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Automatic Vignette update (#984)
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Co-authored-by: sbfnk <[email protected]>
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github-actions[bot] and sbfnk authored Feb 4, 2025
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101 changes: 48 additions & 53 deletions vignettes/epinow.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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
```

Expand Down Expand Up @@ -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$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2203 (1259 -- 3956) Likely decreasing
#> 2: testland 2237 (1281 -- 4185) Likely decreasing
#> Region New infections per day Expected change in reports
#> <char> <char> <fctr>
#> 1: realland 2284 (1405 -- 3710) Likely decreasing
#> 2: testland 2237 (1344 -- 3795) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.89 (0.71 -- 1.1) -0.031 (-0.096 -- 0.041)
#> 2: 0.9 (0.71 -- 1.1) -0.027 (-0.097 -- 0.051)
#> 1: 0.91 (0.73 -- 1.1) -0.026 (-0.093 -- 0.04)
#> 2: 0.9 (0.71 -- 1.1) -0.028 (-0.099 -- 0.041)
#> Doubling/halving time (days)
#> <char>
#> 1: -22 (17 -- -7.2)
#> 2: -26 (14 -- -7.2)
#> 1: -27 (17 -- -7.4)
#> 2: -25 (17 -- -7)
## plot
region_rt$summary$plots$R
```
Expand All @@ -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$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2072 (1008 -- 4386) Likely decreasing
#> 2: testland 2264 (1344 -- 3892) Likely decreasing
#> Region New infections per day Expected change in reports
#> <char> <char> <fctr>
#> 1: realland 2017 (1042 -- 3839) Likely decreasing
#> 2: testland 2266 (1356 -- 3666) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.85 (0.6 -- 1.2) -0.039 (-0.11 -- 0.049)
#> 2: 0.9 (0.71 -- 1.1) -0.026 (-0.091 -- 0.041)
#> 1: 0.84 (0.6 -- 1.2) -0.042 (-0.11 -- 0.038)
#> 2: 0.9 (0.71 -- 1.1) -0.028 (-0.098 -- 0.039)
#> Doubling/halving time (days)
#> <char>
#> 1: -18 (14 -- -6.2)
#> 2: -26 (17 -- -7.6)
#> 1: -16 (18 -- -6.2)
#> 2: -25 (18 -- -7.1)
## plot
region_separate_rt$summary$plots$R
```
Expand Down

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