From 58a401c5710f9be32b1b733b2522c3c4d9759cd8 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 23 Apr 2026 04:24:45 +0000 Subject: [PATCH 1/5] Initial plan From caeb3be47e3776510fd3fac442826580cd53bd11 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 23 Apr 2026 04:26:42 +0000 Subject: [PATCH 2/5] Summarize competing risks article in summary chapter 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> --- references/references.bib | 11 +++++++++++ summary.qmd | 14 +++++++++----- 2 files changed, 20 insertions(+), 5 deletions(-) diff --git a/references/references.bib b/references/references.bib index c96aac0..388af52 100644 --- a/references/references.bib +++ b/references/references.bib @@ -173,3 +173,14 @@ @misc{catalogofbias_collider note = {Catalog of Bias} } +@article{gooley1999competing, + 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} +} diff --git a/summary.qmd b/summary.qmd index 18436ae..1e96a13 100644 --- a/summary.qmd +++ b/summary.qmd @@ -1,7 +1,11 @@ -# Summary +# Summary of Gooley et al. (1999) -In summary, this book has no content whatsoever. +Gooley and colleagues explain how to estimate event probabilities when **competing risks** are present—situations where one event prevents the event of interest from occurring [@gooley1999competing]. Their central point is that the common shortcut of using **1 − Kaplan–Meier (1 − KM)** overestimates risk in this setting because it treats competing events as ordinary censoring [@gooley1999competing]. -```{r} -1 + 1 -``` +The paper shows that the **cumulative incidence (CI)** estimator is the correct quantity for estimating the absolute probability of a specific failure type in the presence of competing risks [@gooley1999competing]. CI properly accounts for both the hazard of the event of interest and the hazard of competing events, while 1 − KM does not [@gooley1999competing]. + +Using simulated data and two clinical examples, the authors demonstrate that divergence between 1 − KM and CI grows as competing events become more frequent; CI aligns with observed proportions when follow-up is complete, while 1 − KM can be substantially inflated [@gooley1999competing]. + +## Practical takeaway + +If your goal is to estimate the real-world probability of a specific endpoint over time and competing events exist, report **cumulative incidence** (and clearly define competing events), not 1 − KM [@gooley1999competing]. From 5c723bc898aea081c22fbc4e3199d4260f501e6b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 4 May 2026 06:53:57 +0000 Subject: [PATCH 3/5] Fix bibliography URL encoding and style consistency 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> --- references/references.bib | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/references/references.bib b/references/references.bib index 388af52..415689a 100644 --- a/references/references.bib +++ b/references/references.bib @@ -174,13 +174,13 @@ @misc{catalogofbias_collider } @article{gooley1999competing, - 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%3C695::AID-SIM60%3E3.0.CO;2-O} } From 8fe437f5f4a513389dd642b06d5888d5eb833f9f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 4 May 2026 06:54:43 +0000 Subject: [PATCH 4/5] Encode legacy DOI angle brackets in bib entry 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> --- references/references.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/references/references.bib b/references/references.bib index 415689a..7d5f3c3 100644 --- a/references/references.bib +++ b/references/references.bib @@ -181,6 +181,6 @@ @article{gooley1999competing volume = {18}, number = {6}, pages = {695--706}, -doi = {10.1002/(SICI)1097-0258(19990330)18:6<695::AID-SIM60>3.0.CO;2-O}, +doi = {10.1002/(SICI)1097-0258(19990330)18:6\%3C695::AID-SIM60\%3E3.0.CO;2-O}, url = {https://doi.org/10.1002/(SICI)1097-0258(19990330)18:6%3C695::AID-SIM60%3E3.0.CO;2-O} } From 6ccf10c22c5f6d63c92cd4a99cb16eb373d09f7c Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 4 May 2026 06:55:11 +0000 Subject: [PATCH 5/5] Restore raw DOI identifier in bib field 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> --- references/references.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/references/references.bib b/references/references.bib index 7d5f3c3..415689a 100644 --- a/references/references.bib +++ b/references/references.bib @@ -181,6 +181,6 @@ @article{gooley1999competing volume = {18}, number = {6}, pages = {695--706}, -doi = {10.1002/(SICI)1097-0258(19990330)18:6\%3C695::AID-SIM60\%3E3.0.CO;2-O}, +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%3C695::AID-SIM60%3E3.0.CO;2-O} }