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Assign Per-Class LOS RR to Resistance Profiles (Max Rule)

Source: R/burden.R, R/yll.R
assign_rr_to_profiles.Rd

For each resistance profile delta (from compute_resistance_profiles()), determines the profile-level RR_kd_LOS using the GBD max rule: RR_kd_LOS = max over c in C_R(d) of RR_kc_LOS [if C_R(d) non-empty] = 1 [if d = all-susceptible] where C_R(d) = {c : d_c = 1}. The CI reported for each profile is that of its dominant (max-RR) class.

For each resistance profile delta, determines the profile-level RR using the GBD max rule: RR_kd = max over resistant classes of RR_kc. The CI reported for each profile is that of its dominant (max-RR) class. Also used for mortality ORs when called with rr_col = "OR_death".

Usage

assign_rr_to_profiles(
  profiles_output,
  rr_table,
  pathogen_col = "pathogen",
  class_col = "antibiotic_class",
  rr_col = "RR_LOS",
  fallback_rr = 1
)

assign_rr_to_profiles(
  profiles_output,
  rr_table,
  pathogen_col = "pathogen",
  class_col = "antibiotic_class",
  rr_col = "RR_LOS",
  fallback_rr = 1
)

Arguments

profiles_output

Named list from compute_resistance_profiles().

rr_table

Data frame from fit_mortality_rr_logistic() or a LOS RR table. Must have pathogen_col, class_col, rr_col, and optionally CI_lower / CI_upper.

pathogen_col

Character. Default "pathogen".

class_col

Character. Default "antibiotic_class".

rr_col

Character. Default "RR_LOS". Use "OR_death" for mortality.

fallback_rr

Numeric. RR for classes with no match. Default 1.

Value

Named list (one entry per pathogen): original profiles data frame augmented with RR_LOS_profile, dominant_class, and (if available) CI_lower_profile / CI_upper_profile.

Named list (one per pathogen): profiles data frame augmented with RR_LOS_profile, dominant_class, and CI columns.