EpiNow2

EpiNow2 copied to clipboard

As noted in #631 we have `{styler}` in the suggests for no good reason. This PR removes it.

seabbs

switch to directly calculated growth rate and extend model options, take 2

1

Attempts to resurrect #307 as work in progress. Copying text from there: This PR is meant to supersede #213 and #214. It - finalises the work commenced in #214 to...

sbfnk

## Description This PR closes #519. It adds a `weight_priors` argument (having realise that "weigh" is the wrong verb!) to `generation_time_opts()`, `delay_opts()` and `trunc_opts()`. I'm not sure this is a...

sbfnk

Vignette on approximations and speedups

5

Type of issue: Proposal for a new vignette Detail: People often state that estimation in the package is slow (e.g. https://journals.plos.org/digitalhealth/article/figure?id=10.1371/journal.pdig.0000052.t002). This is to some degree a function of the...

sbfnk

New maintainer

2

Would anyone - especially someone already funded to do `EpiNow2` development (i.e @sbfnk or @jamesmbaazam) be interested in taking over as a maintainer? I think I need to take a...

seabbs

Return forecasts for easy processing with `scoringutils`

3

Is your feature request related to a problem? Please describe: Forecast evaluation is an important part of broader workflows around forecasting. [scoringutils](https://epiforecasts.io/scoringutils) is an R package for evaluating forecasts. It...

sbfnk

Change "back-calculation" to "non-mechanistic" infection model throughout

1

At some point we should change back-calculation to nonparametric infection model throughout as that's what we're calling it in the model definition vignette. _Originally posted by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/521#discussion_r1407455280_

jamesmbaazam

Remove references to "confirmed" cases

2

At the moment the main functions in the package expect a data frame with columns `date` and `confirm`. Also much of the reporting refers to "confirmed cases". However, the package...

sbfnk

After #605 is addressed, would be good to pass the new arguments to a `preprocessing_opts()` function. _Originally posted by @sbfnk in https://github.com/epiforecasts/EpiNow2/issues/346#issuecomment-1988022878_

jamesmbaazam

- [ ] rename first argument of all three models to `data` _Originally posted by @sbfnk in https://github.com/epiforecasts/EpiNow2/issues/346#issuecomment-1988022878_

jamesmbaazam