Split Polymicrobial Episodes by Strategy — prep_split_poly_episode • anumaan

Applies a chosen strategy for handling polymicrobial episodes:

fractional: Keep all rows; poly_weight is applied downstream during DALY calculation.
exclude: Drop polymicrobial episodes from the main analysis frame.
separate: Retain polymicrobial episodes in a separate data frame stored in attr(result, "poly_data") for sensitivity analyses.

Usage

prep_split_poly_episode(
  data,
  strategy = c("fractional", "exclude", "separate"),
  polymicrobial_col = "is_polymicrobial"
)

Arguments

data: Data frame with is_polymicrobial column (output of prep_flag_polymicrobial()).
strategy: Character. "fractional" (default), "exclude", or "separate".
polymicrobial_col: Character. Polymicrobial flag column (0/1). Default "is_polymicrobial".

Value

Data frame with polymicrobial rows handled per strategy. When strategy = "separate", the poly subset is in attr(result, "poly_data").