Merge pull request #37 from phuse-org/updates

Contribute updates and (-) update
phuse-org · Sep 26, 2024 · 8c49650 · 8c49650
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diff --git a/OSmodels.qmd b/OSmodels.qmd
@@ -10,17 +10,7 @@ title: "(-) OS Business Models"
 
 -   [Wikipedia page](https://en.wikipedia.org/wiki/Business_models_for_open-source_software){target="_blank"}
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [What open source models are available for businesses?](https://github.com/phuse-org/OSTCDA/discussions/16){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
-
-
diff --git a/_quarto.yml b/_quarto.yml
@@ -37,6 +37,7 @@ book:
     - legal.qmd
     - OSmodels.qmd
     - whatelse.qmd
+    - contribute.qmd
     - references.qmd
 
 bibliography: references.bib

diff --git a/art.qmd b/art.qmd
@@ -114,15 +114,7 @@ This list is not exhaustive by any means, but each tool gives additional informa
 
 The best solution is to combine a tool such as {logrx} with a well managed container environment deployment of R as described above. This proves that the container was unchanged from the original, tested and documented environment. And assuming that original container is held under Software Development Life Cycle change control, we can be confident of accuracy, reproducibility and traceability, and hence a "validated" environment.
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [How do you establish reproducibility and traceability with open source solutions?](https://github.com/phuse-org/OSTCDA/discussions/8){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/contribute.qmd b/contribute.qmd
@@ -0,0 +1,24 @@
+# Contribute {.unnumbered}
+
+## Join discussions
+
+Share your industry expertise and contribute to the collective knowledge by joining our [discussions](https://github.com/phuse-org/OSTCDA/discussions). These discussions are a valuable resource, providing citable and sometimes quotable input that will culminate in a "state of the union"-style manuscript. This manuscript aims to address questions that have been sufficiently explored and to focus on those that still need attention.
+
+We encourage you to visit the [Discussions section](https://github.com/phuse-org/OSTCDA/discussions) to share your thoughts, resources, or perspectives. If you identify a key question that has been overlooked, feel free to start a new discussion thread!
+
+## Provide Feedback, Questions, Suggestions 
+
+Your feedback is crucial to our progress. Please use the [Issues](https://github.com/phuse-org/OSTCDA/issues) area to share general feedback, ask questions, or make suggestions. You can also propose new paragraphs or information that you believe would be valuable for inclusion.
+
+## Pull Requests
+
+If you are familiar with git, we welcome you to contribute directly by submitting [Pull Requests](https://github.com/phuse-org/OSTCDA/pulls). Your contributions are highly appreciated and will help improve the manuscript.
+
+
+## Guidance
+
+-   Share your thoughts and perspectives to enrich the discussions.
+-   Provide references to relevant articles, webinars, and presentations (citations and links are encouraged).
+-   Maintain a respectful and constructive tone within the community.
+
+Your active participation is essential to the success of this project. Together, we can advance our understanding and address the remaining questions effectively.
diff --git a/cost.qmd b/cost.qmd
@@ -8,15 +8,7 @@ title: "(-) Cost of Open Source"
 
 -   What resources are required for proper implementation?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [What is the true cost of implementing open source solutions into clinical data analytic processes??](https://github.com/phuse-org/OSTCDA/discussions/4)
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/doc_trust.qmd b/doc_trust.qmd
@@ -77,15 +77,7 @@ These packages help a user perform and document risk assessments on R packages,
 
 PHUSE's [End-to-End Open-Source Collaboration Guidance](https://phuse-org.github.io/E2E-OS-Guidance/) references a [Case Studies Repository](https://github.com/pharmaR/case_studies), "which contains examples from Roche, Merck and Novartis on how they approach validation and risk mitigation." The main takeaway, according to James Black, is of "the 4 companies that shared their process for assessing R packages, each company currently takes a very different approach." Coline Zeballos presented on Roche's to package validation at the [R/Pharma conference](https://rinpharma.com/), both in [2021](https://www.youtube.com/watch?v=xksxuvXVimM) and [2022](https://www.youtube.com/watch?v=ZfZpypQ1jSM) (co-presenting with Doug Kelkhoff).
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [How do you document your trust in an open source solution to satisfy a third-party inquiry?](https://github.com/phuse-org/OSTCDA/discussions/5)
-
-All contributions should:
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/fundOS.qmd b/fundOS.qmd
@@ -12,15 +12,7 @@ title: "(-) Funding OS"
 
 -   Are there examples of this in other industries?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Is it possible for industry fund open source?](https://github.com/phuse-org/OSTCDA/discussions/13){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/legal.qmd b/legal.qmd
@@ -119,15 +119,7 @@ While the specifics of the act are still being finalized, it's clear that it wil
 
 For single-individual open-source projects, the impact might be less direct. However, it could still influence the way these projects are managed. For instance, the act might encourage individual developers to adopt more robust security practices, such as conducting regular vulnerability assessments and ensuring timely patching and updates.
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Are there any legal concerns or ramifications from open source development (on the user, developer, organization)?](https://github.com/phuse-org/OSTCDA/discussions/15){target="_blank"}
-
-All contributions should:
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/liability.qmd b/liability.qmd
@@ -56,15 +56,7 @@ Examples:
 
     >This software is provided by the copyright holders and contributors “as is” and any express or **implied warranties**, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose **are disclaimed**. In **no event shall the copyright holder or contributors be liable** for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Are contributors to open source exposing themselves to any liability of their solutions?](https://github.com/phuse-org/OSTCDA/discussions/14){target="_blank"}
-
-All contributions should:
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/longrun.qmd b/longrun.qmd
@@ -12,16 +12,7 @@ When these solutions are embedded in data pipelines, if development and maintena
 
