Sebastian Funk

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...

Return forecasts for easy processing with `scoringutils`

6

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...

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...

Rather than one option for the whole model

create `gt_opts` as an alias for `generation_time_opts`

4

As we move towards extending the `_opts` interface to specifying the data and preprocessing (#346) we are adding complexity to the user interaction. Where in the past a user would...

Time-varying parameters (i.e. conversion to latent variables)

4

Once #504 and #525 are done this opens the option of extending the distribution interface to allow any parameter to vary over time. An interface for Gaussian processes could e.g....

fold secondary options into observation model

4

`secondary_opts` has just one named option: `type` ("incidence" or "prevalence"). This could be added to the observation model options instead, and a `calculate_secondary` call be added to the `estimate_infections` model...

Before releasing 1.5.0 we should check that - [ ] all deprecation warnings point to the correct version - [ ] no functions remain which have their deprecation cycle completed...

The [reference page](https://epiforecasts.io/EpiNow2/dev/reference/index.html) lists quite a few functions as "internal" but in reality they're a mixture of functions users might interact with (the `..._opts` functions) and ones they'll never call...

Bundle repeated checks

2

We should probably bundle these checks into one as it's getting repeated in several places. _Originally posted by @jamesmbaazam in https://github.com/epiforecasts/EpiNow2/pull/557#discussion_r1494641426_