Conditionally throw message for obs_opts(na = "missing")

[jamesmbaazam]

Description

This PR closes #771 by adding a message to inform users about how NA's are treated in the default model. It also points to alternatives given the user's use case. This PR also adds missing tests for obs_opts().

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
• I have added or updated unit tests where necessary.
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After the initial Pull Request

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[sbfnk]

Nice - some suggestions for (I think) slightly clearer wording. I think we should be more restrictive about when this message is shown (e.g. it should be suppressed when there is no missing data).

[sbfnk]

Thanks, this looks good.

It's adding a fair amount of infrastructure (an additional function + return value in obs_opts() that needs to be removed) just to be able to show that message. Shall we give it an expiry (and use keyword "deprecated" somewhere)?

[sbfnk]

Hardcoding these column names will require coming back to this when addressing #505 - perhaps we should just pass this as an argument (where the function asking for the tests specifies what to check)?

[jamesmbaazam]

Thanks, this looks good.

It's adding a fair amount of infrastructure (an additional function + return value in obs_opts() that needs to be removed) just to be able to show that message. Shall we give it an expiry (and use keyword "deprecated" somewhere)?

Was this what you meant? https://github.com/epiforecasts/EpiNow2/pull/774/files#diff-6cd987920443d42098a4963d43b2e0efec9fd16f9198d66705e6d95094e3b87aR185-R194.

[sbfnk]

Thanks, this looks good.
It's adding a fair amount of infrastructure (an additional function + return value in obs_opts() that needs to be removed) just to be able to show that message. Shall we give it an expiry (and use keyword "deprecated" somewhere)?

Was this what you meant? https://github.com/epiforecasts/EpiNow2/pull/774/files#diff-6cd987920443d42098a4963d43b2e0efec9fd16f9198d66705e6d95094e3b87aR185-R194.

Yes, I think this will do.