Add R packages overview to survival analysis chapter by Copilot · Pull Request #349 · d-morrison/rme

Copilot · 2026-01-27T21:21:56Z

Original prompt

This section details on the original issue you should resolve

<issue_title>add an overview of R packages for survival analysis</issue_title>
<issue_description>- https://cran.r-project.org/web/packages/survival/index.html

http://danieldsjoberg.com/ggsurvfit/

https://cran.r-project.org/web/packages/ggfortify/index.html

any others you can find on CRAN or github</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes add an overview of R packages for survival analysis #348

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

… capitalization, use HTTPS Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

_sec-surv-r-packages-overview.qmd

Copilot

Pull request overview

This pull request adds comprehensive documentation of the R survival analysis ecosystem to help readers navigate available tools in the survival analysis chapter.

Changes:

Adds new section documenting core, visualization, and specialized modeling packages for survival analysis
Provides package selection guidance organized by use case
Updates WORDLIST with relevant technical terms

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
`_sec-surv-r-packages-overview.qmd`	New comprehensive overview of R packages for survival analysis, including core packages, visualization tools, and specialized modeling packages with usage guidance
`intro-to-survival-analysis.qmd`	Integrates the new packages overview section after the "Using the `survival` package in R" section
`inst/WORDLIST`	Adds technical terms used in the new content (package names, author names, and survival analysis terminology)

Copilot · 2026-01-28T01:36:04Z

_sec-surv-r-packages-overview.qmd

+- Produces publication-ready legends without showing raw variable names
+- All plot elements are native ggplot2 layers,
+making customization straightforward
+- Available on [CRAN](https://cran.r-project.org/package=ggsurvfit) and [GitHub](https://github.com/pharmaverse/ggsurvfit)


The CRAN link for ggsurvfit uses a different URL pattern than the other CRAN package links in this file. The survival, survminer, and ggfortify packages all use the pattern https://cran.r-project.org/web/packages/PACKAGE/index.html, but ggsurvfit uses https://cran.r-project.org/package=ggsurvfit. While both URL formats are valid CRAN URLs, using a consistent format throughout the document would improve maintainability. Consider changing this to https://cran.r-project.org/web/packages/ggsurvfit/index.html to match the other CRAN package links.

Suggested change

- Available on [CRAN](https://cran.r-project.org/package=ggsurvfit) and [GitHub](https://github.com/pharmaverse/ggsurvfit)

- Available on [CRAN](https://cran.r-project.org/web/packages/ggsurvfit/index.html) and [GitHub](https://github.com/pharmaverse/ggsurvfit)

Fixed in commit 2e5831b. Changed to use the consistent CRAN URL pattern matching other packages in the document.

Copilot · 2026-01-28T01:36:04Z

_sec-surv-r-packages-overview.qmd

+- **`flexsurv`**: Flexible parametric survival models with a wide range of distributions
+- **`rms`** (Regression Modeling Strategies): 
+Advanced regression modeling including survival models with tools for model validation and calibration
+- **`cmprsk`**: Competing risks regression using the Fine-Gray model
+- **`mstate`**: Multi-state survival models for complex event histories
+- **`timereg`**: Flexible regression models for survival data,
+including additive hazards models
+- **`frailtypack`**: Frailty models for clustered or recurrent event data
+- **`riskRegression`**: Risk prediction models and performance evaluation
+- **`pec`**: Prediction error curves for survival model validation
+- **`prodlim`**: Fast estimation of survival models including competing risks


The packages listed in the "Additional Modeling Packages" section lack hyperlinks to their documentation, which is inconsistent with the "Visualization Packages" section where all packages include links to their documentation. Adding CRAN links (and GitHub links where relevant) for these packages would make it easier for readers to find more information. For example, flexsurv, cmprsk, mstate, etc. should have links to their CRAN pages similar to how survival, ggsurvfit, survminer, and ggfortify are documented.

