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Fit relative LOS using Gamma GLM with log link

Source: R/daly_rr_and_los.R
daly_fit_los_rr.Rd

Estimates class-specific relative length of stay (RR_LOS) for each pathogen using a Gamma generalized linear model with log link:

Usage

daly_fit_los_rr(
  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",
  age_col = "Age",
  sex_col = "Gender",
  unit_type_col = NULL,
  comorbidity_col = NULL,
  syndrome_name = NULL,
  organism_name = NULL,
  hai_threshold_hours = 48,
  max_los = 365,
  min_n = 20L,
  min_resistant = 5L,
  min_susceptible = 5L,
  add_centre_fe = TRUE
)

Arguments

data

Data frame.

patient_id_col

Character. Patient identifier column.

facility_col

Character or NULL. Facility / centre column. When NULL, no hospital effect is included in the model and a single pooled RR is returned (hospital column will be NA). When provided, the model is fit separately per hospital and the result contains one row per pathogen-class-hospital combination (hospital-specific RR).

organism_col

Character. Pathogen column.

syndrome_col

Character. Syndrome column.

infection_type_col

Character. Raw infection type column.

antibiotic_class_col

Character. Antibiotic class column.

antibiotic_name_col

Character. Antibiotic name column.

antibiotic_value_col

Character. Antibiotic susceptibility column.

date_admission_col

Character. Admission date column.

date_discharge_col

Character. Discharge / final outcome date column.

date_culture_col

Character. First positive culture date column.

final_outcome_col

Character. Final outcome column.

final_outcome_value

Character. Value indicating discharged patients.

age_col

Character. Age column.

sex_col

Character. Sex column.

unit_type_col

Character or NULL. ICU / ward location column.

comorbidity_col

Character or NULL. Comorbidity column.

syndrome_name

Character or NULL. Restrict to one syndrome.

organism_name

Character vector or NULL. Restrict to these pathogens.

hai_threshold_hours

Numeric. HAI derivation threshold.

max_los

Numeric. Maximum retained LOS in days.

min_n

Integer. Minimum patients required in a class model.

min_resistant

Integer. Minimum resistant patients required.

min_susceptible

Integer. Minimum susceptible patients required.

add_centre_fe

Logical. Retained for backward compatibility; ignored when facility_col is provided (per-hospital fitting is used) or NULL (no facility information available).

Value

Data frame with pathogen, antibiotic_class, hospital (NA when facility_col is NULL), RR_LOS, CI_lower, CI_upper, beta_log_rr, mean_los_resistant, mean_los_susceptible, n_patients, n_resistant, n_susceptible, model_family, link_function, and syndrome_scope.

Details

E(LOS_i) = exp(beta0 + beta1*Resistance_ci + beta2*HAI_i + beta3*Age_i + beta4*Sex_i + beta5*ICU_i + beta6*Comorbidity_i + centre fixed effects)

RR_LOS for a resistance class is exp(beta1).