 -   How do we ensure long term maintainability?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [How do we ensure that the solutions being developed today will exist in the long run?](https://github.com/phuse-org/OSTCDA/discussions/12){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
-
diff --git a/match.qmd b/match.qmd
@@ -1,5 +1,5 @@
 ---
-title: "(-) Numerical Matching"
+title: "Numerical Matching"
 ---
 
 ## What if open source languages and commercial software (such as SAS), do not match numerically with the analysis results they give?
@@ -124,21 +124,13 @@ Both of these issues can be resolved but adding options to the code to specify t
 
 SAP should be updated (for example) to say: Kaplan-Meier plots (with 95% CIs **calculated using the log-log method**) of Overall Survival will be presented by treatment group. Overall survival will be analyzed using a stratified log-rank test with hazard ratio and 95% CI from the cox-proportional hazards model **calculated using** **the efron method in the case of tied survival times**.
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Do we need to match SAS numerically when using a different language?](https://github.com/phuse-org/OSTCDA/discussions/11){target="_blank"}
 
 Contribute to the CAMIS repository [here](https://psiaims.github.io/CAMIS/contribution/contribution.html).
 
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
-
 ## References
 
 1.  https://www.sas.com/en_us/company-information/history.html

diff --git a/reg_accept.qmd b/reg_accept.qmd
@@ -40,19 +40,11 @@ Yet still some doubts persist. If a sponsor submits analytical results using Too
 
 And what about agencies who typically do not re-analyse sponsor data? How can the industry provide reassurance and proof that analytical environments are validated: accurate, reproducible and traceable? When installation of software into an environment is a one-step process, we can be pretty sure of consistency across analysts. But if there are multiple steps involved, and the software can change almost daily, then how do we ensure this consistency and reproducibility? This is not just the job of IT organisations within sponsor companies, but the responsibility of the individual analyst, to ensure that they are working compliant with organisational processes and in validated environments. Audit trails and traceability helps ensure this, but it is a potential source of doubt for both sponsor and regulatory authority.
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Will the **FDA** accept data and analyses generated with solutions developed and available as open source?](https://github.com/phuse-org/OSTCDA/discussions/6){target="_blank"}
 
-All contributions should:
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
-
 ## References
 
 Bell, B "Issues with Open Source Statistical Software in Industry: Validation, Legal Issues, and Regulatory Requirements" ASA JSM 2006.

diff --git a/summary.qmd b/summary.qmd
@@ -1,5 +1,5 @@
 ---
-title: "(-) What is Open Source?"
+title: "What is Open Source?"
 ---
 
 ## What is Open Source?
@@ -22,21 +22,8 @@ Data submitted for review by a health authority to approve a medicine, therapy,
 
 In this publication, we aim to explore the numerous questions that have been raised by practitioners of data analytics for clinical research. These questions are aimed at managing the perceived risk of leveraging tools built on open source software for analyzing clinical trial data to support market applications of medicines, therapies, and vaccines based on evidence of safety and efficacy. The answers to some of these questions are becoming well understood in the industry while other answers are less complete. Our objective is to comprehensively compile this knowledge for ease of reference by others.
 
-## How to Contribute
+## Discussion
 
 You may continue to contribute to this discussion here in GitHub Discussions:\
 [What is open source?](https://github.com/phuse-org/OSTCDA/discussions/1){target="_blank"}
 
--   Comment on content already developed
-
--   Add additional content or perspectives for consideration
-
--   Upvote content that is particularly valuable
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/trust.qmd b/trust.qmd
@@ -8,15 +8,7 @@ title: "(-) Establishing Trust"
 
 -   What are the relevant considerations?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [Can an open source solution be trusted to be accurate?](https://github.com/phuse-org/OSTCDA/discussions/3){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/user_dev.qmd b/user_dev.qmd
@@ -26,15 +26,7 @@ Many Data Scientists are:
 
 How will we transform the traditional Statistical Programmer into the future Data Scientist?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [How do you transform the traditional Statistical Programmer into the future Data Scientist?](https://github.com/phuse-org/OSTCDA/discussions/10-){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/users.qmd b/users.qmd
@@ -10,15 +10,7 @@ The conventional user (programmer) processing clinical trial data may be used to
 
 -   How can we help users to address unexpected challenges due to changes in their computational environment?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [How do we support users in managing an ever-evolving environment of Open Source solutions?](https://github.com/phuse-org/OSTCDA/discussions/9){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/whatelse.qmd b/whatelse.qmd
@@ -10,15 +10,7 @@ This is very open ended and initially intended as a catch-all for the future con
 
 -   What other questions are being asked and/or need to be addressed?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [What else can we do?](https://github.com/phuse-org/OSTCDA/discussions/17){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community
diff --git a/why.qmd b/why.qmd
@@ -10,15 +10,7 @@ title: "(-) Why Open Source?"
 
 -   Why are leaders of organizations in Data Management, Biostatistics, and Programming devoting resources toward the development, testing, and adoption of open source solutions?
 
-## How to Contribute
+## Discussion
 
 Contribute to the discussion here in GitHub Discussions:\
 [What is the 'why' for open source?](https://github.com/phuse-org/OSTCDA/discussions/2){target="_blank"}
-
-## Guidance
-
--   Provide your thoughts and perspectives
-
--   Provide references to articles, webinars, presentations (citations, links)
-
--   Be respectful in this community