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Closes #111 dataset contents ref pages #130

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vbshuliar
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@vbshuliar vbshuliar commented Nov 8, 2024 •
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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 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!

@vbshuliar vbshuliar added the documentation Improvements or additions to documentation label Nov 8, 2024
@vbshuliar vbshuliar self-assigned this Nov 8, 2024
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github-actions bot commented Nov 8, 2024 •
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Code Coverage

Package Line Rate Health
pharmaversesdtm 0% ❌
Summary 0% (0 / 41) ❌

@vbshuliar vbshuliar linked an issue Nov 8, 2024 that may be closed by this pull request
Show dataset contents in reference pages #111
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bundfussr
bundfussr requested changes Nov 15, 2024
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  • A comment should be added to the R/*.R that these are generated and shouldn't be edited manually.
  • README.md should be updated to describe the new documentation process.

@manciniedoardo
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  • A comment should be added to the R/*.R that these are generated and shouldn't be edited manually.
  • README.md should be updated to describe the new documentation process.

@vbshuliar once you update README.md could you also do the same in pharmaverseadam as we are now following the same process across both packages? thanks

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@manciniedoardo @bundfussr Please take a look at the updated version.

manciniedoardo
manciniedoardo requested changes Dec 2, 2024
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Thanks @vbshuliar - I tested the actual process and looks great. I've added a couple of comments.

In addition to the above I also tried rendering the site. Looks good, but can you please restructure the reference page so that it mentions datasets and not functions:

image

Edit: get_terms() should still be under functions.

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I updated the layout as you requested. Please, proceed with the rereview @manciniedoardo

image
image

bundfussr
bundfussr requested changes Dec 3, 2024
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Could you update such that the labels are displayed on the reference page? For example:
image

inst/extdata/sdtms-specs.xlsx
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Could we use a JSON file?

Then it is possible to see changes in github.

data-raw/create_sdtms_data.R
@@ -0,0 +1,134 @@
# Load the XLSX file with metadata
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Could you add a header describing the purpose of the script?

data-raw/create_sdtms_data.R

# Create documentation for the current dataset
doc_string <- paste(
sprintf("# This file is automatically generated."),
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Could we add more information? For example:

Suggested change
sprintf("# This file is automatically generated."),
sprintf("# This file is automatically generated by data-raw/create_sdtms_data.R."),
sprintf("# For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R."),

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@bundfussr bundfussr bundfussr requested changes

@manciniedoardo manciniedoardo Awaiting requested review from manciniedoardo

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Show dataset contents in reference pages
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@vbshuliar @manciniedoardo @bundfussr