Issue 188: Add delay samples functionality

[athowes]

Description

This draft PR will close #188.

Checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
• I have read the contribution guidelines.
• I have tested my changes locally.
• I have added or updated unit tests where necessary.
• I have updated the documentation if required.
• My code follows the established coding standards.
• I have added a news item linked to this PR.
• I have reviewed CI checks for this PR and addressed them as far as I am able.

[athowes]

To do before merge:

• Add issue about helping the user with newdata Help user pass newdata as sensible things (e.g. all strata) #213
• Add issue about adding functionality for full custom family implementation things Posterior prediction for lognormal #214
• Add issue about summary function built on top of this Create delay_summary function built on predict_delay_parameters #215
• Discuss choice of name (maybe different to delay_samples). Could use word draws, could mention extracting. Want to be similar to the summary function

[athowes]

I think this is ready for review. I have created follow up issues.

Other thing is that for some reason it's failing a Ubuntu R-CMD-check but in a way that seems not related to the code changes. Any pointers?

[seabbs]

The error is here:

Error ('test-unit-postprocess.R:5:3'): add_mean_sd.lognormal_samples works with posterior samples from the latent lognormal model ──
Error: Error: All list elements must have the same length.

You also have a few unrelated to this PR notes and warnings that we should flag and ideally fix

[seabbs]

This is looking good. Just naming to discuss I think

[athowes]

Added issue about fixing possible check notes #217

[athowes]

The error is here:

Error ('test-unit-postprocess.R:5:3'): add_mean_sd.lognormal_samples works with posterior samples from the latent lognormal model ──
Error: Error: All list elements must have the same length.

How did you see this? I can just see:

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-unit-postprocess.R:5:3'): add_mean_sd.lognormal_samples works with posterior samples from the latent lognormal model ──
Error in read_cmdstan_csv(files = self$output_files(include_failed = FALSE), variables = variables, sampler_diagnostics = sampler_diagnostics, format = format): Assertion on 'files' failed: File does not exist: '/tmp/RtmpVPgfDE/working_dir/Rtmpkb8cQq/model_ea52f49f447bb88d6fe4ace47415d149-202407312111-1-1098f0.csv'.

[athowes]

Should we have functionality for getting a "properly" discretised PMF in this package or somewhere else?

[seabbs]

How did you see this? I can just see:

I just looked through the log? What was the fix that made this go away?

[seabbs]

Should we have functionality for getting a "properly" discretised PMF in this package or somewhere else?

My vote is somewhere else so that i.e epinowcast can use it and then also use it here but we could dev something here and then port out. Note that epinowcast already has a simulate based approach to this but really the approach taken in EpiAware (numeric integration) is the way to go I think

[athowes]

How did you see this? I can just see:

I just looked through the log? What was the fix that made this go away?

I didn't do anything it just went away.

[seabbs]

This is great. I think there are a few errors in the handling of newdata. I know we are doing the new data stuff separately but I think we need a few minimal checks here to be sure it works as is and avoid broken code going to main

[athowes]

Good spot! Agree we should fix these newdata things.

[athowes]

I've added tests for this (and indeed they did bring up another code issue! Which is now fixed).

[seabbs]

Nice. Looks great.