This PR builds on the template structure of a VISC report.
I've changed this PR a bit since standup. There is now a function called use_visc_report() which creates a template VISC PT report (previously you may have done this through rmarkdown::draft() or the RStudio GUI) and a directory called "methods" which contains assay-specific methods for biological endpoints, lab methods, and statistical methods.
Major changes:
There is a new function called use_visc_report() which creates a VISC Report with template language. With this PR, there are options for an "empty", "generic", or "bama" report (other assays to be added in future PRs).
In the PT report skeleton, the biological endpoints, lab methods, and statistical methods sections are set up as "child" R Markdown documents.
Instead of gently encouraging the user to use a project-level background section and study schema, this is more explicitly laid out in the PT report template.
Minor changes:
To improve the writing, editing, and reviewing experience, I used semantic line breaks in the template text.
Changed the names of the report templates (what you see in the R Studio GUI window) from "Empty Report" to "VISC Empty Report" and from "VISC PT Report (Generic)" to "VISC PT Report".
Feedback:
Alicia and Celia: Can you please comment on the methods language and structure? This is taken directly from the current PT report template and BAMA assay memo that you wrote, so if you want to make update, this would be a good time. The files you should look at in this PR are: bama-biological-endpoints.Rmd, bama-lab-methods.Rmd, bama-statistical-methods.Rmd, generic-biological-endpoints.Rmd, generic-lab-methods.Rmd, and generic-statistical-methods.Rmd. If you need help navigating to these files, please let me know.
Chelsey: We had a discussion about box plots in C100 but I'm not sure how that issue was resolved. Can you please take a look at bama-statistical-methods.Rmd and generic-statistical-methods.Rmd and suggest changes to the graphical analysis section that would help guide SRAs on this issue? We can chat about it and discuss approaches.
Jimmy: Could you please look at the code in general and new functions? We chatted about including a check for the methods files, but I'm not sure I want to include that right now. Let's chat more about that in a package development meeting. I think it could be another PR anyway.
Others: General comments or other suggestions welcome.
This PR builds on the template structure of a VISC report.
I've changed this PR a bit since standup. There is now a function called
use_visc_report()which creates a template VISC PT report (previously you may have done this throughrmarkdown::draft()or the RStudio GUI) and a directory called "methods" which contains assay-specific methods for biological endpoints, lab methods, and statistical methods.Major changes:
use_visc_report()which creates a VISC Report with template language. With this PR, there are options for an "empty", "generic", or "bama" report (other assays to be added in future PRs).Minor changes:
Feedback:
bama-biological-endpoints.Rmd,bama-lab-methods.Rmd,bama-statistical-methods.Rmd,generic-biological-endpoints.Rmd,generic-lab-methods.Rmd, andgeneric-statistical-methods.Rmd. If you need help navigating to these files, please let me know.bama-statistical-methods.Rmdandgeneric-statistical-methods.Rmdand suggest changes to the graphical analysis section that would help guide SRAs on this issue? We can chat about it and discuss approaches.