Ranks pathogens by the number of records (rows) in the dataset, optionally filtered to a specific syndrome, specimen, facility, or outcome. Returns the top N pathogens overall or broken down per facility.
Usage
get_top_pathogens(
data,
pathogen_col,
n = 5L,
syndrome_col = NULL,
syndrome_name = NULL,
specimen_col = NULL,
specimen_name = NULL,
outcome_col = NULL,
outcome_name = NULL,
facility_col = NULL,
facility_name = NULL
)Arguments
- data
Data frame of facility-level records.
- pathogen_col
Character. Pathogen column.
- n
Integer. Number of top pathogens to return. Default 5.
- syndrome_col
Character or NULL. Filter to this syndrome column.
- syndrome_name
Character or NULL. Syndrome value to filter to.
- specimen_col
Character or NULL. Filter to this specimen column.
- specimen_name
Character or NULL. Specimen value to filter to.
- outcome_col
Character or NULL. Filter to this outcome column.
- outcome_name
Character or NULL. Outcome value to filter to (e.g.,
"Died"or"Discharged").- facility_col
Character or NULL. Facility identifier column. When provided without
facility_name, returns top N per facility.- facility_name
Character or NULL. If provided, restricts to that facility only before ranking.
Value
Data frame with columns: pathogen_col, n_records,
rank (1 = most common), and facility_col if supplied.
Details
Use this to decide which pathogens to focus on before calling
calculate_P_Lk_prime_BSI(), calculate_cfr_lk(), or
calculate_YLD().