surv_sensitivity: Sensitivity analysis across methods

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Sensitivity analysis across methods

Description

Runs all three prevalence estimators and delay/no-delay variants on the same design, producing a comparison table. Essential for robustness checks in publications.

Usage

surv_sensitivity(
  design,
  lineage,
  delay_fit = NULL,
  time = "epiweek",
  conf_level = 0.95
)

Arguments

design	A surv_design object.
lineage	Character. Target lineage.
delay_fit	Optional surv_delay_fit object. If provided, includes delay-adjusted estimates.
time	Character. Default "epiweek".
conf_level	Numeric. Default 0.95.

Value

A tibble with one row per method-time combination, columns: method, time, prevalence, se, ci_lower, ci_upper.

See Also

surv_lineage_prevalence(), surv_adjusted_prevalence()

Examples

sim <- surv_simulate(n_regions = 3, n_weeks = 10, seed = 1)
d <- surv_design(sim$sequences, ~ region,
                 sim$population[c("region", "seq_rate")], sim$population)
surv_sensitivity(d, "BA.2.86")

survinger documentation built on April 27, 2026, 9:10 a.m.