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recompile vignettes
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@sbfnk
sbfnk committed Oct 23, 2023
1 parent e3dbb89 commit 4841ad5
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95 changes: 49 additions & 46 deletions vignettes/epinow.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,6 @@ reporting_delay <- dist_spec(
sd = convert_to_logsd(2, 1), sd_sd = 0, max = 10
)
delay <- example_incubation_period + reporting_delay
#> Error in eval(expr, envir, enclos): object 'example_incubation_period' not found
rt_prior <- list(mean = 2, sd = 0.1)
```

Expand All @@ -50,12 +49,16 @@ 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//Rtmpb9LWrR/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmprzMMcb/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//Rtmpb9LWrR/epinow/2020-04-21.log
#> Error in eval(expr, envir, enclos): object 'example_generation_time' not found
#> Writing EpiNow2.epinow logs to the console and: /tmp/RtmprzMMcb/epinow/2020-04-21.log
#> WARN [2023-10-21 09:32:12] epinow: There were 17 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 [2023-10-21 09:32:12] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
res$plots$R
#> Error in eval(expr, envir, enclos): object 'res' not found
#> NULL
```

The initial messages here indicate where log files can be found, and summarised results and plots are in the folder given by `target_folder` (here: `results/`).
Expand Down Expand Up @@ -86,34 +89,34 @@ region_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior),
)
#> INFO [2023-10-19 16:50:18] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-21 09:32:19] 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//Rtmpb9LWrR/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmprzMMcb/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//Rtmpb9LWrR/epinow/2020-04-21.log
#> INFO [2023-10-19 16:50:18] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-19 16:50:18] No target directory specified so returning output
#> INFO [2023-10-19 16:50:18] Producing estimates for: testland, realland
#> INFO [2023-10-19 16:50:18] Regions excluded: none
#> INFO [2023-10-19 16:52:38] Completed estimates for: testland
#> INFO [2023-10-19 16:54:34] Completed estimates for: realland
#> INFO [2023-10-19 16:54:34] Completed regional estimates
#> INFO [2023-10-19 16:54:34] Regions with estimates: 2
#> INFO [2023-10-19 16:54:34] Regions with runtime errors: 0
#> INFO [2023-10-19 16:54:34] Producing summary
#> INFO [2023-10-19 16:54:34] No summary directory specified so returning summary output
#> INFO [2023-10-19 16:54:34] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmprzMMcb/epinow/2020-04-21.log
#> INFO [2023-10-21 09:32:19] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-21 09:32:19] No target directory specified so returning output
#> INFO [2023-10-21 09:32:19] Producing estimates for: testland, realland
#> INFO [2023-10-21 09:32:19] Regions excluded: none
#> INFO [2023-10-21 09:33:56] Completed estimates for: testland
#> INFO [2023-10-21 09:35:26] Completed estimates for: realland
#> INFO [2023-10-21 09:35:26] Completed regional estimates
#> INFO [2023-10-21 09:35:26] Regions with estimates: 2
#> INFO [2023-10-21 09:35:26] Regions with runtime errors: 0
#> INFO [2023-10-21 09:35:26] Producing summary
#> INFO [2023-10-21 09:35:26] No summary directory specified so returning summary output
#> INFO [2023-10-21 09:35:26] No target directory specified so returning timings
## summary
region_rt$summary$summarised_results$table
#> Region New confirmed cases by infection date
#> 1: realland 2178 (945 -- 4053)
#> 2: testland 2150 (915 -- 4118)
#> 1: realland 2119 (876 -- 4309)
#> 2: testland 2082 (823 -- 4219)
#> Expected change in daily cases Effective reproduction no.
#> 1: Likely decreasing 0.89 (0.62 -- 1.1)
#> 2: Likely decreasing 0.89 (0.61 -- 1.1)
#> 1: Likely decreasing 0.89 (0.61 -- 1.2)
#> 2: Likely decreasing 0.88 (0.6 -- 1.2)
#> Rate of growth Doubling/halving time (days)
#> 1: -0.031 (-0.13 -- 0.04) -22 (18 -- -5.2)
#> 2: -0.032 (-0.13 -- 0.038) -22 (18 -- -5.2)
#> 1: -0.033 (-0.14 -- 0.041) -21 (17 -- -5.1)
#> 2: -0.035 (-0.14 -- 0.04) -20 (17 -- -5)
## plot
region_rt$summary$plots$R
```
Expand All @@ -133,34 +136,34 @@ region_separate_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2023-10-19 16:54:35] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-21 09:35:27] 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//Rtmpb9LWrR/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmprzMMcb/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//Rtmpb9LWrR/epinow/2020-04-21.log
#> INFO [2023-10-19 16:54:35] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-19 16:54:35] No target directory specified so returning output
#> INFO [2023-10-19 16:54:35] Producing estimates for: testland, realland
#> INFO [2023-10-19 16:54:35] Regions excluded: none
#> INFO [2023-10-19 16:57:36] Completed estimates for: testland
#> INFO [2023-10-19 16:58:20] Completed estimates for: realland
#> INFO [2023-10-19 16:58:20] Completed regional estimates
#> INFO [2023-10-19 16:58:20] Regions with estimates: 2
#> INFO [2023-10-19 16:58:20] Regions with runtime errors: 0
#> INFO [2023-10-19 16:58:20] Producing summary
#> INFO [2023-10-19 16:58:20] No summary directory specified so returning summary output
#> INFO [2023-10-19 16:58:21] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmprzMMcb/epinow/2020-04-21.log
#> INFO [2023-10-21 09:35:27] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-21 09:35:27] No target directory specified so returning output
#> INFO [2023-10-21 09:35:27] Producing estimates for: testland, realland
#> INFO [2023-10-21 09:35:27] Regions excluded: none
#> INFO [2023-10-21 09:37:00] Completed estimates for: testland
#> INFO [2023-10-21 09:37:36] Completed estimates for: realland
#> INFO [2023-10-21 09:37:36] Completed regional estimates
#> INFO [2023-10-21 09:37:36] Regions with estimates: 2
#> INFO [2023-10-21 09:37:36] Regions with runtime errors: 0
#> INFO [2023-10-21 09:37:36] Producing summary
#> INFO [2023-10-21 09:37:36] No summary directory specified so returning summary output
#> INFO [2023-10-21 09:37:36] No target directory specified so returning timings
## summary
region_separate_rt$summary$summarised_results$table
#> Region New confirmed cases by infection date
#> 1: realland 1996 (1006 -- 3934)
#> 2: testland 2073 (896 -- 4109)
#> 1: realland 2013 (953 -- 4182)
#> 2: testland 2052 (855 -- 4277)
#> Expected change in daily cases Effective reproduction no.
#> 1: Likely decreasing 0.88 (0.67 -- 1.1)
#> 1: Likely decreasing 0.88 (0.66 -- 1.2)
#> 2: Likely decreasing 0.88 (0.6 -- 1.2)
#> Rate of growth Doubling/halving time (days)
#> 1: -0.036 (-0.11 -- 0.036) -19 (19 -- -6.2)
#> 2: -0.035 (-0.14 -- 0.04) -20 (17 -- -4.9)
#> 1: -0.035 (-0.12 -- 0.04) -20 (17 -- -6)
#> 2: -0.036 (-0.14 -- 0.045) -19 (16 -- -5)
## plot
region_separate_rt$summary$plots$R
```
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