diff --git a/vignettes/EpiNow2.Rmd b/vignettes/EpiNow2.Rmd index 763e0febf..b5b5dad0d 100644 --- a/vignettes/EpiNow2.Rmd +++ b/vignettes/EpiNow2.Rmd @@ -91,7 +91,6 @@ Users can also pass a non-parametric delay distribution vector using the `NonPar for both the generation interval and reporting delays. It is important to note that if doing so, both delay distributions are 0-indexed, meaning the first element corresponds to the probability mass at day 0 of an individual's infection. Because the discretised renewal equation doesn't support mass on day 0, the generation interval should be passed in as a 0-indexed vector with a mass of zero on day 0. -If this is not the case, a warning will indicate that the vector is being left-truncated and renormalized. ``` r @@ -253,19 +252,19 @@ estimates <- regional_epinow( gp = NULL, stan = stan_opts(cores = 4, warmup = 250, samples = 1000) ) -#> INFO [2024-10-02 12:26:54] Producing following optional outputs: regions, summary, samples, plots, latest -#> INFO [2024-10-02 12:26:54] Reporting estimates using data up to: 2020-04-21 -#> INFO [2024-10-02 12:26:54] No target directory specified so returning output -#> INFO [2024-10-02 12:26:54] Producing estimates for: testland, realland -#> INFO [2024-10-02 12:26:54] Regions excluded: none -#> INFO [2024-10-02 12:27:15] Completed estimates for: testland -#> INFO [2024-10-02 12:27:37] Completed estimates for: realland -#> INFO [2024-10-02 12:27:37] Completed regional estimates -#> INFO [2024-10-02 12:27:37] Regions with estimates: 2 -#> INFO [2024-10-02 12:27:37] Regions with runtime errors: 0 -#> INFO [2024-10-02 12:27:37] Producing summary -#> INFO [2024-10-02 12:27:37] No summary directory specified so returning summary output -#> INFO [2024-10-02 12:27:37] No target directory specified so returning timings +#> INFO [2024-10-15 17:53:24] Producing following optional outputs: regions, summary, samples, plots, latest +#> INFO [2024-10-15 17:53:24] Reporting estimates using data up to: 2020-04-21 +#> INFO [2024-10-15 17:53:24] No target directory specified so returning output +#> INFO [2024-10-15 17:53:24] Producing estimates for: testland, realland +#> INFO [2024-10-15 17:53:24] Regions excluded: none +#> INFO [2024-10-15 17:53:46] Completed estimates for: testland +#> INFO [2024-10-15 17:54:09] Completed estimates for: realland +#> INFO [2024-10-15 17:54:09] Completed regional estimates +#> INFO [2024-10-15 17:54:09] Regions with estimates: 2 +#> INFO [2024-10-15 17:54:09] Regions with runtime errors: 0 +#> INFO [2024-10-15 17:54:09] Producing summary +#> INFO [2024-10-15 17:54:09] No summary directory specified so returning summary output +#> INFO [2024-10-15 17:54:10] 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.