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Flag Polymicrobial Infections (No Specimen Type, No Episode ID)

Source: R/weight.R
flag_polymicrobial.Rd

Flags polymicrobial status by counting distinct organisms per patient (optionally within facility/syndrome scope). No specimen type and no episode_id are used.

Usage

flag_polymicrobial(
  data,
  patient_col = "patient_id",
  organism_col = "organism_normalized",
  facility_col = NULL,
  facility_name = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame with patient and organism columns.

patient_col

Character. Patient ID column. Default "patient_id".

organism_col

Character. Organism column. Default "organism_normalized".

facility_col

Character or NULL. Facility column. When supplied, polymicrobial status is scoped within each facility.

facility_name

Character or NULL. When supplied with facility_col, data are first filtered to that facility.

syndrome_col

Character or NULL. Syndrome column. When supplied, polymicrobial status is scoped within each syndrome.

syndrome_name

Character or NULL. When supplied with syndrome_col, data are first filtered to that syndrome.

Value

Data frame with n_organisms and is_polymicrobial (0/1).