Automatic Vignette update

Author: sbfnk

vignettes/prior_choice_guide-workflow-step3-1.png

@@ -50,20 +50,27 @@ We load the _EpiNow2_ package and the _posterior_ and _data.table_ packages whic
 
 ``` r
 library(EpiNow2)
+#> 
+#> Attaching package: 'EpiNow2'
+#> The following object is masked from 'package:stats':
+#> 
+#>     Gamma
 library(posterior)
-#> This is posterior version 1.6.1.9000
+#> This is posterior version 1.7.0
 #> 
 #> Attaching package: 'posterior'
-#> The following objects are masked from 'package:rstan':
-#> 
-#>     ess_bulk, ess_tail
 #> The following objects are masked from 'package:stats':
 #> 
 #>     mad, sd, var
 #> The following objects are masked from 'package:base':
 #> 
 #>     %in%, match
 library(data.table)
+#> 
+#> Attaching package: 'data.table'
+#> The following object is masked from 'package:base':
+#> 
+#>     %notin%
 ```
 
 We also set up example data and parameters that will be used in code examples throughout this vignette.
@@ -90,8 +97,18 @@ delay <- example_incubation_period + reporting_delay
 # Fast Stan settings for vignette building
 # (Use default settings for actual analyses)
 stan <- stan_opts(
-  samples = 100,
-  warmup = 100,
+  samples = 500,
+  warmup = 250,
+  chains = 2,
+  control = list(adapt_delta = 0.9)
+)
+
+# estimate_secondary() needs a few more post-warmup samples for a stable tail
+# effective sample size at these fast settings; the other models are fine with
+# `stan` above.
+stan_secondary <- stan_opts(
+  samples = 1000,
+  warmup = 500,
   chains = 2,
   control = list(adapt_delta = 0.9)
 )
@@ -518,12 +535,6 @@ fit_rw <- estimate_infections(
   gp = NULL,  # Disable GP when using random walk
   stan = stan
 )
-#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
-#> https://mc-stan.org/misc/warnings.html#bfmi-low
-#> Warning: Examine the pairs() plot to diagnose sampling problems
-#> Warning: The largest R-hat is NA, indicating chains have not mixed.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#r-hat
 #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
 #> Running the chains for more iterations may help. See
 #> https://mc-stan.org/misc/warnings.html#bulk-ess
@@ -992,9 +1003,6 @@ fit_renewal <- estimate_infections(
   rt = rt_opts(prior = LogNormal(mean = 2, sd = 0.5)),
   stan = stan
 )
-#> Warning: The largest R-hat is NA, indicating chains have not mixed.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#r-hat
 #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
 #> Running the chains for more iterations may help. See
 #> https://mc-stan.org/misc/warnings.html#bulk-ess
@@ -1014,15 +1022,6 @@ fit_nonmech <- estimate_infections(
 #>   day, i.e. the reproduction number is the same as the daily growth rate.
 #> ℹ If this was intended then this warning can be silenced by setting `dist =
 #>   Fixed(1)`'.
-#> Warning: The largest R-hat is NA, indicating chains have not mixed.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#r-hat
-#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#bulk-ess
-#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#tail-ess
 ```
 
 ## Priors for estimate_secondary()
@@ -1055,7 +1054,7 @@ from primary observations (cases, admissions) with a delay and scaling.
 fit_secondary_fixed <- estimate_secondary(
   secondary_data,
   delays = delay_opts(LogNormal(mean = 14, sd = 5, max = 30)),
-  stan = stan
+  stan = stan_secondary
 )
 
 # Uncertain delay (long time series)
@@ -1068,8 +1067,14 @@ fit_secondary_uncertain <- estimate_secondary(
       max = 30
     )
   ),
-  stan = stan
+  stan = stan_secondary
 )
+#> WARN [2026-09-02 15:53:08] estimate_secondary (chain: 1, 2): Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#bulk-ess -
+#> WARN [2026-09-02 15:53:08] estimate_secondary (chain: 1, 2): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#tail-ess -
 ```
 
 ## Priors for estimate_truncation()
@@ -1110,6 +1115,12 @@ fit_trunc_fast <- estimate_truncation(
   ),
   stan = stan
 )
+#> WARN [2026-09-02 15:53:10] estimate_truncation (chain: 1, 2): Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#bulk-ess -
+#> WARN [2026-09-02 15:53:10] estimate_truncation (chain: 1, 2): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#tail-ess -
 
