Skip to content

Summarize competing-risks article in summary.qmd with proper citation wiring - #30

Open
d-morrison with Copilot wants to merge 5 commits into
mainfrom
copilot/summarize-article
Open

Summarize competing-risks article in summary.qmd with proper citation wiring#30
d-morrison with Copilot wants to merge 5 commits into
mainfrom
copilot/summarize-article

Conversation

Copilot AI commented Apr 23, 2026

Copy link
Copy Markdown
Contributor
  • Inspect PR comments and identify actionable review feedback
  • Check repository state and locate affected bibliography entry
  • Update references/references.bib to match style and fix DOI URL encoding issue
  • Run targeted validation for changed files
  • Run final automated validation
  • Reply to the new PR comment with the fixing commit hash

Copilot AI requested review from Copilot and removed request for Copilot April 23, 2026 04:24
Copilot AI linked an issue Apr 23, 2026 that may be closed by this pull request
Agent-Logs-Url: https://github.com/d-morrison/cie/sessions/db8367f0-5edb-434a-9c84-df3cdca34503

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI requested review from Copilot and removed request for Copilot April 23, 2026 04:26
Copilot AI changed the title [WIP] Add summary for CIE with competing events article Summarize competing-risks article in summary.qmd with proper citation wiring Apr 23, 2026
Copilot AI requested a review from d-morrison April 23, 2026 04:28
@d-morrison
d-morrison marked this pull request as ready for review April 23, 2026 04:36
Copilot AI review requested due to automatic review settings April 23, 2026 04:36

Copilot AI left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Pull request overview

This PR replaces placeholder content in the book’s summary.qmd chapter with a cited synopsis of Gooley et al. (1999) on cumulative incidence vs. 1−Kaplan–Meier under competing risks, and adds the corresponding BibTeX entry so the citations render.

Changes:

  • Rewrote summary.qmd to summarize the competing-risks estimator comparison and provide a practical takeaway, with inline citations.
  • Added a @gooley1999competing entry to references/references.bib and referenced it from the new summary text.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File Description
summary.qmd Replaces placeholder chapter content with a cited methodological summary and takeaway.
references/references.bib Adds the Gooley et al. (1999) bibliography entry used by the new summary citations.

Comment thread references/references.bib Outdated
number = {6},
pages = {695--706},
doi = {10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O},
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}

Copilot AI Apr 23, 2026

Copy link

Choose a reason for hiding this comment

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

The url field contains raw < and > characters, which makes the URL invalid and can break link rendering in HTML/PDF outputs. Consider percent-encoding these characters (e.g., %3C / %3E) or using an alternative canonical URL that does not include angle brackets.

Suggested change
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6%3C695::AID-SIM60%3E3.0.CO;2-O}

Copilot uses AI. Check for mistakes.
Comment thread references/references.bib Outdated
Comment on lines +177 to +185
author = {Gooley, Ted A. and Leisenring, Wendy and Crowley, John and Storer, Barry E.},
title = {Estimation of Failure Probabilities in the Presence of Competing Risks: New Representations of Old Estimators},
journal = {Statistics in Medicine},
year = {1999},
volume = {18},
number = {6},
pages = {695--706},
doi = {10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O},
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}

Copilot AI Apr 23, 2026

Copy link

Choose a reason for hiding this comment

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

This new BibTeX entry is the only one in the file that indents fields with extra leading spaces. For consistency with the rest of references.bib, consider aligning the formatting (remove the extra indentation before field names).

Suggested change
author = {Gooley, Ted A. and Leisenring, Wendy and Crowley, John and Storer, Barry E.},
title = {Estimation of Failure Probabilities in the Presence of Competing Risks: New Representations of Old Estimators},
journal = {Statistics in Medicine},
year = {1999},
volume = {18},
number = {6},
pages = {695--706},
doi = {10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O},
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}
author = {Gooley, Ted A. and Leisenring, Wendy and Crowley, John and Storer, Barry E.},
title = {Estimation of Failure Probabilities in the Presence of Competing Risks: New Representations of Old Estimators},
journal = {Statistics in Medicine},
year = {1999},
volume = {18},
number = {6},
pages = {695--706},
doi = {10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O},
url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}

Copilot uses AI. Check for mistakes.
@github-actions

github-actions Bot commented Apr 23, 2026

Copy link
Copy Markdown
PR Preview Action v1.8.1-2-g6ad689f

QR code for preview link

🚀 View preview at
https://d-morrison.github.io/cie/pr-preview/pr-30/

Built to branch gh-pages at 2026-05-04 06:58 UTC.
Preview will be ready when the GitHub Pages deployment is complete.

@d-morrison

Copy link
Copy Markdown
Owner

@copilot apply changes based on the comments in this thread

@d-morrison
d-morrison removed their request for review May 4, 2026 06:49
Copilot AI and others added 2 commits May 4, 2026 06:53
Agent-Logs-Url: https://github.com/d-morrison/cie/sessions/91e679ab-393e-412c-8b1e-fbcc7173635f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Agent-Logs-Url: https://github.com/d-morrison/cie/sessions/91e679ab-393e-412c-8b1e-fbcc7173635f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI requested review from Copilot and removed request for Copilot May 4, 2026 06:54
Agent-Logs-Url: https://github.com/d-morrison/cie/sessions/91e679ab-393e-412c-8b1e-fbcc7173635f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Copilot AI requested review from Copilot and removed request for Copilot May 4, 2026 06:55

Copilot AI commented May 4, 2026

Copy link
Copy Markdown
Contributor Author

@copilot apply changes based on the comments in this thread

Applied the requested thread changes in references/references.bib: normalized field indentation for @gooley1999competing and updated the DOI URL to use encoded angle brackets. Included in commit 6ccf10c.

Copilot AI requested a review from d-morrison May 4, 2026 06:56
@d-morrison
d-morrison removed their request for review May 4, 2026 08:13
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.

summarize this article

3 participants