Identify top N pathogens by occurrence

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

daly_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().