surv_report: Generate a comprehensive surveillance system report

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Generate a comprehensive surveillance system report

Description

Produces a summary of the current surveillance design's strengths, weaknesses, and recommendations.

Usage

surv_report(design, target_lineage = NULL, target_prevalence = 0.01)

Arguments

design	A surv_design object.
target_lineage	Character or NULL. Lineage to focus on. If NULL, uses the most common non-"Other" lineage.
target_prevalence	Numeric. Assumed prevalence for detection calculations. Default 0.01.

Value

Invisibly returns a named list of computed metrics including n_obs, n_strata, rate_range, gini, effective_n, detection_prob, and mean_bias.

See Also

surv_design(), surv_lineage_prevalence(), surv_detection_probability(), surv_optimize_allocation()

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_report(d)

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