 # Slower reporting (e.g., deaths, 7-14 days)
 fit_trunc_slow <- estimate_truncation(
@@ -1123,6 +1134,12 @@ fit_trunc_slow <- estimate_truncation(
   ),
   stan = stan
 )
+#> WARN [2026-09-02 15:53:12] estimate_truncation (chain: 1, 2): Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#bulk-ess -
+#> WARN [2026-09-02 15:53:13] estimate_truncation (chain: 1, 2): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+#> Running the chains for more iterations may help. See
+#> https://mc-stan.org/misc/warnings.html#tail-ess -
 ```
 
 # Practical workflow for prior specification
@@ -1140,9 +1157,6 @@ estimates <- estimate_infections(
   delays = delay_opts(example_incubation_period + reporting_delay),
   stan = stan
 )
-#> Warning: The largest R-hat is NA, indicating chains have not mixed.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#r-hat
 #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
 #> Running the chains for more iterations may help. See
 #> https://mc-stan.org/misc/warnings.html#bulk-ess
@@ -1175,15 +1189,9 @@ estimates_r0 <- estimate_infections(
   rt = rt_opts(prior = LogNormal(mean = 2.5, sd = 0.5)),
   stan = stan
 )
-#> Warning: The largest R-hat is NA, indicating chains have not mixed.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#r-hat
 #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
 #> Running the chains for more iterations may help. See
 #> https://mc-stan.org/misc/warnings.html#bulk-ess
-#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
-#> Running the chains for more iterations may help. See
-#> https://mc-stan.org/misc/warnings.html#tail-ess
 
 # Compare results
 plot(estimates)
@@ -1226,50 +1234,47 @@ fit <- estimates_r0$fit
 
 # Check Rhat (should be < 1.01)
 summarise_draws(fit, "rhat")
-#> # A tibble: 522 × 2
+#> # A tibble: 496 × 2
 #>    variable   rhat
 #>    <chr>     <dbl>
-#>  1 params[1] 1.02 
+#>  1 params[1] 1.01 
 #>  2 params[2] 1.00 
-#>  3 params[3] 1.01 
-#>  4 eta[1]    0.995
-#>  5 eta[2]    0.995
-#>  6 eta[3]    1.06 
-#>  7 eta[4]    0.991
-#>  8 eta[5]    1.03 
-#>  9 eta[6]    1.00 
-#> 10 eta[7]    1.02 
-#> # ℹ 512 more rows
+#>  3 params[3] 1.000
+#>  4 eta[1]    1.00 
+#>  5 eta[2]    1.01 
+#>  6 eta[3]    1.00 
+#>  7 eta[4]    1.01 
+#>  8 eta[5]    1.02 
+#>  9 eta[6]    1.01 
+#> 10 eta[7]    1.000
+#> # ℹ 486 more rows
 
 # Check effective sample size (should be > 400 for reliable inference)
 summarise_draws(fit, "ess_bulk", "ess_tail")
-#> Warning: The ESS has been capped to avoid unstable estimates.
-#> Warning: The ESS has been capped to avoid unstable estimates.
-#> Warning: The ESS has been capped to avoid unstable estimates.
-#> # A tibble: 522 × 3
+#> # A tibble: 496 × 3
 #>    variable  ess_bulk ess_tail
 #>    <chr>        <dbl>    <dbl>
-#>  1 params[1]    129.      71.9
-#>  2 params[2]    104.     117. 
-#>  3 params[3]     66.3     60.2
-#>  4 eta[1]       110.      70.2
-#>  5 eta[2]       101.      67.7
-#>  6 eta[3]        93.4     79.9
-#>  7 eta[4]       129.     116. 
-#>  8 eta[5]        73.0     53.8
-#>  9 eta[6]       144.      41.9
-#> 10 eta[7]        83.6     58.0
-#> # ℹ 512 more rows
+#>  1 params[1]     305.     243.
+#>  2 params[2]     463.     334.
+#>  3 params[3]     414.     440.
+#>  4 eta[1]        339.     320.
+#>  5 eta[2]        287.     332.
+#>  6 eta[3]        258.     355.
+#>  7 eta[4]        460.     391.
+#>  8 eta[5]        532.     315.
+#>  9 eta[6]        525.     398.
+#> 10 eta[7]        707.     341.
+#> # ℹ 486 more rows
 
 # You can also use the summary method which includes these diagnostics
 summary(estimates_r0)
 #>                         measure                estimate
 #>                          <char>                  <char>
-#> 1:       New infections per day     2139 (1415 -- 3150)
+#> 1:       New infections per day     2195 (1355 -- 3636)
 #> 2:   Expected change in reports       Likely decreasing
-#> 3:   Effective reproduction no.        0.88 (0.71 -- 1)
-#> 4:               Rate of growth -0.033 (-0.09 -- 0.023)
-#> 5: Doubling/halving time (days)        -21 (30 -- -7.7)
+#> 3:   Effective reproduction no.       0.88 (0.7 -- 1.1)
+#> 4:               Rate of growth -0.03 (-0.096 -- 0.036)
+#> 5: Doubling/halving time (days)        -23 (19 -- -7.2)
 ```
 
 Key diagnostics to check: