James Azam

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_

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_

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

Architecture diagram for the package

4

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...

Group deprecated functions together in `pkgdown` Reference Page

1

It would be nice to add a section in the `pkgdown` Reference, similar to [this section on superseded functions in dplyr](https://dplyr.tidyverse.org/reference/index.html#superseded) and [purrr](https://purrr.tidyverse.org/reference/index.html#superseded). That will probably help users identify which...

Simplify "Getting Started" | Split into smaller chunks

7

I think the "Getting Started" vignette is well-written but quite long. May I suggest writing a simpler version of the current one and splitting the current one into smaller chunks,...

Address `devtools::check()` warning and note

2

When you run `devtools::check()`, you get the following warning and note that should probably be addressed: ``` ❯ checking S3 generic/method consistency ... WARNING as.igraph: function(x, ...) as.igraph.epicontacts: function(x) See...

I'm just learning about [`lifecycle::is_present()`](https://lifecycle.r-lib.org/reference/deprecated.html). Might be worse applying the recommendations in the linked reference since we're already importing {lifecycle}. Yet to weigh the cons of this approach vs what...

Clarify how to specify priors

6

@seabbs I've updated the tests to check aspects of the structure of the expected prior used. It's made me realise that the documentation of the `prior` argument in `epinowcast()` could...

General improvements to Getting Started vignette

1

The current Getting Started vignette can be improved in various areas, some of which were mentioned in the review of #375, including: - [ ] Use consistent function specification style...