Add RMST in R and RMST R vs. SAS comparison - #598
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DrLynTaylor
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Jul 13, 2026
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@yannickvandendijck please could you add package survRM2 to your version of the renv lock file so we can bring this PR in, thanks. |
This was referenced Aug 21, 2026
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abiterry
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Sep 24, 2026
CI has failed at "Set up renv" on every branch since ~24 July 2026, including pushes straight to main. The trigger was GitHub migrating ubuntu-latest to a new image: setup-renv keys its package cache on sessionInfo()$running, so the migration invalidated every cache at once. That exposed a latent problem. renv.lock pointed at packagemanager.posit.co/cran/latest, which only ever serves the *current* version of each package, and 154 of the 374 pinned versions were no longer current. With no binary available, renv fell back to compiling old source tarballs from the CRAN archive, which fails on the new runner. A warm cache had hidden this for months. Changes: - Pin the repository to a dated snapshot (cran/2026-08-14) and re-snapshot so every recorded version matches that date. Verified that all 365 repository-sourced records resolve on macOS arm64, Windows and Linux, and that all 170 compiled packages are served as prebuilt binaries for both noble and resolute. CI now compiles nothing. - Stop recording the 15 packages that ship with R (mgcv, Matrix, survival, lattice, ...). Their versions track the R build rather than CRAN, so no snapshot date can ever satisfy them; this is also what broke local installs on macOS. utils/quarto_check_pkg_dependencies.R already handles these having no hash. - Add survRM2 1.0-4 and its dependency muhaz, to unblock #598. - Drop survMisc: CRAN archived it on 17 March 2026, it is no longer a survminer dependency, and it is only mentioned in prose. km.ci, KMsurv, plyr, reshape2 and rgl go with it as transitive dependencies that current versions no longer need. - Pin runs-on to ubuntu-24.04 in both workflows so a future image migration cannot silently invalidate the caches again. Note: 138 package versions change, so the Quarto freeze cache will be largely invalidated and most pages will re-execute on the first run.
DrLynTaylor
approved these changes
Sep 30, 2026
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Request to add two new pages:
A page on Restricted Mean Survival Time (RMST) in R to act as the equivalent of the existing page for SAS. Both pages use the same data and methods.
A page comparing RMST outputs in R and SAS. Note that the page on RMST in SAS does not provide the output for one analysis (Method 2: Pseudo-value estimation), so R-SAS comparisons were not possible for that method.