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Compute Baseline Mortality Rate Among Fully Susceptible Patients (p0)

Source: R/yll.R
compute_p0.Rd

Computes the baseline death probability \(p_0\) among patients who are fully susceptible – i.e. all antibiotic test results are "S". Any patient with at least one "R" result is excluded. Used as the denominator correction for OR -> RR conversion (Zhang & Yu 1998).

Usage

compute_p0(
  data,
  patient_col,
  antibiotic_value_col,
  outcome_col,
  death_value = "Death",
  resistant_value = "R",
  syndrome_col = NULL,
  syndrome_name = NULL,
  facility_col = NULL,
  facility_name = NULL
)

Arguments

data

Data frame. One row per patient x antibiotic test.

patient_col

Character. Unique patient identifier column.

antibiotic_value_col

Character. Antibiotic result column ("S", "R", "I").

outcome_col

Character. Final outcome column.

death_value

Character. Death indicator. Default "Death".

resistant_value

Character. Resistance indicator used to exclude patients. Default "R".

syndrome_col

Character or NULL.

syndrome_name

Character or NULL.

facility_col

Character or NULL. Facility identifier column. Required when facility_name is specified.

facility_name

Character or NULL. If provided, filters data to the specified facility before computing p0.

Value

Named list: p0 (scalar), n_susceptible, n_susceptible_deaths, summary (one-row data frame).

References

Zhang J, Yu KF. What's the relative risk? JAMA. 1998;280(19):1690-1.