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update vignettes
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@sbfnk
sbfnk committed Oct 11, 2023
1 parent 22c5182 commit cf94027
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92 changes: 46 additions & 46 deletions vignettes/epinow.Rmd
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Expand Up @@ -55,13 +55,13 @@ res <- epinow(reported_cases,
target_folder = "results"
)
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpyrWM57/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to the console and: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/epinow/2020-04-21.log
#> WARN [2023-10-02 20:01:50] epinow: There were 17 divergent transitions after warmup. See
#> Writing EpiNow2.epinow logs to the console and: /tmp/RtmpyrWM57/epinow/2020-04-21.log
#> WARN [2023-10-11 13:27:59] epinow: There were 11 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 [2023-10-02 20:01:50] epinow: Examine the pairs() plot to diagnose sampling problems
#> WARN [2023-10-11 13:27:59] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
res$plots$R
#> NULL
Expand Down Expand Up @@ -95,34 +95,34 @@ region_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior),
)
#> INFO [2023-10-02 20:01:56] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-11 13:28:05] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpyrWM57/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/epinow/2020-04-21.log
#> INFO [2023-10-02 20:01:56] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-02 20:01:56] No target directory specified so returning output
#> INFO [2023-10-02 20:01:56] Producing estimates for: testland, realland
#> INFO [2023-10-02 20:01:56] Regions excluded: none
#> INFO [2023-10-02 20:03:16] Completed estimates for: testland
#> INFO [2023-10-02 20:04:44] Completed estimates for: realland
#> INFO [2023-10-02 20:04:44] Completed regional estimates
#> INFO [2023-10-02 20:04:44] Regions with estimates: 2
#> INFO [2023-10-02 20:04:44] Regions with runtime errors: 0
#> INFO [2023-10-02 20:04:44] Producing summary
#> INFO [2023-10-02 20:04:44] No summary directory specified so returning summary output
#> INFO [2023-10-02 20:04:45] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmpyrWM57/epinow/2020-04-21.log
#> INFO [2023-10-11 13:28:05] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-11 13:28:05] No target directory specified so returning output
#> INFO [2023-10-11 13:28:05] Producing estimates for: testland, realland
#> INFO [2023-10-11 13:28:05] Regions excluded: none
#> INFO [2023-10-11 13:29:30] Completed estimates for: testland
#> INFO [2023-10-11 13:30:38] Completed estimates for: realland
#> INFO [2023-10-11 13:30:38] Completed regional estimates
#> INFO [2023-10-11 13:30:38] Regions with estimates: 2
#> INFO [2023-10-11 13:30:38] Regions with runtime errors: 0
#> INFO [2023-10-11 13:30:38] Producing summary
#> INFO [2023-10-11 13:30:38] No summary directory specified so returning summary output
#> INFO [2023-10-11 13:30:38] No target directory specified so returning timings
## summary
region_rt$summary$summarised_results$table
#> Region New confirmed cases by infection date
#> 1: realland 2243 (1148 -- 4405)
#> 2: testland 2327 (1127 -- 4494)
#> 1: realland 2299 (1120 -- 4463)
#> 2: testland 2327 (1154 -- 4455)
#> Expected change in daily cases Effective reproduction no.
#> 1: Likely decreasing 0.88 (0.62 -- 1.2)
#> 2: Likely decreasing 0.89 (0.61 -- 1.2)
#> 1: Likely decreasing 0.89 (0.61 -- 1.2)
#> 2: Likely decreasing 0.89 (0.62 -- 1.2)
#> Rate of growth Doubling/halving time (days)
#> 1: -0.028 (-0.095 -- 0.037) -25 (19 -- -7.3)
#> 2: -0.025 (-0.098 -- 0.042) -27 (17 -- -7.1)
#> 1: -0.024 (-0.096 -- 0.042) -28 (17 -- -7.2)
#> 2: -0.025 (-0.095 -- 0.038) -28 (18 -- -7.3)
## plot
region_rt$summary$plots$R
```
Expand All @@ -142,34 +142,34 @@ region_separate_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2023-10-02 20:04:45] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-11 13:30:39] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpyrWM57/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/gd/x84kkjzd6bn9rlf3f2v830c00000gp/T//Rtmp2g83K0/epinow/2020-04-21.log
#> INFO [2023-10-02 20:04:45] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-02 20:04:45] No target directory specified so returning output
#> INFO [2023-10-02 20:04:45] Producing estimates for: testland, realland
#> INFO [2023-10-02 20:04:45] Regions excluded: none
#> INFO [2023-10-02 20:06:46] Completed estimates for: testland
#> INFO [2023-10-02 20:07:21] Completed estimates for: realland
#> INFO [2023-10-02 20:07:21] Completed regional estimates
#> INFO [2023-10-02 20:07:21] Regions with estimates: 2
#> INFO [2023-10-02 20:07:21] Regions with runtime errors: 0
#> INFO [2023-10-02 20:07:21] Producing summary
#> INFO [2023-10-02 20:07:21] No summary directory specified so returning summary output
#> INFO [2023-10-02 20:07:21] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmpyrWM57/epinow/2020-04-21.log
#> INFO [2023-10-11 13:30:39] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-11 13:30:39] No target directory specified so returning output
#> INFO [2023-10-11 13:30:39] Producing estimates for: testland, realland
#> INFO [2023-10-11 13:30:39] Regions excluded: none
#> INFO [2023-10-11 13:32:06] Completed estimates for: testland
#> INFO [2023-10-11 13:32:36] Completed estimates for: realland
#> INFO [2023-10-11 13:32:36] Completed regional estimates
#> INFO [2023-10-11 13:32:36] Regions with estimates: 2
#> INFO [2023-10-11 13:32:36] Regions with runtime errors: 0
#> INFO [2023-10-11 13:32:36] Producing summary
#> INFO [2023-10-11 13:32:36] No summary directory specified so returning summary output
#> INFO [2023-10-11 13:32:36] No target directory specified so returning timings
## summary
region_separate_rt$summary$summarised_results$table
#> Region New confirmed cases by infection date
#> 1: realland 2168 (1094 -- 4167)
#> 2: testland 2233 (1014 -- 4477)
#> 1: realland 2125 (1135 -- 4129)
#> 2: testland 2189 (934 -- 4255)
#> Expected change in daily cases Effective reproduction no.
#> 1: Likely decreasing 0.86 (0.61 -- 1.2)
#> 2: Likely decreasing 0.88 (0.56 -- 1.2)
#> 1: Likely decreasing 0.85 (0.63 -- 1.2)
#> 2: Likely decreasing 0.86 (0.55 -- 1.2)
#> Rate of growth Doubling/halving time (days)
#> 1: -0.032 (-0.096 -- 0.034) -22 (20 -- -7.2)
#> 2: -0.028 (-0.11 -- 0.044) -25 (16 -- -6.1)
#> 1: -0.034 (-0.091 -- 0.032) -20 (22 -- -7.6)
#> 2: -0.031 (-0.12 -- 0.036) -22 (19 -- -5.9)
## plot
region_separate_rt$summary$plots$R
```
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