cran-task-views / ctv

CRAN Task View Initiative
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CRAN task view proposal: Pharmaverse #60

Closed mstackhouse closed 1 month ago

mstackhouse commented 9 months ago

Scope

The packages included within the pharmaverse focus on a specific subset of clinical trial activities, specifically on the clinical reporting pipelines used within the pharmaceutical industry. These activities follow specific standards, such as CDISC Data Standards and ICH E3. The scope of pharmaverse packages ranges from CRF (Case Report Forms - or data collection for a clinical trial) through clinical trial analysis reporting, including formatting of data to match SDTM (Study Data Tabulation Model) and ADaM (Analysis Data Model) standards, and production of TLGs (Tables, Listings, and Graphs). Furthermore, pharmaverse packages help supporting the orchestration activities of clinical trial data analysis through regulatory requirements.

The scope of the pharmaverse is only a small subset of the larger range of clinical trial activities for with R can be applied. For more information on R packages for clinical trials, see r view("ClinicalTrials"). Pharmaverse also has more resources outside of CRAN, which you can read about on www.pharmaverse.org.

Packages

Study Data Tabulation Model (SDTM)

Analysis Data Model (ADaM)

Tables

Plots

Interactive

Frameworks

Electronic Submissions (eSUB)

Metadata

Utility

Package Validation

Synthetic Data

Other Useful Packages

Overlap

The most abundant potential overlap is with both Clinical Trials and Survival. The scope of pharmaverse itself is more narrow, focusing on activities and procedures around creating regulatory reports.

Maintainers

Notes

A full draft of the task view is available here: https://github.com/pharmaverse/pharmaverse_task-view/blob/main/Pharmaverse.md

zeileis commented 9 months ago

Thanks for the proposal! This is an interesting topic and the timing is also good, given that the "ClinicalTrials" task view is also going to be relaunched, see: https://github.com/cran-task-views/ctv/issues/59

For the current draft, I see the following main issues:

mstackhouse commented 8 months ago

@zeileis Both the ClinicalTrials and proposed Pharmaverse have met as a group. We mutually decided that right now it's better to keep our proposed task views separate and reassess in the future if it makes sense to combine them. We will continue to address feedback here. We will be updating with other proposed feedback you have suggested.

zeileis commented 8 months ago

OK, thanks for the follow-up. Then we will assess the proposals separately. I have already raised my main concerns above. Maybe my fellow co-editors want to add to this list @rsbivand @eddelbuettel @tuxette

tuxette commented 8 months ago

Thanks for the proposal. My impression is that your proposal would be a task view version of the website https://pharmaverse.org/ . Hence, at the moment, I don't clearly see its scope: As mentioned by @zeileis , it seems to be at the intersection of ClinicalTrial and ReproducibleResearch but I don't clearly see the focus specific to pharmaceutical studies or even clinical reporting. I you could elaborate a bit on that, it would help us better assessing your proposal. And, also for me, the name does not work well because "Pharmaverse" is not a field or a topic.

rsbivand commented 8 months ago

I agree with @tuxette , but maybe the website could be linked to from ClinicalTrial and ReproducibleResearch to increase its visibility in the relevant domains. I agree that the title is not viable.

mstackhouse commented 8 months ago

Hi @tuxette,

The name change for the purpose of the task view makes sense. To additionally help clarify the scope, I'm thinking the title "RegulatoryClinicalReporting" might make sense, which is supported by the first paragraph of our the scope within the proposal.

I think an additional clarification of scope is that that in addition to conforming to regulatory and industry standards, the packages in pharmaverse (or RegulatoryClinicalReporting) focus on repeatability in addition to reproducibility. Given the standardization of regulatory reporting, these packages supporting making a pipeline that operates more like a factory than a bespoke analysis. So there's a heavy focus on efficiency.

mstackhouse commented 8 months ago

Updates based on comments.

RegulatoryClinicalReporting

Scope

The packages included within the RegulatoryClinicalReporting focus on a specific subset of clinical trial activities, specifically on the clinical reporting pipelines used within the pharmaceutical industry. These activities follow specific standards, such as CDISC Data Standards and ICH E3. The scope of pharmaverse packages ranges from CRF (Case Report Forms - or data collection for a clinical trial) through clinical trial analysis reporting, including formatting of data to match SDTM (Study Data Tabulation Model) and ADaM (Analysis Data Model) standards, and production of TLGs (Tables, Listings, and Graphs). Furthermore, RegulatoryClinicalReporting packages help supporting the orchestration activities of clinical trial data analysis through regulatory requirements. A specific distinction that sets these packages apart from those in task views such as r view("ClinicalTrials") is the focus on conformance to industry standards and efficiency. In addition to reproducibility, repeatability is a critical component of the clinical reporting pipeline given the volume of trials and analysis ongoing for pharmaceutical or medical organizations working with regulatory agencies,

The scope of the RegulatoryClinicalReporting is only a small subset of the larger range of clinical trial activities for with R can be applied. For more information on R packages for clinical trials, see r view("ClinicalTrials"). Pharmaverse also has more resources outside of CRAN, which you can read about on www.pharmaverse.org.

Packages

Study Data Tabulation Model (SDTM)

Analysis Data Model (ADaM)

Tables

Plots

Interactive

Frameworks

Electronic Submissions (eSUB)

Metadata

Utility

Package Validation

Synthetic Data

Overlap

The most abundant potential overlap is with both Clinical Trials and Survival. Additionally, there is overlap with ReproducibleResearch. The scope of pharmaverse itself is more narrow, focusing on activities and procedures around creating regulatory reports.

Maintainers

Notes

A full draft of the task view is available here: https://github.com/pharmaverse/pharmaverse_task-view/blob/main/Pharmaverse.md

tuxette commented 8 months ago

Thanks @mstackhouse : it clarifies a bit the proposal for me. However, looking carefully at your new proposal, I have additional remarks:

mstackhouse commented 8 months ago

Moving metadata up would be a fine adjustment for now. Otherwise, the flow of the packages is based on the clinical reporting lifecycle. In clinical reporting:

After that flow we have more of the utility packages placed.

As for packages present on CRAN, the only one in the list that I've posted above that is not present on CRAN is valtools, and that's my mistake. While the pharmaverse has more packages listed, I filtered out github packages and our view should only include packages present on CRAN.

As you state that a large proportion are only on GitHub, please let me know if I'm mistaken in my list below.

All of these packages are included on CRAN currently:

Packages

Study Data Tabulation Model (SDTM)

Analysis Data Model (ADaM)

Tables

Plots

Interactive

Frameworks

Electronic Submissions (eSUB)

Metadata

Utility

Package Validation

Synthetic Data

tuxette commented 8 months ago

Thanks @mstackhouse :

zeileis commented 8 months ago

Thanks for the useful discussions and updates, Mike @mstackhouse and Nathalie @tuxette. Some comments:

tuxette commented 2 months ago

@mstackhouse : I do not see activity for this proposal since February. However, to me, we were heading to something interesting with the few minor adjustments that have been suggested. Do you still plan to submit this task view?

zeileis commented 1 month ago

Unfortunately, we did not have any follow-up in more than half a year. Hence I'm closing this issue/proposal now. However, I agree with Nathalie @tuxette that we had been quite close to an interesting submission. Michael @mstackhouse, if you do feel that you want to move this forward, please post a new issue incorporating the feedback we provided.