Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Better truncation handling #44

Merged
merged 22 commits into from
Sep 6, 2024
Merged

Better truncation handling #44

merged 22 commits into from
Sep 6, 2024

Conversation

seabbs
Copy link
Contributor

@seabbs seabbs commented Sep 6, 2024

Description

This PR partly addresses #34 and some concerns in #37 about the handling of truncation. It moves to using normalisation outside the integral everywhere rather than just in the vectorised code. As @SamuelBrand1 pointed out this is more correct.

It also

  • adds a variety of speed-ups to the R code to make estimation more efficient
  • Improves and adds tests that compare sampling with numerical methods
  • Improves coverage of pprimarycensoreddist
  • Updates all documentation
  • Recharaterises the Stan integral as being from delay - window to delay rather than 0 to window. Testing found this to be more stable

I investigated using xc and found this made the integral fail to solve at any tolerance level.

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.

@seabbs seabbs marked this pull request as ready for review September 6, 2024 19:19

This comment was marked as outdated.

Copy link
Contributor Author

@seabbs seabbs left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@seabbs seabbs merged commit e648b4f into main Sep 6, 2024
12 checks passed
@seabbs seabbs deleted the explore-int-as-delay branch September 6, 2024 20:21
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant