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Add RR Pathogen and Drug Class Mappings

Source: R/daly_rr_and_los.R
daly_add_rr_mappings.Rd

Maps organism names to GBD RR pathogen categories and antibiotic class names to RR drug categories in a single pass. Either mapping is skipped silently when the corresponding column is absent from data.

Usage

daly_add_rr_mappings(
  data,
  organism_col = "organism_normalized",
  class_col = "antibiotic_class"
)

Arguments

data

Data frame with organism and/or antibiotic class columns.

organism_col

Character. Column with organism names to map to rr_pathogen. Set to NULL to skip. Default "organism_normalized".

class_col

Character. Column with antibiotic class names to map to rr_drug. Set to NULL to skip. Default "antibiotic_class".

Value

Data frame with rr_pathogen and/or rr_drug columns appended.

Details

Pathogen mapping uses the organism taxonomy (get_organism_taxonomy()); drug class mapping uses inst/extdata/WHO_aware_class.csv.