EpiNow2

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CRAN release

7

We (mostly thanks to @sbfnk) are starting to accumulate a lot of nice new features all (I think) are well implemented enough not to break backwards compatibility. Given that we...

seabbs

Rather than one option for the whole model

sbfnk

Clarify documentation for passing uncertainty from estimate_truncation to estimate_infections

1

See https://github.com/epiforecasts/EpiNow2/discussions/365 for a user question highlighting the current issues and explanations of the current functionality. Ideally, we would improve areas of the documentation to make the various options clearer....

seabbs

reported_cases_opts()

29

Currently, all inputs except for `reported_cases` are managed via a helper function (i.e `delay_opts()`) that enables specifying options. It would make sense to standardized `reported_cases` to be in line with...

seabbs

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...

sbfnk

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

2

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....

sbfnk

fold secondary options into observation model

1

`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...

sbfnk

Would it be worth sketching up the architecture of this package? This might help users and contributors quickly understand how the various models relate to each other and how data...

jamesmbaazam

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...

sbfnk

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...

sbfnk