update case study of hierarchical models for binary trials

[mitzimorris]

Updated models and notebook for Stan case study "Hierarchical Partial Pooling for Repeated Binary Trials"

• use affine transform for non-centered hierarchical logit model
• use include directives for data, transformed data, and generated quantities code shared across all models
• rework Rmd notebook so that it runs with CmdStanR

[mitzimorris]

This PR updates the Rmd notebook and the HTML
A subsequent PR will break this case study into multiple parts and create Jupyter notebooks.

[WardBrian]

To actually update the one people see I think there needs to be a separate PR to https://github.com/stan-dev/stan-dev.github.io, right?

I’ll take a look at this tomorrow

[mitzimorris]

If you OK this PR, that should be sufficient review for the stan-dev.github.io pages as well.

[mitzimorris]

can we turn off compilation for the include fragments? if so, how?

[WardBrian]

I think @rok-cesnovar put it together. My guess is provably naming them something other than .stan would work, but then you lose syntax highlighting etc

[mitzimorris]

@rok-cesnovar - the include files are in a directory named "include" - can we do something with this information?
for this case study, using includes makes a lot of sense. also, it's good to have more examples of how this works somewhere.

[WardBrian]

A few comments on the Rmd file. The reorganization of the stan files using #include looks good

[WardBrian]

This is a minor detail, but generally using \[ \] is preferred over $$ $$. The later is a pure-TeX shorthand which can cause some issues with LaTeX macros. Not sure it matters for us, but just thought I'd note. More on Wikibooks

[mitzimorris]

yes, but only $$ works in Jupyter notebooks.

[WardBrian]

Is this being run in a jupyter notebook now? Or is the idea that it will be recreated in one?

[mitzimorris]

yes, it would be good to be able to run these in jupyter, either in Python or R.

I used jupyter to update this notebook, so I hit this right off the bat.
awhile back I installed juptext on my machine and I prefer jupyter to RStudio - https://mc-stan.org/users/documentation/case-studies/jupyter_colab_notebooks_2020.html#challenge-putting-the-r-in-jupyter

With juptext and IRkernal, I can run the notebook while keeping it in .Rmd format which means that it's easy to edit via the browser of in emacs. but that's just me.

[WardBrian]

Suggested change

	Because these models contain a number of [include directives](https://mc-stan.org/docs/reference-manual/includes-section.html),
	Because these models contain a number of [include directives](https://mc-stan.org/docs/reference-manual/includes.html),

With -section it will link to the 2_27 version (at least until we fix that redirect)

[WardBrian]

This still needs to be changed (I think you changed a different copy of the link which I hadn't caught)

[rok-cesnovar]

Feel free to ignore the testing errors, will fix the GHA script later this week to ignore the files you mentioned.

[WardBrian]

It doesn't let me comment directly on the rendered HTML, but here are some thoughts on the way the output looks:

• Can we hide the 'A newer version of CmdStan is available. See ?install_cmdstan() to install it.' message? If possible it would also be great to hide some (if not all) of these setup messages such as the cmdstan path
• There's some strange formatting around the code blocks at the end. Some of the titles seem to stretch onto the next line while still in typewritertext
• I'm not sure how the html is built from the Rmd in this case - would it be possible to get syntax highlighting of the Stan code?

[mitzimorris]

Can we hide the 'A newer version of CmdStan is available. See ?install_cmdstan() to install it.' message? If possible it would also be great to hide some (if not all) of these setup messages such as the cmdstan path

I think this is an CmdStanR bug. I actually have CmdStan 2.28.2 installed. I also have a version of develop in my .cmdstan directory and I named that dir cmdstan-develop - CmdStanPy ignores it, but CmdStanR wanted to use that and not 2.28.2. @rok-cesnovar - what are the rules for CmdStanR?

[WardBrian]

It mentions an environment variable to disable it for now

[mitzimorris]

I just converted it to a draft because there's more work to be done here.

will investigate formatting issues.

it would definitely be nice to get Stan syntax highlighting into the HTML
and I'm pretty sure we can hack the .Rmd to make that happen.

[WardBrian]

What program is used to ultimately create the HTML? Pandoc?

[rok-cesnovar]

@rok-cesnovar - what are the rules for CmdStanR?

We sort the folder in .cmdstan, not sure why -develop would be ahead though. Will check.