sarscov2_surveillance: Example SARS-CoV-2 genomic surveillance data

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Example SARS-CoV-2 genomic surveillance data

Description

Simulated genomic surveillance dataset with 5 regions, 26 weeks, highly unequal sequencing rates (15% to 0.5%), three sample sources, and negative binomial reporting delays. Contains known ground truth for benchmarking.

Usage

sarscov2_surveillance

Format

A named list with four elements:

sequences

Tibble of sequence records: sequence_id, region, source_type, lineage, collection_date, report_date, epiweek.

population

Tibble with one row per region: region, n_positive, n_sequenced, seq_rate, pop_total.

truth

Tibble of true lineage prevalence by region and week.

parameters

List of simulation parameters.

Source

Simulated using surv_simulate(seed = 20240101).

Examples

data(sarscov2_surveillance)
head(sarscov2_surveillance$sequences)
sarscov2_surveillance$population

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