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Count incident cases by syndrome from facility data

Source: R/burden.R
count_incident_cases.Rd

Counts the number of unique patients per infectious syndrome directly from facility-level data. This is the direct-count approach to incidence – no CFR, no CR_L adjustment, no pathogen weighting. Use this when you want raw facility-reported case counts rather than the formula-derived estimate from calculate_incidence_L().

Usage

count_incident_cases(
  data,
  syndrome_col,
  syndrome_name,
  patient_col,
  facility_col = NULL,
  facility_name = NULL,
  pathogen_col = NULL,
  pathogen_name = NULL
)

Arguments

data

Data frame of facility-level records.

syndrome_col

Character. Column containing infectious syndrome labels.

syndrome_name

Character. Syndrome to count cases for (e.g., "Bloodstream infections").

patient_col

Character. Unique patient identifier column. Cases are counted as distinct patients, not rows.

facility_col

Character or NULL. Facility identifier column. When provided without facility_name, counts are broken down per facility. Default NULL.

facility_name

Character or NULL. If provided, restricts the count to that facility only. Default NULL.

pathogen_col

Character or NULL. Pathogen identifier column. Required when pathogen_name is specified. Default NULL.

pathogen_name

Character or NULL. If provided, restricts the count to the specified pathogen(s). Default NULL.

Value

Data frame with columns: syndrome_col, n_cases (unique patient count), and facility_col if supplied.

Details

Results are returned facility-wise when facility_col is supplied and facility_name is NULL. When facility_name is specified, only that facility is returned. When no facility information is provided, a single pooled count across all records is returned.