Skip to content

Closes #49 add formulas/document the methods of CI interval calculation in LaTeX #63

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 11 commits into from
Mar 8, 2024

Conversation

zdz2101
Copy link
Contributor

@zdz2101 zdz2101 commented Feb 28, 2024

What changes are proposed in this pull request?

  • Style this entry in a way that can be copied directly into NEWS.md. (#, @)

Provide more detail here as needed.
write latex formulas of all the prop ci calculations


Pre-review Checklist (if item does not apply, mark is as complete)

  • All GitHub Action workflows pass with a ✅
  • PR branch has pulled the most recent updates from master branch: usethis::pr_merge_main()
  • If a bug was fixed, a unit test was added.
  • Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): devtools::test_coverage()
  • Request a reviewer

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

  • If a bug was fixed, a unit test was added.
  • Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
  • Code coverage is suitable for any new functions/features: devtools::test_coverage()

When the branch is ready to be merged:

  • Update NEWS.md with the changes from this pull request under the heading "# cards (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).
  • All GitHub Action workflows pass with a ✅
  • Approve Pull Request
  • Merge the PR. Please use "Squash and merge" or "Rebase and merge".

@zdz2101 zdz2101 linked an issue Feb 28, 2024 that may be closed by this pull request
@zdz2101
Copy link
Contributor Author

zdz2101 commented Feb 28, 2024

image

for easier review/look, not quite sure what you had in mind entirely of how to document this but this is probably at least a good start?

Also not quite sure how to handle the errors related to rendering the webiste down below

@codecov-commenter
Copy link

codecov-commenter commented Feb 28, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.49%. Comparing base (c849ad4) to head (d3cb4ec).
Report is 1 commits behind head on main.

❗ Current head d3cb4ec differs from pull request most recent head dc9277d. Consider uploading reports for the commit dc9277d to get more accurate results

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #63   +/-   ##
=======================================
  Coverage   99.49%   99.49%           
=======================================
  Files          16       16           
  Lines         789      789           
=======================================
  Hits          785      785           
  Misses          4        4           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@ddsjoberg
Copy link
Collaborator

@zdz2101 this is beautiful!! ❤️

what do you think of adding this as a section to the function help file instead of a standalone article? we could add it to the proportion_ci.R file like this

#' @section Method Details:
#'
#' ### Wald
#' 
#' $$      
#' \hat{p} \pm z_{\alpha/2} \sqrt{\frac{\hat{p}(1 - \hat{p})}{n}}
#' $$

Here's an example of Latex in a roxygen2 help file https://github.com/MSKCC-Epi-Bio/tidycmprsk/blob/543851ce4b3eeb82c037188f01e8c901a6448344/R/cuminc.R#L12

@zdz2101 zdz2101 marked this pull request as ready for review March 5, 2024 18:04
@zdz2101 zdz2101 requested a review from ddsjoberg March 5, 2024 18:07
Copy link
Contributor

github-actions bot commented Mar 5, 2024

badge

Code Coverage Summary

Filename                    Stmts    Miss  Cover    Missing
------------------------  -------  ------  -------  ------------------------------------
R/ard_car_anova.R              41       2  95.12%   57, 60
R/ard_chisqtest.R              31       0  100.00%
R/ard_cohens_d.R               73       0  100.00%
R/ard_fishertest.R             33       0  100.00%
R/ard_hedges_g.R               60       0  100.00%
R/ard_kruskaltest.R            27       0  100.00%
R/ard_mcnemartest.R            41       0  100.00%
R/ard_moodtest.R               40       0  100.00%
R/ard_proportion_ci.R          40       5  87.50%   63-67
R/ard_proptest.R               71       0  100.00%
R/ard_regression_basic.R       14       1  92.86%   44
R/ard_regression.R             49       0  100.00%
R/ard_smd.R                    40       0  100.00%
R/ard_ttest.R                  78       0  100.00%
R/ard_wilcoxtest.R             83       0  100.00%
R/proportion_ci.R             188      28  85.11%   275, 278, 287-292, 300, 315, 415-438
TOTAL                         909      36  96.04%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: a956878

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

Copy link
Contributor

github-actions bot commented Mar 5, 2024

Unit Tests Summary

 1 files  26 suites   4s ⏱️
25 tests 20 ✅  5 💤 0 ❌
67 runs  51 ✅ 16 💤 0 ❌

Results for commit a956878.

♻️ This comment has been updated with latest results.

@ddsjoberg
Copy link
Collaborator

@zdz2101 this looks so so good!

My only request is if we can replace the old-school division sign with a large slash? If not, that is ok too. Thanks!

image

@zdz2101
Copy link
Contributor Author

zdz2101 commented Mar 8, 2024

@zdz2101 this looks so so good!

My only request is if we can replace the old-school division sign with a large slash? If not, that is ok too. Thanks!

image

done!

@zdz2101
Copy link
Contributor Author

zdz2101 commented Mar 8, 2024

@ddsjoberg not quite sure why one of the r-cmd-check (oldrel-1) is breaking now but I made the swap

edit: reran the failed job and now it works

Copy link
Collaborator

@ddsjoberg ddsjoberg left a comment

Choose a reason for hiding this comment

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

just lovely!!! ❤️ thank you!

@ddsjoberg ddsjoberg merged commit db79851 into main Mar 8, 2024
@ddsjoberg ddsjoberg deleted the 49-document-the-method-for-proportion-cis branch March 8, 2024 16:29
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.

Document the method for proportion CIs
3 participants