Flags polymicrobial status by counting distinct organisms per patient (optionally scoped within facility and/or syndrome).
Usage
prep_flag_polymicrobial(
data,
patient_col = "patient_id",
organism_col = "organism_normalized",
facility_col = NULL,
facility_name = NULL,
syndrome_col = NULL,
syndrome_name = NULL
)
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.
- patient_col
Character. Patient ID column. Default "patient_id".
- organism_col
Character. Organism column. Default "organism_normalized".
- facility_col
Character or NULL. Facility column for scoped counting.
- facility_name
Character or NULL. Filter to this facility before flagging.
- syndrome_col
Character or NULL. Syndrome column for scoped counting.
- syndrome_name
Character or NULL. Filter to this syndrome before flagging.