R version 4.6.0 alpha (2026-03-27 r89733 ucrt) Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(survinger) > > test_check("survinger") -- Lineage Prevalence Estimate ------------------------------------------------- Lineage: "BA.2.86" Method: "hajek" Confidence level: 0.95 Time periods: 1 # A tibble: 1 x 5 time prevalence se ci_lower ci_upper 1 2024-W01 0.3 0.05 0.2 0.4 -- Optimal Sequencing Allocation ----------------------------------------------- Objective: min_mse Total capacity: 100 sequences Strata: 1 # A tibble: 1 x 2 stratum n_allocated 1 A 100 -- Reporting Delay Distribution ------------------------------------------------ Distribution: "negbin" Strata: none (pooled) Observations: 100 Mean delay: 10 days # A tibble: 1 x 3 stratum mu size 1 all 10 3 -- Genomic Surveillance Design ------------------------------------------------- Observations: 421 Strata: 3 (region) Date range: 2024-01-01 to 2024-01-28 Lineages: 4 Sources: clinical, sentinel, wastewater Weight range: [5.354, 20.231] -- Surveillance Design Summary ------------------------------------------------- Sequences: 421 Strata: 3 (region) Period: 2024-01-01 to 2024-01-28 -- Top lineages BA.5: 252 XBB.1.5: 121 Other: 34 BA.2.86: 14 -- Sampling weights Min. 1st Qu. Median Mean 3rd Qu. Max. 5.354 8.813 12.273 12.619 16.252 20.231 -- Optimal Sequencing Allocation ----------------------------------------------- Objective: min_mse Total capacity: 100 sequences Strata: 3 # A tibble: 3 x 3 region n_allocated proportion 1 Region_A 24 0.24 2 Region_B 8 0.08 3 Region_C 68 0.68 -- Reporting Delay Distribution ------------------------------------------------ Distribution: "negbin" Strata: none (pooled) Observations: 768 Mean delay: 10 days # A tibble: 1 x 5 stratum distribution mu size converged 1 all negbin 10.1 2.96 TRUE -- Design-Weighted Delay-Adjusted Prevalence ----------------------------------- Correction: "design:hajek+delay:direct" # A tibble: 10 x 9 time lineage n_obs_raw n_obs_adjusted prevalence se ci_lower ci_upper 1 2024-W01 BA.2.86 56 56.0 0.0147 0.0256 0 0.0649 2 2024-W02 BA.2.86 58 58.0 0.117 0.0726 0 0.260 3 2024-W03 BA.2.86 52 52.0 0 0 0 0 4 2024-W04 BA.2.86 53 53.0 0.0361 0.0257 0 0.0863 5 2024-W05 BA.2.86 52 52.0 0.0135 0.0256 0 0.0638 6 2024-W06 BA.2.86 68 68.0 0.0444 0.0409 0 0.125 7 2024-W07 BA.2.86 46 46.0 0 0 0 0 8 2024-W08 BA.2.86 51 51.0 0.0693 0.0518 0 0.171 9 2024-W09 BA.2.86 48 48.0 0.0659 0.0610 0 0.185 10 2024-W10 BA.2.86 66 66.2 0.0549 0.0465 0 0.146 # i 1 more variable: mean_report_prob -- Surveillance System Report -------------------------------------------------- -- Design Structure -- Total sequences: 3,031 Strata: 3 Period: 2024-01-01 to 2024-02-25 -- Sequencing Inequality -- Rate range: 3.29% to 45.56% Rate ratio: 13.8x Gini coefficient: 0.365 i Moderate inequality. Weighting recommended. -- Estimation Impact -- Effective sample size: 1501 (49.5% of total) Mean |weighted - naive| bias: 2.07 percentage points -- Detection Power -- Target: detect BA.5 at 1% prevalence Weekly detection probability: 97.8% Sequences needed for 95% detection: 299 -- Detection Power Curve ------------------------------------------------------- Prevalence range: 0.1% to 5% -- Thresholds 50% detection requires 0.2% prevalence 80% detection requires 0.5% prevalence 95% detection requires 0.8% prevalence [ FAIL 0 | WARN 1 | SKIP 0 | PASS 154 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 154 ] > > proc.time() user system elapsed 14.32 0.35 14.71