Skip to content
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

Closes #2142 Supersede get_summary_records() and enhance derive_summary_records() #2158

Merged
merged 43 commits into from
Nov 9, 2023

Conversation

zdz2101
Copy link
Collaborator

@zdz2101 zdz2101 commented Oct 6, 2023

Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the devel branch until you have checked off each task.

  • Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
  • Code is formatted according to the tidyverse style guide. Run styler::style_file() to style R and Rmd files
  • Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See Unit Test Guide
  • If you removed/replaced any function and/or function parameters, did you fully follow the deprecation guidance?
  • Update to all relevant roxygen headers and examples, including keywords and families. Refer to the categorization of functions to tag appropriate keyword/family.
  • Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
  • Address any updates needed for vignettes and/or templates
  • Update NEWS.md under the header # admiral (development version) if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
  • Build admiral site pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
  • Address or fix all lintr warnings and errors - lintr::lint_package()
  • Run R CMD check locally and address all errors and warnings - devtools::check()
  • Link the issue in the Development Section on the right hand side.
  • Address all merge conflicts and resolve appropriately
  • Pat yourself on the back for a job well done! Much love to your accomplishment!

@zdz2101 zdz2101 changed the title feat: #2142 intiial superseding step Closes #2142 Supersede get_summary_records() and enhance derive_summary_records() Oct 6, 2023
@github-actions
Copy link

github-actions bot commented Oct 6, 2023

Code Coverage

Package Line Rate Health
admiral 98%
Summary 98% (4587 / 4673)

@zdz2101 zdz2101 marked this pull request as ready for review October 26, 2023 22:05
@zdz2101 zdz2101 requested a review from ddsjoberg October 27, 2023 17:49
DESCRIPTION Outdated
@@ -38,6 +38,7 @@ LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: R (>= 4.0)
Remotes: pharmaverse/admiraldev
Copy link
Collaborator Author

Choose a reason for hiding this comment

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

@ddsjoberg is this all I would have to do? or does I need to remove the imports line too?

Copy link
Collaborator

Choose a reason for hiding this comment

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

You'll want to make one small change to include the min version number required.

Remotes: pharmaverse/admiraldev (>= 0.5.0.9000)

Then if anyone does any dev work, like redocumenting, and they don't have this version installed, they'll get a note that they need to install the updated version.

NEWS.md Outdated
@@ -12,6 +12,8 @@
were enhanced such that more than one summary variable can be derived, e.g.,
`AVAL` as the sum and `ADT` as the maximum of the contributing records. (#1792)

- `derive_summary_records()` was enhanced with the following optional arguments: `dataset_add`, `dataset_ref`, `missing_values`. These arguments respectively, generate summary variables from additional datasets, retain/add specific records that and impute user-defined missing values. (#2142)
Copy link
Collaborator

Choose a reason for hiding this comment

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

is the that supposed to have something after it?

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

fixed

Comment on lines 8 to 9
#' switching to using the `dataset_add` argument in `derive_summary_records()`,
#' which is easier to use, has more features, and still under active development.
Copy link
Collaborator

Choose a reason for hiding this comment

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

I don't think we should say easier to use and under active development.

I think this is fine:

#' Development on get_summary_records() is complete, and for new code we recommend
#' switching to using the dataset_add argument in derive_summary_records().

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

fixed

R/derive_summary_records.R Outdated Show resolved Hide resolved
R/derive_summary_records.R Outdated Show resolved Hide resolved
R/derive_param_exposure.R Outdated Show resolved Hide resolved
R/derive_param_exposure.R Outdated Show resolved Hide resolved
inst/templates/ad_adex.R Outdated Show resolved Hide resolved
R/derive_summary_records.R Outdated Show resolved Hide resolved
@zdz2101
Copy link
Collaborator Author

zdz2101 commented Nov 6, 2023

@bundfussr all feedback should be addressed now, please take a look specifically at test 6 for derive_summary_records() here to visually see my interpretation of your missing_values commentary

R/derive_summary_records.R Outdated Show resolved Hide resolved
R/derive_summary_records.R Outdated Show resolved Hide resolved
R/derive_param_exposure.R Show resolved Hide resolved
R/derive_summary_records.R Outdated Show resolved Hide resolved
NEWS.md Show resolved Hide resolved
R/derive_summary_records.R Outdated Show resolved Hide resolved
R/derive_param_exposure.R Outdated Show resolved Hide resolved
@zdz2101 zdz2101 requested review from bundfussr and bms63 November 7, 2023 19:02
R/derive_param_exposure.R Outdated Show resolved Hide resolved
R/derive_param_exposure.R Outdated Show resolved Hide resolved
@zdz2101 zdz2101 merged commit 205e0d1 into main Nov 9, 2023
16 of 17 checks passed
@zdz2101 zdz2101 deleted the 2142_derive_summary_records_get_summary_records_mods branch November 9, 2023 14:14
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.

Feature Request: Enhance derive_summary_records() and supersede get_summary_records()
5 participants