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Compute Polymicrobial Weights

Source: R/prep_polymicrobial.R
prep_compute_poly_weights.Rd

Calculates proportional weights for polymicrobial infections. Monomicrobial patients always receive weight = 1.0. For polymicrobial patients, weight is computed per organism within each episode using one of three methods.

Usage

prep_compute_poly_weights(
  data,
  episode_col = "episode_id",
  organism_col = "organism_normalized",
  polymicrobial_col = "is_polymicrobial",
  method = "monomicrobial_proportion",
  weight_map = NULL,
  facility_col = NULL,
  facility_name = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

compute_polymicrobial_weight(
  data,
  episode_col = "episode_id",
  organism_col = "organism_normalized",
  polymicrobial_col = "is_polymicrobial",
  method = "monomicrobial_proportion",
  weight_map = NULL,
  facility_col = NULL,
  facility_name = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame with episode_id, is_polymicrobial (0/1), and organism columns (output of prep_flag_polymicrobial()).

episode_col

Character. Episode ID column. Default "episode_id".

organism_col

Character. Organism column. Default "organism_normalized".

polymicrobial_col

Character. Polymicrobial flag column (0/1). Default "is_polymicrobial".

method

Character. One of "monomicrobial_proportion" (default), "equal", or "manual".

weight_map

Named numeric vector. Custom organism weights when method = "manual".

facility_col

Character or NULL. Scope monomicrobial reference pool per facility.

facility_name

Character or NULL. Filter to this facility.

syndrome_col

Character or NULL. Scope reference pool per syndrome.

syndrome_name

Character or NULL. Filter to this syndrome.

Value

Data frame with poly_weight, weight_method, and weight_confidence columns.