Compute PAF for length of stay per resistance profile

Computes the population attributable fraction (PAF) for length of stay from a named list of profile data frames, each containing resistance-profile probabilities and profile-level relative risk of LOS.

Usage

daly_calc_paf_los(
  profiles_with_rr,
  probability_col = "probability",
  rr_profile_col = "RR_LOS_profile",
  profile_col = "profile"
)

Arguments

profiles_with_rr

Named list returned by assign_rr_to_profiles() or filter_profiles_to_rr_classes(). Each entry is a data frame of resistance profiles for one pathogen.

probability_col

Character. Column name for profile probability (must sum to 1 within each pathogen). Default "probability".

rr_profile_col

Character. Column name for profile-level LOS relative risk. Default "RR_LOS_profile".

profile_col

Character. Column name for the profile identifier. Default "profile".

Value

Named list (one entry per pathogen) with columns profile, probability, rr_profile_col, numerator, PAF_LOS, and denominator added to the input profile data frame.

Details

For each pathogen the formula is: PAF = sum_d R'_kd * (RR_kd - 1) / (1 + sum_d R'_kd * (RR_kd - 1))

where R'_kd is the probability of resistance profile d and RR_kd is the corresponding relative LOS multiplier.