Restructure GGIR vignettes

[vincentvanhees]

In the past couple of months Jairo and I have been preparing a restructuring of the vignette documentation.
We now have a github-pages framework that we will fill with narrative chapters to describe everything there is to say about GGIR in an accessible way. As a result, the CRAN pages can be be refocused to have a more practical focus with output and parameters dictionaries, as well as reference tables for cut-points.

I am creating this issue to keep track of outstanding tasks:

Chapters 1-7:

• Draft and peer-review among ourselves (offline)
• Add to branch
• Check all looks good locally
• Merge with master branch and check all look good online

Chapters 8-12:

• Draft and peer-review among ourselves (offline)
• Add to branch
• Check all looks good locally
• Merge with master branch and check all look good online

Additional chapters

• Create new vignette focussed on inspecting the output with a focus on variable names. Make it available in both gh-pages and on CRAN.

Cross references

• Add reference from GGIR-package.Rd to github pages.
• Add hyperlinks in between chapters and republish.

Revise main CRAN vignette

• Make it complementary to the github pages and useful from a CRAN perspective. For example, brief introduction followed by demo(s) and references to other documentation resources.

Search field

• Make sure all function documentation is ignored by search field, because GGIR and gh-pages are focussed on users. Contributors can check function documentation inside the code, no need to put this in the gh-pages.

Additional points:

• Explain somewhere in the githubpages: dec_reports and sep_reports => probably chapter 2 is a good place
• Remove beginning of chapter 2 once chapter 1 has been added.
• https://wadpac.github.io/GGIR/articles/chapter0_Support.html is out of date as links still refer to CRAN
• Make sure open-source pitch highlights reproducibility crisis in the field, where many studies are done without a reference to code.
• check that appending files is explained
• In clipping detection paragraph, update 80% to 30%
• minor rephrasing of Axivity file processing, see email Lena 22March2024
• make sure p5 time series are well explained
• explain that part 5 can be used for studying volume, intensity, frequency of behaviour
• Remove reference to CRAN in parameters vignette
• Tidy up annex for HouseHoldCoanalysis.html which still refers to CRAN vignettes at the top.
• Simplify CRAN vignettes even more and remove some of them to avoid ambiguity about where to find information.
• Reflect on if and where to report number of publications that have used GGIR.
• Reflect on whether to link to complementary packages such as the work done in Habitus. Maybe introduction chapter is a good place.
• Reduce length of tables in GGIRoutput.Rmd as git struggles to track changes and then labels the entire table as changed which complicates merging branches.