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Update EpiNow2 vignette #959

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Update EpiNow2 vignette #959

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26 changes: 13 additions & 13 deletions vignettes/EpiNow2.Rmd
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Expand Up @@ -252,19 +252,19 @@ estimates <- regional_epinow(
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2025-01-31 17:34:01] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2025-01-31 17:34:01] Reporting estimates using data up to: 2020-04-21
#> INFO [2025-01-31 17:34:01] No target directory specified so returning output
#> INFO [2025-01-31 17:34:01] Producing estimates for: testland, realland
#> INFO [2025-01-31 17:34:01] Regions excluded: none
#> INFO [2025-01-31 17:34:21] Completed estimates for: testland
#> INFO [2025-01-31 17:34:41] Completed estimates for: realland
#> INFO [2025-01-31 17:34:41] Completed regional estimates
#> INFO [2025-01-31 17:34:41] Regions with estimates: 2
#> INFO [2025-01-31 17:34:41] Regions with runtime errors: 0
#> INFO [2025-01-31 17:34:41] Producing summary
#> INFO [2025-01-31 17:34:41] No summary directory specified so returning summary output
#> INFO [2025-01-31 17:34:41] No target directory specified so returning timings
#> INFO [2025-02-01 00:22:07] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2025-02-01 00:22:07] Reporting estimates using data up to: 2020-04-21
#> INFO [2025-02-01 00:22:07] No target directory specified so returning output
#> INFO [2025-02-01 00:22:07] Producing estimates for: testland, realland
#> INFO [2025-02-01 00:22:07] Regions excluded: none
#> INFO [2025-02-01 00:22:26] Completed estimates for: testland
#> INFO [2025-02-01 00:22:46] Completed estimates for: realland
#> INFO [2025-02-01 00:22:46] Completed regional estimates
#> INFO [2025-02-01 00:22:46] Regions with estimates: 2
#> INFO [2025-02-01 00:22:46] Regions with runtime errors: 0
#> INFO [2025-02-01 00:22:46] Producing summary
#> INFO [2025-02-01 00:22:46] No summary directory specified so returning summary output
#> INFO [2025-02-01 00:22:47] No target directory specified so returning timings
```

Results from each region are stored in a `regional` list with across region summary measures and plots stored in a `summary` list. All results can be set to be internally saved by setting the `target_folder` and `summary_dir` arguments. Each region can be estimated in parallel using the `{future}` package (when in most scenarios `cores` should be set to 1). For routine use each MCMC chain can also be run in parallel (with `future` = TRUE) with a time out (`max_execution_time`) allowing for partial results to be returned if a subset of chains is running longer than expected. See the documentation for the `{future}` package for details on nested futures.
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