Stop spurious NA R-hat warnings from estimate_secondary (#1516)

Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk>

Author: sbfnk-bot

NEWS.md

@@ -14,6 +14,7 @@
 
 - A bug was fixed where disabling the weekly reporting effect produced a spurious convergence warning from a degenerate day-of-week simplex.
 - A bug was fixed where `estimate_infections()` could emit a spurious "the largest R-hat is NA" convergence warning caused by deterministic delay PMFs being monitored; these are no longer monitored.
+- A bug was fixed where `estimate_secondary()` emitted the same spurious "the largest R-hat is NA" convergence warning from a deterministic delay PMF being monitored; it is no longer monitored.
 - A bug was fixed where `get_predictions()` on an `estimate_truncation()` result assigned reconstructed observations to the wrong datasets and dates.
 - A bug was fixed where the prior on the initial reproduction number was applied with an incorrect Jacobian, shifting it upwards by a factor of `exp(sdlog^2)`. A `LogNormal(mean = 2, sd = 1)` prior was applied as though it had a mean of 2.5.
 - A bug was fixed where the mean reproduction number over the observation window was left uninitialised, so chains started from a value drawn across the whole of `exp(-2)` to `exp(2)` rather than from the user's Rt prior.

R/create.R

@@ -727,8 +727,11 @@ create_stan_args <- function(stan = stan_opts(),
   if (!fixed_param && inherits(stan_args$object, "stanmodel") &&
         is.null(stan_args$pars)) {
     exclude <- character(0)
+    if (model %in% c("estimate_infections", "estimate_secondary")) {
+      exclude <- c(exclude, "delay_np_pmf_use")
+    }
     if (identical(model, "estimate_infections")) {
-      exclude <- c(exclude, "delay_np_pmf_use", "gt_rev_pmf")
+      exclude <- c(exclude, "gt_rev_pmf")
     }
     if (isTRUE(data$week_effect == 1)) {
       exclude <- c(exclude, "day_of_week_simplex")

vignettes/prior_choice_guide.Rmd.orig

@@ -83,8 +83,8 @@ 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)
 )