BRMS tutorial: add `rstan` example by falkmielke · Pull Request #346 · inbo/tutorials · GitHub

Description

This PR adds an example of rstan usage with a raw Stan model to the existing brms tutorial.
I also rearranged that tutorial a bit (separate section for data).

I was able to test the Rmd code, all runs as intended. However, I did not knit or publish any of this to html, the structure and publication procedure of this repo seem too sophisticated for me (though great that it is based on hugo ssg!). I hope it will not crash GHA.

Thank you in advance for review and suggestions!

Task list

My tutorial or article is placed in a subfolder of tutorials/content
The filename of my tutorial or article is index.md. In case of an Rmarkdown tutorial I have knitted my index.Rmd to index.md (both files are pushed to the repo).
I have included tags in the YAML header (see the tags listed in the tutorials website side bar for tags that have been used before)
I have added categories to the YAML header and my category tags are from the list of category tags
I was not able to compile the tutorial into html files, and would appreciate if you original authors and tutorial maintainers could take over.

Hi Falk

Very nice addition.

I checked the Dutch version. I will assume the same comments apply for the English version.
General remarks:

Could you keep the term burnin instead of warmup. I like burnin more.
Any particular reason you provide the poisson_model.stan file in brms_eng folder and not in the brms_nl folder?
I think I would like to put your section ("Deep Dive: rstan") in a separate section between "Vergelijken met frequentist statistics" and "Referenties". I think the use of rstan is quite advanced for the general users in INBO. Therefore, I think it is better that it is not in the middle of our tutorial, but behind it. People get a view of the whole process of bayesian statistisc (in brms), and if they want (or if they heard about stan somewhere and want to look into it), they can progress further to your section. What do you think?

wat bedoel je met "een model beveiligen"?

This was a translation fault of a faulty English sentence, which on top of that I overlooked in proofreading. My apologies! It is corrected.

Ik zou hier ook zelf een burn-in gebruiken zoals we in de brms-voorbeelden hebben gedaan. Dan is het nog meer gelijkaardig als hierboven.

Thank you for pointing this out, @wlangera !
I briefly asked @hansvancalster and googled "burn-in tuning warmup Bayesian stats". There is a to-the-point discussion here. My notion of changing came from the fact that we don't physically "burn" or "burn in" anything; thus I was surprised that apparently the term was considered appropriate for some MCMC algorithms. "Tuning", my actual favorite 🤘, is reserved for a certain sub-part of the warm-up phase (Merci, Hans!).

Anyways, the experts seem to prefer "warm-up", and if you agree and confirm, I will in turn adjust this throughout the tutorial.

Ok that sounds good. Thanks

From looking at the content/tutorials/r_brms/index.md file, I think that the html's should be rendered locally and commited to the repo in this folder.

Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

From looking at the content/tutorials/r_brms/index.md file, I think that the html's should be rendered locally and commited to the repo in this folder.

Thanks, I will try that, and we see where checks lead us.

Any particular reason you provide the poisson_model.stan file in brms_eng folder and not in the brms_nl folder?

Good point; I was thinking about git / data redundancy.
Thinking one step further:

should they rather be in the [...]/html folder, close to what people actually read?
... or shouldn't they best be in a top level /data folder, or in /inst, to be generally accessible?
Thank you for advice @wlangera @hansvancalster ! I will move the file and adjust links.

Any particular reason you provide the poisson_model.stan file in brms_eng folder and not in the brms_nl folder?

Good point; I was thinking about git / data redundancy. Thinking one step further:

should they rather be in the [...]/html folder, close to what people actually read?

... or shouldn't they best be in a top level /data folder, or in /inst, to be generally accessible?
Thank you for advice @wlangera @hansvancalster ! I will move the file and adjust links.

I would put it in the base folder of your tutorial: content/tutorials/r_brms/ or equally fine in a subfolder of that: content/tutorials/r_brms/<subfolder>. The name for the <subfolder> perhaps model, model_files, stan, stan_files or ...?

I incorporated the change suggestions and re-knitted the html reports. This also yielded two image-related issues, here and here.

the cmdstanr package is explicitly mentioned (suggestion by @hansvancalster )
general code files are now in a general folder
knit with low res images

Thank you for re-checking and publishing!

Hi Falk, I have send you the images via mail.

Thanks for the changes

falkmielke added 3 commits November 21, 2024 14:18

brms_rstan: general updates

d09e99e

brms_rstan: poisson model, plain+hierarchical

7b170ac

brms_rstan: windows testing, index, author

bfa0a19

falkmielke added the enhancement tutorial label Nov 22, 2024

falkmielke requested review from hansvancalster and wlangera November 22, 2024 08:22

falkmielke self-assigned this Nov 22, 2024

wlangera requested changes Nov 25, 2024

View reviewed changes

falkmielke and others added 5 commits November 26, 2024 07:31

brms-rstan: wording

d3a0159

Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

brms-rstan: wording (nl)

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Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

brms-rstan: wording (nl)

b487a1e

Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

brms-rstan: wording (nl)

fc2f757

Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

brms-rstan: wording (nl)

194ee75

Co-authored-by: Ward Langeraert <60934857+wlangera@users.noreply.github.com>

falkmielke added 3 commits November 26, 2024 08:09

brms-rstan: rstan moved as suggested.

bb32e0d

brms-rstan: generalizing frequentists; translation

0d113dd

brms-rstan: generalizing frequentists (en)

58dc8af

falkmielke added 3 commits November 26, 2024 08:58

brms-rstan: mentioning cmdstanr backend

4740347

brms-rstan: re-organize static files

4f731a9

brms-rstan: knit files; image issues

75efd94

falkmielke requested review from ToonVanDaele and wlangera November 26, 2024 12:37

wlangera approved these changes Nov 28, 2024

View reviewed changes

falkmielke merged commit 8c46fb7 into master Dec 6, 2024

falkmielke deleted the rstan branch December 6, 2024 10:14

+              Het relatieve gebruiksgemak gaat echter ten koste van de flexibiliteit en in zekere mate de leesbaarheid.
+              Stan en `rstan` daarentegen leunen meer op de wiskundige formulering van modellen.
+              Elk aspect van het model moet expliciet worden ingesteld, wat een voordeel kan zijn (bijvoorbeeld als u te maken hebt met niet-standaard use cases) of een nadeel (bijvoorbeeld als u modellen op niet-optionele manieren beveiligt).


		Sampling doet vrijwel hetzelfde als hierboven, want in de kern is `brms` gewoon `stan`.

		```{r stan_sampling}

BRMS tutorial: add `rstan` example by falkmielke · Pull Request #346 · inbo/tutorials · GitHub

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BRMS tutorial: add rstan example - #346

BRMS tutorial: add rstan example#346falkmielke merged 14 commits intomasterinbo/tutorials:masterfrom rstaninbo/tutorials:rstanCopy head branch name to clipboard

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BRMS tutorial: add rstan example#346
falkmielke merged 14 commits into
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rstan

falkmielke commented Nov 22, 2024 •
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