Automatic Vignette update

epiforecasts · Oct 2, 2024 · b314494 · b314494
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diff --git a/vignettes/estimate_infections_workflow-plot_combined_delay-1.png b/vignettes/estimate_infections_workflow-plot_combined_delay-1.png
diff --git a/vignettes/estimate_infections_workflow-plot_fixed_gamma-1.png b/vignettes/estimate_infections_workflow-plot_fixed_gamma-1.png
diff --git a/vignettes/estimate_infections_workflow-plot_uncertain_gamma-1.png b/vignettes/estimate_infections_workflow-plot_uncertain_gamma-1.png
diff --git a/vignettes/estimate_infections_workflow-results-1.png b/vignettes/estimate_infections_workflow-results-1.png
diff --git a/vignettes/estimate_infections_workflow.Rmd b/vignettes/estimate_infections_workflow.Rmd
@@ -112,11 +112,12 @@ For example, to define a variable gamma distribution where uncertainty in the me
 
 ``` r
 uncertain_gamma <- Gamma(mean = Normal(3, 2), sd = Normal(1, 0.1), max = 10)
-#> Warning: ! Uncertain gamma distribution specified in terms of parameters that are not the "natural"
-#>   parameters of the distribution shape and rate.
-#> ℹ Converting using a crude and very approximate method that is likely to produce biased results.
-#> ℹ If possible it is preferable to specify the distribution directly in terms of the natural
-#>   parameters.
+#> Warning: ! Uncertain gamma distribution specified in terms of parameters that are not
+#>   the "natural" parameters of the distribution shape and rate.
+#> ℹ Converting using a crude and very approximate method that is likely to
+#>   produce biased results.
+#> ℹ If possible it is preferable to specify the distribution directly in terms of
+#>   the natural parameters.
 uncertain_gamma
 #> - gamma distribution (max: 10):
 #>   shape:
@@ -300,7 +301,6 @@ def <- estimate_infections(
   delays = delay_opts(delay),
   rt = rt_opts(prior = rt_prior)
 )
-#> DEBUG [2024-09-26 20:23:03] estimate_infections: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 147 time steps of which 7 are a forecast
 #> Warning: There were 6 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.