Filter Resistance Profiles to Classes with RR Estimates

Drops profiles whose resistant classes have no RR estimate in rr_table and re-normalises the remaining probabilities. The all-susceptible reference profile is always kept.

Usage

daly_filter_profiles_to_rr_classes(
  profiles_with_rr,
  rr_table,
  pathogen_col = "pathogen",
  class_col = "antibiotic_class",
  probability_col = "probability",
  fallback_rr = 1
)

Arguments

profiles_with_rr

Named list returned by daly_assign_rr_to_profiles().

rr_table

Data frame of RR estimates.

pathogen_col

Character. Default "pathogen".

class_col

Character. Default "antibiotic_class".

probability_col

Character. Default "probability".

fallback_rr

Numeric. Default 1.

Value

Named list (one entry per pathogen) with filtered and re-normalised profiles.