Suggested change

- **`flexsurv`**: Flexible parametric survival models with a wide range of distributions

- **`rms`** (Regression Modeling Strategies):

Advanced regression modeling including survival models with tools for model validation and calibration

- **`cmprsk`**: Competing risks regression using the Fine-Gray model

- **`mstate`**: Multi-state survival models for complex event histories

- **`timereg`**: Flexible regression models for survival data,

including additive hazards models

- **`frailtypack`**: Frailty models for clustered or recurrent event data

- **`riskRegression`**: Risk prediction models and performance evaluation

- **`pec`**: Prediction error curves for survival model validation

- **`prodlim`**: Fast estimation of survival models including competing risks

- **[`flexsurv`](https://cran.r-project.org/package=flexsurv)**: Flexible parametric survival models with a wide range of distributions

- **[`rms`](https://cran.r-project.org/package=rms)** (Regression Modeling Strategies):

Advanced regression modeling including survival models with tools for model validation and calibration

- **[`cmprsk`](https://cran.r-project.org/package=cmprsk)**: Competing risks regression using the Fine-Gray model

- **[`mstate`](https://cran.r-project.org/package=mstate)**: Multi-state survival models for complex event histories

- **[`timereg`](https://cran.r-project.org/package=timereg)**: Flexible regression models for survival data,

including additive hazards models

- **[`frailtypack`](https://cran.r-project.org/package=frailtypack)**: Frailty models for clustered or recurrent event data

- **[`riskRegression`](https://cran.r-project.org/package=riskRegression)**: Risk prediction models and performance evaluation

- **[`pec`](https://cran.r-project.org/package=pec)**: Prediction error curves for survival model validation

- **[`prodlim`](https://cran.r-project.org/package=prodlim)**: Fast estimation of survival models including competing risks

Fixed in commit 2e5831b. Added CRAN links to all packages in the Additional Modeling Packages section using the same URL pattern as the visualization packages.

github-actions · 2026-01-28T01:46:32Z

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d-morrison · 2026-01-30T02:51:21Z

intro-to-survival-analysis.qmd

@@ -47,6 +47,10 @@ The term *survival analysis* is a bit misleading. Survival outcomes can sometime

 {{< include _sec-surv-R.qmd >}}

+## R Packages for Survival Analysis
+
+{{< include _sec-surv-r-packages-overview.qmd >}}
+


should these two sections be combined?

Combined in commit 2e5831b. The packages overview is now integrated as a subsection of "Using the survival package in R" after the plotting examples, creating a more cohesive flow from basic usage to the broader ecosystem.

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

d-morrison

move the new content into a sub file

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-02-02T03:54:10Z

move the new content into a sub file

Done in commit bec50a0. Moved the R packages ecosystem content into _sec-surv-r-packages-ecosystem.qmd and included it in _sec-surv-R.qmd.

Initial plan

fc5de41

Copilot AI assigned Copilot and d-morrison Jan 27, 2026

Copilot started work on behalf of d-morrison January 27, 2026 21:22 View session

Copilot AI and others added 2 commits January 27, 2026 21:31

Add comprehensive overview of R packages for survival analysis

28e82e7

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Address code review feedback: add pec package description, fix GitHub…

3a90cbc

… capitalization, use HTTPS Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add overview of R packages for survival analysis~~ Add R packages overview to survival analysis chapter Jan 27, 2026

Copilot AI requested a review from d-morrison January 27, 2026 21:34

Copilot finished work on behalf of d-morrison January 27, 2026 21:34

Update author link for ggsurvfit package

fc478fb

d-morrison approved these changes Jan 28, 2026

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d-morrison marked this pull request as ready for review January 28, 2026 01:32

Copilot AI review requested due to automatic review settings January 28, 2026 01:32

Copilot started reviewing on behalf of d-morrison January 28, 2026 01:32 View session

Copilot AI reviewed Jan 28, 2026

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d-morrison requested changes Jan 30, 2026

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Copilot started work on behalf of d-morrison January 30, 2026 02:52 View session

Copilot AI and others added 2 commits January 30, 2026 02:55

Combine R packages sections and add hyperlinks to all packages

2e5831b

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Clarify ggfortify reference to plotting example

8ea826f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot AI requested a review from d-morrison January 30, 2026 02:58

Copilot finished work on behalf of d-morrison January 30, 2026 02:58

d-morrison requested changes Feb 2, 2026

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Copilot started work on behalf of d-morrison February 2, 2026 03:50 View session

Move R packages ecosystem content into separate subfile

bec50a0

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot finished work on behalf of d-morrison February 2, 2026 03:54

Copilot AI requested a review from d-morrison February 2, 2026 03:54

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Add R packages overview to survival analysis chapter#349

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Copilot AI commented Jan 27, 2026 •

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	- Available on [CRAN](https://cran.r-project.org/package=ggsurvfit) and [GitHub](https://github.com/pharmaverse/ggsurvfit)
	- Available on [CRAN](https://cran.r-project.org/web/packages/ggsurvfit/index.html) and [GitHub](https://github.com/pharmaverse/ggsurvfit)

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