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Compute YLL Attributable to AMR

Source: R/daly_yll.R
daly_calc_yll_attributable.Rd

Takes the per-patient YLL data produced by daly_calc_yll_associated() (which already contains life_expectancy, death_weight, and yll_contribution) and multiplies by the mortality PAF from daly_calc_paf_mortality() to produce AMR-attributable YLL.

Usage

daly_calc_yll_attributable(
  yll_patient_data,
  paf_mort,
  pathogen_col,
  patient_col,
  age_bin_col,
  sex_col = ".sex_norm",
  resistance_profile_col = NULL,
  profile_col = "profile",
  facility_col = NULL,
  syndrome_col = NULL,
  stratify_by = NULL
)

Arguments

yll_patient_data

Data frame: the patient_data element from daly_calc_yll_associated(), with life_expectancy, death_weight, and yll_contribution columns.

paf_mort

Named list returned by daly_calc_paf_mortality().

pathogen_col

Character. Pathogen column.

patient_col

Character. Patient identifier column.

age_bin_col

Character. Age bin column.

sex_col

Character. Normalised sex column. Default ".sex_norm".

resistance_profile_col

Character or NULL. Column holding the resistance profile identifier per patient row. When supplied, per-profile PAF is applied instead of a scalar PAF_k. Default NULL.

profile_col

Character. Profile identifier column in the paf_mort per-profile data frames. Default "profile".

facility_col

Character or NULL. Facility identifier column. When supplied results include a by_facility breakdown. Default NULL.

syndrome_col

Character or NULL. Syndrome column.

stratify_by

Character vector or NULL. Additional columns to aggregate results by. Default NULL.

Value

A list:

total

Scalar: total AMR-attributable YLL.

per_pathogen

One row per pathogen: pathogen_col, n_patients, YLL_associated_k, PAF_k_mort, YLL_attributable_k.

by_age_sex

YLL attributable stratified by age_bin x sex.

by_pathogen_age_sex

YLL attributable by pathogen x age_bin x sex.

by_facility

Per-facility breakdown (when facility_col supplied).

by_syndrome

Per-syndrome breakdown (when syndrome_col supplied).

by_syndrome_pathogen

Per-syndrome x pathogen (when syndrome_col supplied).

stratified

User-defined stratification (when stratify_by supplied).

patient_data

Patient-level data augmented with PAF_kd and YLL_attributable_contribution.

Details

Two PAF modes:

PAF_k scalar mode (default)

When resistance_profile_col is NULL, the overall mortality PAF per pathogen k (PAF_k_mort) from paf_mort is used as a scalar multiplier.

Per-profile mode

When resistance_profile_col is supplied, each patient row is matched to its resistance profile delta and the profile-specific PAF_mortality is applied. Patients whose profile does not appear in paf_mort receive NA and a warning is issued.

$$\text{YLL}^{\text{attr}}_{i,k} = \text{yll\_contribution}_{i,k} \times \text{PAF}_{k(,\delta)}$$

Examples

if (FALSE) { # \dontrun{
yll_assoc <- daly_calc_yll_associated(data = cohort, ...)
mort_or <- fit_mortality_rr_logistic(data = rr_data, ...)
profiles_or <- assign_rr_to_profiles(profiles_out,
  rr_table = mort_or,
  rr_col = "OR_death"
)
paf_mort <- daly_calc_paf_mortality(profiles_or)

yll_attr <- daly_calc_yll_attributable(
  yll_patient_data = yll_assoc$patient_data,
  paf_mort         = paf_mort,
  pathogen_col     = "organism_name",
  patient_col      = "PatientInformation_id",
  age_bin_col      = "Age_bin",
  sex_col          = ".sex_norm",
  facility_col     = "center_name",
  syndrome_col     = "infectious_syndrome",
  stratify_by      = c("location", "infectious_syndrome")
)
} # }