diff --git a/vignettes/epinow-epinow-1.png b/vignettes/epinow-epinow-1.png index 7048c4c1b..61a6721a5 100644 Binary files a/vignettes/epinow-epinow-1.png and b/vignettes/epinow-epinow-1.png differ diff --git a/vignettes/epinow-regional_epinow-1.png b/vignettes/epinow-regional_epinow-1.png index 0777a674e..af538e703 100644 Binary files a/vignettes/epinow-regional_epinow-1.png and b/vignettes/epinow-regional_epinow-1.png differ diff --git a/vignettes/epinow-regional_epinow_multiple-1.png b/vignettes/epinow-regional_epinow_multiple-1.png index b9817901a..d8f1e32ec 100644 Binary files a/vignettes/epinow-regional_epinow_multiple-1.png and b/vignettes/epinow-regional_epinow_multiple-1.png differ diff --git a/vignettes/epinow.Rmd b/vignettes/epinow.Rmd index 2bf48d881..68a341a15 100644 --- a/vignettes/epinow.Rmd +++ b/vignettes/epinow.Rmd @@ -51,15 +51,10 @@ res <- epinow(reported_cases, ) #> Logging threshold set at INFO for the name logger #> Writing EpiNow2 logs to the console and: -#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'. +#> '/tmp/RtmpTIgwPA/regional-epinow/2020-04-21.log'. #> Logging threshold set at INFO for the name logger #> Writing EpiNow2.epinow logs to the console and: -#> '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'. -#> WARN [2024-12-06 15:12:56] epinow: There were 2 divergent transitions after warmup. See -#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup -#> to find out why this is a problem and how to eliminate them. - -#> WARN [2024-12-06 15:12:56] epinow: Examine the pairs() plot to diagnose sampling problems -#> - +#> '/tmp/RtmpTIgwPA/epinow/2020-04-21.log'. res$plots$R ``` @@ -94,38 +89,38 @@ region_rt <- regional_epinow( delays = delay_opts(delay), rt = rt_opts(prior = rt_prior), ) -#> INFO [2024-12-06 15:12:59] Producing following optional outputs: regions, summary, samples, plots, latest +#> INFO [2025-02-04 19:51:23] Producing following optional outputs: regions, summary, samples, plots, latest #> Logging threshold set at INFO for the name logger #> Writing EpiNow2 logs to the console and: -#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'. +#> '/tmp/RtmpTIgwPA/regional-epinow/2020-04-21.log'. #> Logging threshold set at INFO for the name logger -#> Writing EpiNow2.epinow logs to: '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'. -#> INFO [2024-12-06 15:12:59] Reporting estimates using data up to: 2020-04-21 -#> INFO [2024-12-06 15:12:59] No target directory specified so returning output -#> INFO [2024-12-06 15:12:59] Producing estimates for: testland, realland -#> INFO [2024-12-06 15:12:59] Regions excluded: none -#> INFO [2024-12-06 15:14:04] Completed estimates for: testland -#> INFO [2024-12-06 15:15:08] Completed estimates for: realland -#> INFO [2024-12-06 15:15:08] Completed regional estimates -#> INFO [2024-12-06 15:15:08] Regions with estimates: 2 -#> INFO [2024-12-06 15:15:08] Regions with runtime errors: 0 -#> INFO [2024-12-06 15:15:08] Producing summary -#> INFO [2024-12-06 15:15:08] No summary directory specified so returning summary output -#> INFO [2024-12-06 15:15:08] No target directory specified so returning timings +#> Writing EpiNow2.epinow logs to: '/tmp/RtmpTIgwPA/epinow/2020-04-21.log'. +#> INFO [2025-02-04 19:51:23] Reporting estimates using data up to: 2020-04-21 +#> INFO [2025-02-04 19:51:23] No target directory specified so returning output +#> INFO [2025-02-04 19:51:23] Producing estimates for: testland, realland +#> INFO [2025-02-04 19:51:23] Regions excluded: none +#> INFO [2025-02-04 19:54:18] Completed estimates for: testland +#> INFO [2025-02-04 19:55:24] Completed estimates for: realland +#> INFO [2025-02-04 19:55:24] Completed regional estimates +#> INFO [2025-02-04 19:55:24] Regions with estimates: 2 +#> INFO [2025-02-04 19:55:24] Regions with runtime errors: 0 +#> INFO [2025-02-04 19:55:24] Producing summary +#> INFO [2025-02-04 19:55:24] No summary directory specified so returning summary output +#> INFO [2025-02-04 19:55:24] No target directory specified so returning timings ## summary region_rt$summary$summarised_results$table -#> Region New infections per day Expected change in daily reports -#> -#> 1: realland 2203 (1259 -- 3956) Likely decreasing -#> 2: testland 2237 (1281 -- 4185) Likely decreasing +#> Region New infections per day Expected change in reports +#> +#> 1: realland 2284 (1405 -- 3710) Likely decreasing +#> 2: testland 2237 (1344 -- 3795) Likely decreasing #> Effective reproduction no. Rate of growth #> -#> 1: 0.89 (0.71 -- 1.1) -0.031 (-0.096 -- 0.041) -#> 2: 0.9 (0.71 -- 1.1) -0.027 (-0.097 -- 0.051) +#> 1: 0.91 (0.73 -- 1.1) -0.026 (-0.093 -- 0.04) +#> 2: 0.9 (0.71 -- 1.1) -0.028 (-0.099 -- 0.041) #> Doubling/halving time (days) #> -#> 1: -22 (17 -- -7.2) -#> 2: -26 (14 -- -7.2) +#> 1: -27 (17 -- -7.4) +#> 2: -25 (17 -- -7) ## plot region_rt$summary$plots$R ``` @@ -145,38 +140,38 @@ region_separate_rt <- regional_epinow( delays = delay_opts(delay), rt = rt, gp = gp, ) -#> INFO [2024-12-06 15:15:09] Producing following optional outputs: regions, summary, samples, plots, latest +#> INFO [2025-02-04 19:55:25] Producing following optional outputs: regions, summary, samples, plots, latest #> Logging threshold set at INFO for the name logger #> Writing EpiNow2 logs to the console and: -#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'. +#> '/tmp/RtmpTIgwPA/regional-epinow/2020-04-21.log'. #> Logging threshold set at INFO for the name logger -#> Writing EpiNow2.epinow logs to: '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'. -#> INFO [2024-12-06 15:15:09] Reporting estimates using data up to: 2020-04-21 -#> INFO [2024-12-06 15:15:09] No target directory specified so returning output -#> INFO [2024-12-06 15:15:09] Producing estimates for: testland, realland -#> INFO [2024-12-06 15:15:09] Regions excluded: none -#> INFO [2024-12-06 15:16:23] Completed estimates for: testland -#> INFO [2024-12-06 15:17:02] Completed estimates for: realland -#> INFO [2024-12-06 15:17:02] Completed regional estimates -#> INFO [2024-12-06 15:17:02] Regions with estimates: 2 -#> INFO [2024-12-06 15:17:02] Regions with runtime errors: 0 -#> INFO [2024-12-06 15:17:02] Producing summary -#> INFO [2024-12-06 15:17:02] No summary directory specified so returning summary output -#> INFO [2024-12-06 15:17:02] No target directory specified so returning timings +#> Writing EpiNow2.epinow logs to: '/tmp/RtmpTIgwPA/epinow/2020-04-21.log'. +#> INFO [2025-02-04 19:55:25] Reporting estimates using data up to: 2020-04-21 +#> INFO [2025-02-04 19:55:25] No target directory specified so returning output +#> INFO [2025-02-04 19:55:25] Producing estimates for: testland, realland +#> INFO [2025-02-04 19:55:25] Regions excluded: none +#> INFO [2025-02-04 19:56:30] Completed estimates for: testland +#> INFO [2025-02-04 19:56:59] Completed estimates for: realland +#> INFO [2025-02-04 19:56:59] Completed regional estimates +#> INFO [2025-02-04 19:56:59] Regions with estimates: 2 +#> INFO [2025-02-04 19:56:59] Regions with runtime errors: 0 +#> INFO [2025-02-04 19:56:59] Producing summary +#> INFO [2025-02-04 19:56:59] No summary directory specified so returning summary output +#> INFO [2025-02-04 19:57:00] No target directory specified so returning timings ## summary region_separate_rt$summary$summarised_results$table -#> Region New infections per day Expected change in daily reports -#> -#> 1: realland 2072 (1008 -- 4386) Likely decreasing -#> 2: testland 2264 (1344 -- 3892) Likely decreasing +#> Region New infections per day Expected change in reports +#> +#> 1: realland 2017 (1042 -- 3839) Likely decreasing +#> 2: testland 2266 (1356 -- 3666) Likely decreasing #> Effective reproduction no. Rate of growth #> -#> 1: 0.85 (0.6 -- 1.2) -0.039 (-0.11 -- 0.049) -#> 2: 0.9 (0.71 -- 1.1) -0.026 (-0.091 -- 0.041) +#> 1: 0.84 (0.6 -- 1.2) -0.042 (-0.11 -- 0.038) +#> 2: 0.9 (0.71 -- 1.1) -0.028 (-0.098 -- 0.039) #> Doubling/halving time (days) #> -#> 1: -18 (14 -- -6.2) -#> 2: -26 (17 -- -7.6) +#> 1: -16 (18 -- -6.2) +#> 2: -25 (18 -- -7.1) ## plot region_separate_rt$summary$plots$R ```