicating infection involvement in pop_data. Default "is_infection_death".
groupby_cols: Character vector. Additional stratification columns. Default NULL.

Value

Data frame with columns: cause_col, syndrome_col, any groupby_cols, infection_deaths_LJ (deaths for syndrome L given cause J), infection_deaths_J (total infection deaths for cause J), M_LJ (syndrome fraction 0-1), M_LJ_method, M_LJ_confidence.

Details

This function requires population-level data. 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{
m_lj <- calculate_syndrome_fraction(
  pop_data           = vital_reg,
  cause_col          = "icd10_cause",
  syndrome_col       = "infectious_syndrome",
  infection_flag_col = "is_infectious",
  groupby_cols       = c("Age_bin")
)
} # }