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closes #143 Navitas R blog #150

Merged
merged 7 commits into from
May 2, 2024
Merged

closes #143 Navitas R blog #150

merged 7 commits into from
May 2, 2024

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rossfarrugia
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@rossfarrugia rossfarrugia commented Apr 15, 2024 •
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Thank you for your Pull Request! We have developed this task checklist to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your blog post.

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), and make sure the corresponding issue is linked in the Development section on the right hand side
  • Run the script from CICD.R line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style. Address any incongruences by following the instructions in the file!
  • Choose (possibly several) tag(s) or categories from the current list: c("Metadata", "SDTM", "ADaM", "TLG", "Shiny", "Community", "Conferences", "Submissions", "Technical") for your blog post. If you cannot find anything that fits your blog post, add your own tag! We occasionally tidy up all tags for consistency.
  • Add a short description for your blog post in the description field at the top of the markdown document.
  • Blog post is short, personalized, reproducible and readable
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    This blog contains opinions that are of the authors alone and do not necessarily reflect the strategy of their respective organizations.)
  • Address all merge conflicts and resolve appropriately
  • Assign two of us (@bms63, @manciniedoardo, @StefanThoma, @kaz462) as reviewers in the PR.
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@rossfarrugia rossfarrugia linked an issue Apr 15, 2024 that may be closed by this pull request
Blog Post: De-Mystifying R Programming in Clinical Trials #143
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@rossfarrugia rossfarrugia changed the title closes #143 draft blog closes #143 Navitas R blog Apr 15, 2024
@rossfarrugia
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@NavitasLifeSciences i made a draft PR with your blog converted to Quarto, and sent you write access so you can push updates to this blog.

Instead of me reviewing via the PR I just made updates directly to this draft blog for my comments as follows. Of course feel free to change anything back as you own this blog as author. Once you're happy we can tag others from the team to review this.

  • Added ® after any mention of SAS and removed mention of SAS “high cost” as such negative wording would not be suitable to place in a public blog in my opinion
  • Removed the dual programming section as don’t think it added any value for this blog to show that same table can be created in SAS or R
  • Added reference to pharmaverse as otherwise why post this blog on our site
  • I updated some of the wording such as R “usage is currently below par” as I don’t actually think it’s true – some of the blog reads more like a viewpoint from 2-3 years ago compared to the growing momentum we now see in R in our industry
  • Removed “The notable difference between SAS® and R is that SAS® is proprietary software, whereas R is an open-source programming language” as I feel readers would know this
  • Added reference to R consortium R submissions WG
  • I replaced the package examples given with pharmaverse examples as again this is a pharmaverse blog
  • Mentioned R Validation Hub rather than R Foundation for more specificity
  • Added a note on licensing
  • Learning curve of R removed “steep” and “lacks direct support from the company,” as those are not the case in many of the across-industry experiences I’ve seen
  • Added some images to help brighten the blog

@rossfarrugia
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Response from Navitas (Amrita Surendranath) by email: We are fine with the changes. Please go ahead with the next steps.

@bms63 @manciniedoardo want to take a look now? The spellcheck fails but I'm pretty sure I had added all those from this blog to wordlist so might be from other blogs, or I'm just missing something obvious...

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StefanThoma commented Apr 17, 2024 via email

@rossfarrugia
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There is a short script in the R folder that will add all remaining words to the spellcheck dictionary, for future reference :)

Odd as when I run the sections of CICD.R I get:
No spelling errors found.

So not sure why the check is failing,

@StefanThoma
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There is a short script in the R folder that will add all remaining words to the spellcheck dictionary, for future reference :)

Odd as when I run the sections of CICD.R I get: No spelling errors found.

So not sure why the check is failing,

There appears a strange error in our CICD workflow:
Run testthat::test_that(desc = "No Typo", code = testthat::expect_equal(object = spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE), ignore = readr::read_lines("inst/WORDLIST.txt")), expected = spelling::spell_check_files(path = "inst/WORDLIST.txt", ignore = readr::read_lines("inst/WORDLIST.txt")))) ── Failure (???): No Typo ────────────────────────────────────────────────────── spelling::spell_check_files(...) not equal to spelling::spell_check_files(path = "inst/WORDLIST.txt", ignore = readr::read_lines("inst/WORDLIST.txt")). Attributes: < Component “row.names”: Numeric: lengths (7, 0) differ > Component “word”: Lengths ([7](https://github.com/pharmaverse/blog/actions/runs/8692333877/job/23836728476#step:7:8), 0) differ (string compare on first 0) Component “found”: Length mismatch: comparison on first 0 components

@bms63 any ideas?

@bms63
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bms63 commented Apr 17, 2024

Not sure on this error. Maybe there is a new r-libs spell check we could use?

@manciniedoardo
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@NavitasLifeSciences thanks for your updates! Blog post is ready now 😄

@bms63 @StefanThoma I guess we can merge once we find out what's going on with the spellcheck, or we can live dangerously and merge anyway... What do you think?

@manciniedoardo manciniedoardo self-requested a review April 25, 2024 13:56
@NavitasLifeSciences
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NavitasLifeSciences commented Apr 25, 2024 via email

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bms63 commented Apr 25, 2024

If the Spelling is checked locally and is good, then lets just merge it.

@rossfarrugia rossfarrugia merged commit be8b2fb into main May 2, 2024
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@rossfarrugia rossfarrugia deleted the 143_navitas_R_blog branch May 2, 2024 08:20
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As per Ben and Edoardo's messages i'm merging this one to close it out

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@manciniedoardo manciniedoardo manciniedoardo approved these changes

@bms63 bms63 Awaiting requested review from bms63

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Blog Post: De-Mystifying R Programming in Clinical Trials
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@rossfarrugia @StefanThoma @bms63 @manciniedoardo @NavitasLifeSciences