surv_naive_prevalence: Compute naive (unweighted) lineage prevalence
In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

surv_naive_prevalence

R Documentation

Compute naive (unweighted) lineage prevalence

Description

Simple proportion without design correction. Useful as baseline.

Usage

surv_naive_prevalence(design, lineage, time = "epiweek", conf_level = 0.95)

Arguments

`design`	A `surv_design` object.
`lineage`	Character. Target lineage.
`time`	Character. Time aggregation. Default `"epiweek"`.
`conf_level`	Numeric. Default 0.95.

Value

A surv_prevalence object with method = "naive".

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)
naive <- surv_naive_prevalence(d, "BA.2.86")

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