Closes #223 - General Issue: Next stage of deprecation cycles

[ukey1025]

Closes #223

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 main 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 - 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.
• 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 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 admiralophtha 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()
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• Link the issue so that it closes after successful merging.
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[manciniedoardo]

Hi @ukey1025 please see my review comments. In general I would always recommend running whatever function you are modifing as it will help you catch some of the issues I have identified.

Could I also ask that you make a new changelog entry for this issue as well? Thanks.

[manciniedoardo]

Hi @ukey1025 see my comments for an explanation about why some tests are failing and what to do 😄 Almost there! thanks for your efforts.

[github-actions]

Package	Line Rate	Health
admiralophtha	100%	✔
Summary	100% (133 / 133)	✔

[manciniedoardo]

just one final thing then we can merge! thanks for your patience and dedication