Issue in unevaluated vignette chunk

[Bisaloo]

Initially reported by @avinashladdha.

There is a bug in this unevaluated chunk:

epiparameter/vignettes/epiparameter.Rmd

Lines 339 to 350 in 9524e66

	```{r, epinow2 with epiparameter analysis, eval=FALSE}
	# estimate Rt by date of infection
	out <- epinow(
	reported_cases = reported_cases,
	generation_time = generation_time_list,
	rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
	delays = delay_opts(incubation_period_list, reporting_delay),
	stan = stan_opts(samples = 750, chains = 4),
	return_output = TRUE,
	verbose = FALSE
	)
	```

Logging threshold set at INFO for the EpiNow2 logger
Writing EpiNow2 logs to the console and: /tmp/RtmpHlOqyY/regional-epinow/2020-04-01.log
Logging threshold set at INFO for the EpiNow2.epinow logger
Writing EpiNow2.epinow logs to the console and: /tmp/RtmpHlOqyY/epinow/2020-04-01.log
error occurred during calling the sampler; sampling not done
error occurred during calling the sampler; sampling not done
error occurred during calling the sampler; sampling not done
error occurred during calling the sampler; sampling not done
WARN [2022-11-14 11:51:02] epinow: some chains had errors; consider specifying chains = 1 to debug - .local, object, ...
here are whatever error messages were returned
[[1]]
Stan model 'estimate_infections' does not contain samples.

[[2]]
Stan model 'estimate_infections' does not contain samples.

[[3]]
Stan model 'estimate_infections' does not contain samples.

[[4]]
Stan model 'estimate_infections' does not contain samples.

Error in dimnames(x)$parameters :
$ operator is invalid for atomic vectors

I traced back the error to this line but didn't dig more:

https://github.com/epiforecasts/EpiNow2/blob/f9e9fa653190ac2ed9b650f0bf504d7319134bf4/R/estimate_infections.R#L484

You can browse into the code by using:

out <- estimate_infections(
  reported_cases = reported_cases,
  generation_time = generation_time_list,
  rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
  delays = delay_opts(incubation_period_list, reporting_delay),
  stan = stan_opts(samples = 750, chains = 1),
  verbose = FALSE
)

[joshwlambert]

This code was removed in #132. However, keeping this issue open for when writing the transmission vignette.