Closes #168 University post #213

syon45 · 2024-09-03T12:24:11Z

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, propose a new tag to the maintainers! Note: if you use a tag not from this list, the "Check Post Tags" CICD pipeline will error. 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
Add a disclaimer at the top of your post, if appropriate (example: Disclaimer
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.
Pat yourself on the back for a job well done! Much love to your accomplishment!

manciniedoardo · 2024-09-03T12:42:19Z

Thanks @syon45 - as discussed in person, please try resolve the failing CICD checks while I review your post 😄

manciniedoardo

Thanks @syon45 please take a look at my comments 😄

posts/2024-09-03_university_undergraduate_report/university_undergraduate_report.Rmd

…dergraduate_report.Rmd Co-authored-by: Edoardo Mancini <[email protected]>

StefanThoma

I see there is a qmd and an Rmd file with otherwise the same name and content.
Which do you want to use?

(In the end it should be a qmd file I think)

Otherwise I added some minor changes requested.

Cool post :)

posts/2024-09-03_university_undergraduate_report/university_undergraduate_report.Rmd

StefanThoma · 2024-09-11T09:39:38Z

posts/2024-09-03_university_undergraduate_report/university_undergraduate_report.Rmd

+
+The quantitative project report investigates statistical analyses on preliminary clinical trial data using the R Studio software as instructed by the trainStats program I have authored to help ease new Biostatisticians in the industry. The software was built considering the needs of people who are keen to pursue a career in Biostatistics, and was inspired from some exploratory analyses I had done during my placement year with the Ophthalmology Precision Medicine (OPM) group. It entails both hard abilities such as programming, data visualisation and modelling alongside soft skills like logic, reasoning and communication.
+
+I had a smooth experience with pharmaverse all throughout my business and university project. I was introduced to the package by Ross Farrugia while looking for open-source data to analyse for my project. The package was very easy to read and use, with excellent documentation on the pharamverseadam website. As I was planning to share aggregated outputs (such as tables, listings and graphs) from clinical datasets externally to the university, even using historical clinical data was not allowed since external use of confidential data did not align with Roche's FAIR Data principles.


Pharmaverse is a collection of packages, not just one package. Or do you mean a specific package?

I think it is not due to the FAIR data principles that sharing data outside of Roche is problematic, but rather an issue with data privacy.

StefanThoma · 2024-09-11T09:41:47Z

posts/2024-09-03_university_undergraduate_report/university_undergraduate_report.Rmd

+
+I had a smooth experience with pharmaverse all throughout my business and university project. I was introduced to the package by Ross Farrugia while looking for open-source data to analyse for my project. The package was very easy to read and use, with excellent documentation on the pharamverseadam website. As I was planning to share aggregated outputs (such as tables, listings and graphs) from clinical datasets externally to the university, even using historical clinical data was not allowed since external use of confidential data did not align with Roche's FAIR Data principles.
+
+Throughout the trainStats documentation, I have primarily used the `adoe_ophtha` dataset to allow for a variety of exploratory statistical analyses ranging from producing boxplots of the spread of data by visit day, computing standard deviation and confidence intervals for endpoints, as well as programming linear regression models and patient profiles. As the "adoe_ophtha" ADaM dataset contains visit day, active arm and endpoint data, it was ideal to use for training purposes. In addition, I did use the "adsl" dataset too, to encourage trainStats users to join and merge datasets, taking into account patient demographics such as Age. 


Can you link the trainStats? Is this publicly available?

Not yet! It is not publicly available as of now unfortunately

posts/2024-09-03_university_undergraduate_report/university_undergraduate_report.Rmd

…dergraduate_report.Rmd Co-authored-by: StefanThoma <[email protected]>

StefanThoma

LGTM!

syon45 and others added 3 commits September 3, 2024 12:12

#168 draft post added

45b005a

#168 changed to qmd and added dummy category, image

f38eafa

#168 category change

a75d70a

syon45 requested a review from manciniedoardo September 3, 2024 12:24

syon45 added 2 commits September 3, 2024 13:19

changes for review

804337b

ready for review

ed4abf5

manciniedoardo requested changes Sep 3, 2024

View reviewed changes

syon45 and others added 7 commits September 10, 2024 10:27

Update posts/2024-09-03_university_undergraduate_report/university_un…

e32a969

…dergraduate_report.Rmd Co-authored-by: Edoardo Mancini <[email protected]>

Update posts/2024-09-03_university_undergraduate_report/university_un…

1660bf9

…dergraduate_report.Rmd Co-authored-by: Edoardo Mancini <[email protected]>

Update posts/2024-09-03_university_undergraduate_report/university_un…

5caca42

…dergraduate_report.Rmd Co-authored-by: Edoardo Mancini <[email protected]>

final changes from syon

331b141

#168 formatting/link updates

f02b1db

#168 further formatting updates

e44cb9b

Merge branch 'main' into 168universitypost

e63b50d

manciniedoardo requested review from manciniedoardo and StefanThoma September 11, 2024 08:02

