Sam Abbott

Feature explicit pcr model

1

Adds an explicit PCR probability of detection model and then fits to the summary stats from Hellewell et al. As discussed on call I think this is the least worst...

Finally killing the nice clean code.... *WIP*

Update to support multiple antibody levels + booster shots

2

Data now available with multiple antibody levels + booster shots: https://twitter.com/theosanderson/status/1481675533524127748 This enables the option of some more complex modelling and better handle of multiple rounds of vaccination etc. Needs...

Add optional support to fit to count data with CFR/IFR correction

2

Allows tracking of for example severity over time.

Tab by target and then forecast date in reports

1

At the moment the reports are tabbed by forecast date and then target. This can be quite annoying if you are comparing death forecasts across time as you constantly have...

The current definition is static (?) - it makes sense to make this settable in `scenario_sim`

I have looked through the arguments and it seems like this feature (though still in dev) is linked up and working. Having said that I have been seeing errors when...

As the title says with the latest version of `cmdstanr` (https://github.com/stan-dev/cmdstanr/releases/tag/v0.8.0) there is now support for using a fit `cmdstan` object to initialise a new fit. This would likely be...

Double censoring using numerical integration

1

As discussed in https://github.com/CDCgov/Rt-without-renewal/pull/10 we could use numerical integration to find double censored PDFs rather than using simulation or in the stan code approximating using a uniform distribution. Any changes...

**Is your feature request related to a problem? Please describe.** The current stan documentation (added in #422) follows the suggested format in the stan docs which themselves are based on...