For each pathogen x antibiotic class, splits patients into resistant (R) and susceptible (S) groups, fits a parametric distribution (default: gamma) to each group's LOS, and returns: RR_LOS = mean_LOS(R) / mean_LOS(S)

Usage

fit_los_rr_distribution(
  data,
  patient_id_col = "PatientInformation_id",
  facility_col = "center_name",
  organism_col = "organism_name",
  syndrome_col = "syndrome",
  infection_type_col = "type_of_infection",
  antibiotic_class_col = "antibiotic_class",
  antibiotic_name_col = "antibiotic_name",
  antibiotic_value_col = "antibiotic_value",
  date_admission_col = "date_of_admission",
  date_discharge_col = "final_outcome_date",
  date_culture_col = "date_of_first_positive_culture",
  final_outcome_col = "final_outcome",
  final_outcome_value = "Discharged",
  syndrome_name = NULL,
  organism_name = NULL,
  facility_name = NULL,
  hai_threshold_hours = 48,
  distributions = "gamma",
  max_los = 365,
  min_n = 10L
)

Arguments

data: Data frame of isolate/patient rows (long format).
patient_id_col: Character. Patient identifier column.
facility_col: Character. Facility/centre column.
organism_col: Character. Organism name column.
syndrome_col: Character. Syndrome column (used only when syndrome_name is not NULL).
infection_type_col: Character. Column used to derive HAI/CAI.
antibiotic_class_col: Character. Antibiotic class column.
antibiotic_name_col: Character. Antibiotic name column.
antibiotic_value_col: Character. Antibiotic value column (S/I/R).
date_admission_col: Character. Date of admission column.
date_discharge_col: Character. Date of discharge column.
date_culture_col: Character. Date of culture column.
final_outcome_col: Character. Final outcome column.
final_outcome_value: Character. Value indicating discharge.
syndrome_name: Character or NULL. Restrict to this syndrome.
organism_name: Character vector or NULL. Restrict to these pathogen(s); otherwise all pathogens in the filtered data.
facility_name: Character or NULL. If provided, filters data to the specified facility before fitting. Default NULL.
hai_threshold_hours: Numeric. Hours after admission before a culture is classified as HAI. Default 48.
distributions: Character vector. Candidate distributions to fit. Default "gamma".
max_los: Numeric. Maximum plausible LOS in days. Default 200.
min_n: Integer. Minimum patients required in both R and S groups. Default 10L.

Value

A data frame with one row per pathogen x class:

pathogen: Pathogen name.
antibiotic_class: Antibiotic class name.
RR_LOS: Fitted mean ratio: mean_LOS(R) / mean_LOS(S).
mean_LOS_R: Fitted mean LOS for resistant patients.
mean_LOS_S: Fitted mean LOS for susceptible patients.
best_dist_R: Distribution fitted to the R group.
best_dist_S: Distribution fitted to the S group.
n_R: Number of resistant patients.
n_S: Number of susceptible patients.
syndrome_scope: Syndrome filter applied, or "all".

Details

This is an alternative to fit_los_rr_poisson() that avoids regression and models the full LOS distribution per group. The output flat data frame is fully compatible with assign_rr_to_profiles() and filter_profiles_to_rr_classes().

Estimate Per-Class LOS Relative Risk via Parametric Distribution Fitting

Usage

Arguments

Value

Details

See also