Fixes #127

[bahadzie]

• Fixes issue #125
• Fixes issue #127

[Bisaloo]

Hi @bahadzie, rather than removing the files in _snaps/ altogether, you should run the tests interactively on your local machine, and run testthat::snapshot_accept('vaccination') if you want to validate the change in the recorded snapshot.

More info in the dedicated testthat vignette: https://testthat.r-lib.org/articles/snapshotting.html

[pratikunterwegs]

Hi @bahadzie and @Bisaloo - just checking whether this PR is still current and if it needs to be reviewed? @Bisaloo are you reviewing or would it help for me to step in?

[Bisaloo]

No, this was just a drive by comment based on the check results. I have not reviewed the code. I'll leave it up to your expertise.

[pratikunterwegs]

Okay thanks, we have a P3 meeting scheduled later so will discuss next steps for this PR then. Edit add: of course we'll restore the snapshots.

[bahadzie]

Hi @bahadzie, thanks for adding these changes. Could you:

1. Update the PR description to say what the changes are and ideally tag the issues being fixed;

2. Rebase this branch on `main`;

3. Update your version of {testthat} (v3.2.1 appears latest) as this seems to be causing changes to the test snapshots; you would also need to revert changes to the test snapshots, and then check if any snapshots really need to be updated. In general, I would be very conservative in accepting changes to a test snapshot, and I would always mention why in the PR or in the commit message;

4. Update the code in `epidemic_peak()` to access columns using [one of the two methods mentioned in this SO post](https://stackoverflow.com/a/8096882/7410366) by Matt Dowle. In today's meeting I said I preferred setting variables to `NULL` at the top of the function (Dowle's option 2), but I see that in `new_infections()` I have gone for option 1 instead which uses `get()`.

Once 2 -- 4 are done, we shall get a better idea of whether checks pass - I expect they will.

[bahadzie]

Hi @bahadzie, thanks for adding these changes. Could you:

1. Update the PR description to say what the changes are and ideally tag the issues being fixed;

2. Rebase this branch on `main`;

3. Update your version of {testthat} (v3.2.1 appears latest) as this seems to be causing changes to the test snapshots; you would also need to revert changes to the test snapshots, and then check if any snapshots really need to be updated. In general, I would be very conservative in accepting changes to a test snapshot, and I would always mention why in the PR or in the commit message;

4. Update the code in `epidemic_peak()` to access columns using [one of the two methods mentioned in this SO post](https://stackoverflow.com/a/8096882/7410366) by Matt Dowle. In today's meeting I said I preferred setting variables to `NULL` at the top of the function (Dowle's option 2), but I see that in `new_infections()` I have gone for option 1 instead which uses `get()`.

Once 2 -- 4 are done, we shall get a better idea of whether checks pass - I expect they will.

Done

[pratikunterwegs]

Thanks @bahadzie - I think you might have rebased on an older commit; could you rebase on the current head of origin/main? That would probably resolve the flagged conflict.

[bahadzie]

Hi @pratikunterwegs I've rebased on main.

It's currently running the Github Actions. I'll keep you posted.

[pratikunterwegs]

Thanks, will take a look tomorrow, checks are passing.

[pratikunterwegs]

Just looking at this PR again, I think it might be better to restrict this PR to the epidemic peak function by resetting this PR to before the vaccination rate fn is added, I expect that should be https://github.com/epiverse-trace/epidemics/pull/152/commits/8bee33369235d994219efdddce87d3ac289adb50. I think #202 should resolve the effective vaccination issue documented in #198.

[pratikunterwegs]

Key commits from this branch copied into #240 and merged into main.