Use natural parameters when specifying uncertain distributions

[jamesmbaazam]

Description

This PR closes #870. I switch all uncertain parameters expressed in using the unnatural parameters to the natural ones and align the accompanying text.

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After the initial Pull Request

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[jamesmbaazam]

@sbfnk I'm getting this error in the CI. Is this not allowed or do we need to update the checks in check_stan_delays() OR make it clear that if we want to specify a fixed value, it doesn't have to be passed to Fixed()?

library(EpiNow2)
#> 
#> Attaching package: 'EpiNow2'
#> The following object is masked from 'package:stats':
#> 
#>     Gamma
try(
  delay_opts(
    LogNormal(
      meanlog = EpiNow2::Fixed(2),
      sdlog = EpiNow2::Fixed(1),
      max = 10
    )
  )
)
#> Error in check_stan_delay(dist) : 
#>   ! Delay distributions passed to the model need to have parameters that
#>   are either numeric or normally distributed with numeric parameters and
#>   infinite maximum.

^{Created on 2024-12-12 with reprex v2.1.1}

[sbfnk]

I think it's as the error says - either has to be numeric or Normal. We could extend this to a Fixed distribution, I don't feel strongly either way.

[sbfnk]

The original issue only suggested doing this for parameterisations with uncertainty to avoid the warning. For fixed parameters there is no issue - perhaps keep these as they are?

There are a few instances of examples not yet captured here, e.g. various in dist_spec.r and for delay_opts() and the vignettes. I think a full-text search for "mean = Normal" will get most of them.

[sbfnk]

Great! Just one very minor suggestion.

[jamesmbaazam]

/document