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bms63
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bms63
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This is awesome - just some minor comments feel free to use or not, but looking forward to sharing this widely!!
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Thanks @bms63 - great comments! I've updated for all. I'll give it the rest of April for my colleagues and others from our examples to team to comment on this PR, and then we can merge and publish early next month 🙏 |
| - [`{xportr}`](https://atorus-research.github.io/xportr/): delivers the SAS transport file (XPT) and eSub checks. | ||
| - [`{pkglite}`](https://merck.github.io/pkglite/): enables exchange of closed source R packages via text files. | ||
| - [`{datasetjson}`](https://atorus-research.github.io/datasetjson/): experimental package to deliver Dataset-JSON. | ||
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Hi, @rossfarrugia . Thanks for allowing our review. Could metacore and metatools be considered packages useful for R Submission as well?
Both {metacore} and {metatools} play a vital role in the open-source R landscape for regulatory submissions by empowering users to proactively manage data quality and conformance. By leveraging these tools, we can get closer to ensuring our submitted data aligns with cross-industry standards like CDISC and passes validation checks by tools such as Pinnacle 21.
- metacore (https://atorus-research.github.io/metacore/): This package provides a robust framework for defining and managing metadata, which is crucial for ensuring data structure and content adhere to regulatory guidelines. Its capabilities in defining data dictionaries, controlled terminologies, and variable attributes can greatly assist in the creation of submission-ready datasets.
- metatools (https://pharmaverse.github.io/metatools/): Developed within the Pharmaverse ecosystem, metatools offers a collection of utilities designed to work with metadata, including functionalities for data validation, transformation, and reporting. Its focus on practical applications for clinical data makes it a strong candidate for inclusion in our eSUB toolkit.
I see metacore is in the ADSL example below.
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I'll add a general paragraph here for other pharmaverse packages as trying to not repeat too much that's already in the ADaM example pages
| collate(file_ectd(), file_auto("inst")) %>% | ||
| prune("R/zzz.R") %>% | ||
| pack(output = "ectd/r0pkg.txt") | ||
| ``` |
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For these RG examples mentioned here, when submitting closed-source packages, here are the links to their respective ADRGs if anyone would like to see the actual examples.
Pilot 1, using {pkglite} - https://github.com/RConsortium/submissions-pilot1-to-fda/blob/main/m5/datasets/rconsortiumpilot1/analysis/adam/datasets/adrg.pdf
Pilot 3, using compressed .zip approach - https://github.com/RConsortium/submissions-pilot3-adam-to-fda/blob/main/m5/datasets/rconsortiumpilot3/analysis/adam/datasets/adrg.pdf
| pack(output = "ectd/r0pkg.txt") | ||
| ``` | ||
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| It is worth monitoring this |
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| It is worth monitoring this | |
| For current ADRG guidance, regardless of the programming language used for regulatory submissions, ensuring your documentations meet the ADRG completion guidelines found here [PHUSE ADRG Package](https://advance.hub.phuse.global/wiki/spaces/WEL/pages/26804660/Analysis+Data+Reviewer+s+Guide+ADRG+Package) | |
| will be a great foundation to your open-source submission journey. As we are heading into this open-source R submission journey, it is worth monitoring this | |
| [PHUSE Open-Source Metadata Documentation WG](https://phuse-org.github.io/OSDocuMeta/) | |
| to see how guidance evolves in this documentation space. |
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@bms63 some minor updates made for review from my colleagues. Do you want to take a quick final look and then merge/approve? I'm away monday for UK bank holiday so if you publish this before i get back feel free to share the link out on pharmaverse slack to announce this new example. I hope people will find it useful and we can add to it over time as we see more industry submission experiences shared. |
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Thanks @rossfarrugia for updates. it looks good to me. feel free to publish when you get back from holiday. |
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add esub example article
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