implement `survfit2_hr` and optimize `survfit2_p`

Yunuuuu commented 6 months ago

What changes are proposed in this pull request? add function survfit2_hr to calculate Hazard ratio

Reviewer Checklist (if item does not apply, mark as complete)

[x] Ensure all package dependencies are installed by running renv::install()
[x] PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
[x] If a new function was added, function included in _pkgdown.yml
[x] If a bug was fixed, a unit test was added for the bug check
[x] Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
[x] Overall code coverage remains >99.5%. Review coverage with withr::with_envvar(list(CI = TRUE), code = devtools::test_coverage()). Begin in a fresh R session without any packages loaded.
[x] R CMD Check runs without errors, warnings, and notes
[x] usethis::use_spell_check() runs with no spelling errors in documentation

When the branch is ready to be merged into master:

[ ] Update NEWS.md with the changes from this pull request under the heading "# ggsurvfit (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
[ ] Increment the version number using usethis::use_version(which = "dev")
[ ] Run usethis::use_spell_check() again
[ ] Approve Pull Request
[ ] Merge the PR. Please use "Squash and merge".

Yunuuuu commented 6 months ago

It would be beneficial if the function survfit2_p could directly provide the p-value. Additionally, format can accept purrr-style formula now.

Yunuuuu commented 6 months ago

This also deals with the issue of partial argument matching for some functions like scale_y_continous (labels) and add_quantile (y_value).

ddsjoberg commented 6 months ago

@Yunuuuu thank you for the pull request.

the typical lifecycle here would be to file an issue where the implementation is discussed. after an API/implementation has been agreed upon, then we'd discuss who would make the update.

I took a quick look, and I see there is an issue when there are 3+ groups. The function returns a single p-value when most users would expect multiple HRs.

I think a better first step than a new function would be a simple example adding a table of Cox results as an annotation.

Perhaps create an issue and let's discuss further in the new year?

pharmaverse / ggsurvfit

implement `survfit2_hr` and optimize `survfit2_p` #187