manciniedoardo approved these changes Sep 11, 2024

View reviewed changes

manciniedoardo added 2 commits September 11, 2024 08:06

#168 spelling and styler updates

ac0eccd

#168 another styler fix

d9069b8

StefanThoma requested changes Sep 11, 2024

View reviewed changes

syon45 and others added 6 commits September 13, 2024 16:48

Update posts/2024-09-03_university_undergraduate_report/university_un…

836339b

…dergraduate_report.Rmd Co-authored-by: StefanThoma <[email protected]>

Update posts/2024-09-03_university_undergraduate_report/university_un…

fb93268

…dergraduate_report.Rmd Co-authored-by: StefanThoma <[email protected]>

final changes, ready to post

227d886

all done, updated date

7309c30

Merge branch 'main' into 168universitypost

63c9b88

#168 update prior to posting

f807e54

StefanThoma approved these changes Sep 16, 2024

View reviewed changes

manciniedoardo merged commit 1f07278 into main Sep 16, 2024
5 checks passed

manciniedoardo deleted the 168universitypost branch September 16, 2024 14:35

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Closes #168 University post #213

Closes #168 University post #213

syon45 commented Sep 3, 2024 •

edited by manciniedoardo

Loading

manciniedoardo commented Sep 3, 2024

manciniedoardo left a comment

StefanThoma left a comment

StefanThoma Sep 11, 2024

StefanThoma Sep 11, 2024

syon45 Sep 13, 2024

StefanThoma left a comment


		The quantitative project report investigates statistical analyses on preliminary clinical trial data using the R Studio software as instructed by the trainStats program I have authored to help ease new Biostatisticians in the industry. The software was built considering the needs of people who are keen to pursue a career in Biostatistics, and was inspired from some exploratory analyses I had done during my placement year with the Ophthalmology Precision Medicine (OPM) group. It entails both hard abilities such as programming, data visualisation and modelling alongside soft skills like logic, reasoning and communication.

		I had a smooth experience with pharmaverse all throughout my business and university project. I was introduced to the package by Ross Farrugia while looking for open-source data to analyse for my project. The package was very easy to read and use, with excellent documentation on the pharamverseadam website. As I was planning to share aggregated outputs (such as tables, listings and graphs) from clinical datasets externally to the university, even using historical clinical data was not allowed since external use of confidential data did not align with Roche's FAIR Data principles.


		I had a smooth experience with pharmaverse all throughout my business and university project. I was introduced to the package by Ross Farrugia while looking for open-source data to analyse for my project. The package was very easy to read and use, with excellent documentation on the pharamverseadam website. As I was planning to share aggregated outputs (such as tables, listings and graphs) from clinical datasets externally to the university, even using historical clinical data was not allowed since external use of confidential data did not align with Roche's FAIR Data principles.

		Throughout the trainStats documentation, I have primarily used the `adoe_ophtha` dataset to allow for a variety of exploratory statistical analyses ranging from producing boxplots of the spread of data by visit day, computing standard deviation and confidence intervals for endpoints, as well as programming linear regression models and patient profiles. As the "adoe_ophtha" ADaM dataset contains visit day, active arm and endpoint data, it was ideal to use for training purposes. In addition, I did use the "adsl" dataset too, to encourage trainStats users to join and merge datasets, taking into account patient demographics such as Age.

Closes #168 University post #213

Closes #168 University post #213

Conversation

syon45 commented Sep 3, 2024 • edited by manciniedoardo Loading

manciniedoardo commented Sep 3, 2024

manciniedoardo left a comment

Choose a reason for hiding this comment

StefanThoma left a comment

Choose a reason for hiding this comment

StefanThoma Sep 11, 2024

Choose a reason for hiding this comment

StefanThoma Sep 11, 2024

Choose a reason for hiding this comment

syon45 Sep 13, 2024

Choose a reason for hiding this comment

StefanThoma left a comment

Choose a reason for hiding this comment

syon45 commented Sep 3, 2024 •

edited by manciniedoardo

Loading