Use testthat edition 3 & fix imports

[steffilazerte]

Pull Request - Ready for review

• Updating tests to testthat edition 3 (Use testthat v3 #243)
• Adding snapshot tests where missing (Remove the serialized snapshot value test (replace with something less opaque) #239)
• Adding more tests for coverage
• Moving incidence and incidence2 from imports to suggests (Make incidence and incidence2 suggests not imports? #241)
• Adding rlang::check_installed() to plot(), wallinga_teunis() and estimate_R() where incidence/incidence two functions are required

Checklist

• I have added tests to prove my changes work
• I have added documentation where required
• I have updated NEWS.md with a short description of my change

[steffilazerte]

Hi @sangeetabhatia03, sorry for the delay on this! I've updated the tests to testthat edition 3 which was pretty straightforward, and then added some snapshot tests, especially for the gibs draws functions (which was not too bad but a tad more complicated because of the custom snapshot tests and trying to avoid problems with randomization across different OS). I also added a snapshot test for the Wallinga Teunis function which fails on devel because they changed a randomization procedure. I'm skipping that test on devel for now, but once R updates we'll probably have to update the snapshot, but that seems like a later problem?

The linters are failing because I fixed a warning in plot.R but did not fix all the lint problems there (I think better to do that in a dedicated PR and I should have resisted the urge to fix the warning, but ah well).

I think it's good to go now. Once you've had a look, we can merge into main, and then I think you could merge main into #244, possibly refactor the tests to match the new functions you've created, but I think it shouldn't be strictly necessary (I'm happy to do that if needed). Then we should be able to merge #244 🎉 (I've taken a look and as far as I can tell it's good, but with so many changes it can't hurt to have the tests).

[sangeetabhatia03]

hi @steffilazerte I have added some minor comments; these changes will trigger a build failure with an older version of testthat. e.g. I get the following error:

 ── Error ('test-gibs_draws.R:39:3'): get_shape_R_flat() ────────────────────────
Error in `expect_all_equal(expect_silent(get_shape_R_flat(incid, default_priors())), 
    20.04)`: could not find function "expect_all_equal"
── Failure ('test-weekly.R:686:3'): you can't run estimate_R_agg unless using parametric/non-parametric SI methods ──

when testing with v3.1.7. So we either modify the offending function, or update the DESCRIPTION file.