R version 4.6.0 alpha (2026-03-28 r89738 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. > library(testthat) > library(lineagefreq) > > test_check("lineagefreq") Backtesting ============>------------------ 41% | ETA: 2s Backtesting =======================>------- 77% | ETA: 1s Backtesting ==============================> 100% | ETA: 0s Backtesting =======================>------- 77% | ETA: 1s Backtesting ==============================> 100% | ETA: 0s -- Backtest results 22 predictions across 11 origins Engines: "mlr" Horizons: 7 days # A tibble: 22 x 9 origin_date target_date horizon engine lineage predicted lower upper observed * 1 2026-05-11 2026-05-18 7 mlr A 0.79 0.705 0.87 0.786 2 2026-05-11 2026-05-18 7 mlr ref 0.21 0.13 0.295 0.214 3 2026-05-18 2026-05-25 7 mlr A 0.82 0.73 0.89 0.824 4 2026-05-18 2026-05-25 7 mlr ref 0.18 0.11 0.27 0.176 5 2026-05-25 2026-06-01 7 mlr A 0.85 0.76 0.91 0.834 6 2026-05-25 2026-06-01 7 mlr ref 0.15 0.09 0.24 0.166 7 2026-06-01 2026-06-08 7 mlr A 0.87 0.8 0.93 0.872 8 2026-06-01 2026-06-08 7 mlr ref 0.13 0.07 0.2 0.128 9 2026-06-08 2026-06-15 7 mlr A 0.89 0.81 0.94 0.914 10 2026-06-08 2026-06-15 7 mlr ref 0.11 0.06 0.19 0.086 # i 12 more rows 3 lineages, 12 time points Date range: 2026-03-30 to 2026-06-15 Pivot: "B" 3 lineages, 20 time points Date range: 2026-03-30 to 2026-08-10 Pivot: "ref" -- Lineage frequency forecast Engine: mlr Forecast start: 2026-08-11 | Horizon: 14 days CI level: 95% 60 fitted + 6 forecast rows # A tibble: 66 x 6 .date .lineage .median .lower .upper .type * 1 2026-03-30 A 0.341 0.341 0.341 fitted 2 2026-03-30 B 0.324 0.324 0.324 fitted 3 2026-03-30 ref 0.335 0.335 0.335 fitted 4 2026-04-06 A 0.408 0.408 0.408 fitted 5 2026-04-06 B 0.257 0.257 0.257 fitted 6 2026-04-06 ref 0.335 0.335 0.335 fitted 7 2026-04-13 A 0.476 0.476 0.476 fitted 8 2026-04-13 B 0.198 0.198 0.198 fitted 9 2026-04-13 ref 0.326 0.326 0.326 fitted 10 2026-04-20 A 0.541 0.541 0.541 fitted # i 56 more rows 1 time point have fewer than 10 total sequences. -- Lineage frequency data 2 lineages, 1 time point Date range: 2026-03-30 to 2026-03-30 Lineages: "A, B" 3 lineages, 12 time points Date range: 2026-03-30 to 2026-06-15 Pivot: "B" Collapsing 1 rare lineage into "Other". 2 time points have fewer than 10 total sequences. Backtesting ===============>--------------- 50% | ETA: 1s Backtesting =============================>- 95% | ETA: 0s Backtesting ==============================> 100% | ETA: 0s Registered engine "test_engine". Unregistered engine "test_engine". [ FAIL 0 | WARN 0 | SKIP 6 | PASS 251 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • {cmdstanr} is not installed (6): 'test-engine-fga.R:11:3', 'test-engine-fga.R:33:3', 'test-engine-fga.R:53:3', 'test-engine-garw.R:11:3', 'test-engine-garw.R:34:3', 'test-engine-garw.R:56:3' [ FAIL 0 | WARN 0 | SKIP 6 | PASS 251 ] > > proc.time() user system elapsed 29.28 1.26 30.59