# \#docs

**URL:** https://discourse.mc-stan.org/tag/docs/156.md

[Latest](https://discourse.mc-stan.org/latest.md) · [Categories](https://discourse.mc-stan.org/categories.md) · [Tags](https://discourse.mc-stan.org/tags.md)

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## [New User's Guide Intro, SEM, and user-defined constrained parameters chapters](https://discourse.mc-stan.org/t/new-users-guide-intro-sem-and-user-defined-constrained-parameters-chapters/41430)

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**Author:** [@Bob\_Carpenter](https://discourse.mc-stan.org/u/Bob_Carpenter)\
**Replies:** 11\
**Last updated:** [August 4, 2026, 9:34pm UTC](https://discourse.mc-stan.org/t/new-users-guide-intro-sem-and-user-defined-constrained-parameters-chapters/41430 "2026-08-04T21:34:25Z")

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After feedback from @WardBrian and @mitzimorris, I just merged two new chapters for the User’s Guide right up front in a new introductory part. The Stan Ecosystem How Stan Works I’m not sure what the schedule is for r…

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## [Example stan documentation with doxygen](https://discourse.mc-stan.org/t/example-stan-documentation-with-doxygen/39111)

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**Author:** [@jamesazam](https://discourse.mc-stan.org/u/jamesazam)\
**Replies:** 8\
**Last updated:** [April 7, 2025, 4:26pm UTC](https://discourse.mc-stan.org/t/example-stan-documentation-with-doxygen/39111 "2025-04-07T16:26:35Z")

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Hi everyone, I just wanted to point you to this work we recently did in EpiNow2 to document our stan code (See EpiNow2 Stan Functions: EpiNow2 Stan Functions), using doxygen. We’ve not seen any guides around on how to d…

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## [Very minor mistake in cmdstanr model-method-compile help page](https://discourse.mc-stan.org/t/very-minor-mistake-in-cmdstanr-model-method-compile-help-page/36051)

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**Author:** [@JohnnyZoom4H](https://discourse.mc-stan.org/u/JohnnyZoom4H)\
**Replies:** 6\
**Last updated:** [July 31, 2024, 9:39am UTC](https://discourse.mc-stan.org/t/very-minor-mistake-in-cmdstanr-model-method-compile-help-page/36051 "2024-07-31T09:39:01Z")

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On the model-method-compile help page from the cmdstanr package, there is a trivial mistake in the description of the “pedantic” argument. The link there to the “Pedantic mode” subchapter in the Stan User’s Guide is des…

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## [Not working function in Stan manual(s): permutation\_rng](https://discourse.mc-stan.org/t/not-working-function-in-stan-manual-s-permutation-rng/31415)

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**Author:** [@dankehila](https://discourse.mc-stan.org/u/dankehila)\
**Replies:** 1\
**Last updated:** [May 17, 2023, 1:32pm UTC](https://discourse.mc-stan.org/t/not-working-function-in-stan-manual-s-permutation-rng/31415 "2023-05-17T13:32:07Z")

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The cross validation entry has a function permutation\_rng: functions { array\[\] int permutation\_rng(int N) { int N = rows(x); array\[N\] int y; for (n in 1:N) { y\[n\] = n; } vector\[N\] theta…

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## [Incorrect formula for correlation matrix transform](https://discourse.mc-stan.org/t/incorrect-formula-for-correlation-matrix-transform/24664)

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**Author:** [@hhau](https://discourse.mc-stan.org/u/hhau)\
**Replies:** 6\
**Last updated:** [March 3, 2023, 7:23am UTC](https://discourse.mc-stan.org/t/incorrect-formula-for-correlation-matrix-transform/24664 "2023-03-03T07:23:38Z")

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I am mapping a set of unconstrained values to a correlation matrix and working off 10.9 Correlation matrices | Stan Reference Manual in the manual (for which I am very grateful, as the LKJ papers are not at all easy to u…

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## [A Sphinx extension for documentation Stan code](https://discourse.mc-stan.org/t/a-sphinx-extension-for-documentation-stan-code/30210)

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**Author:** [@tillahoffmann](https://discourse.mc-stan.org/u/tillahoffmann)\
**Replies:** 2\
**Last updated:** [February 1, 2023, 6:55pm UTC](https://discourse.mc-stan.org/t/a-sphinx-extension-for-documentation-stan-code/30210 "2023-02-01T18:55:01Z")

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As part of developing the package for Scalable Gaussian process inference, I wrote a reasonable amount of interface documentation. To avoid scattering documentation across different documents (e.g., Stan code and markdow…

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## [Understanding brackets array syntax documentation](https://discourse.mc-stan.org/t/understanding-brackets-array-syntax-documentation/27437)

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**Author:** [@Richard\_Erickson](https://discourse.mc-stan.org/u/Richard_Erickson)\
**Replies:** 2\
**Last updated:** [May 11, 2022, 4:27pm UTC](https://discourse.mc-stan.org/t/understanding-brackets-array-syntax-documentation/27437 "2022-05-11T16:27:43Z")

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I am trying to update my code to address this error: Warning in '/tmp/RtmpH9sgz3/model-3b673bc8c67.stan', line 38, column 2: Declaration of arrays by placing brackets after a variable name is deprecated and will…

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## [Feature request for documentation](https://discourse.mc-stan.org/t/feature-request-for-documentation/27158)

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**Author:** [@Richard\_Erickson](https://discourse.mc-stan.org/u/Richard_Erickson)\
**Replies:** 2\
**Last updated:** [April 15, 2022, 4:37pm UTC](https://discourse.mc-stan.org/t/feature-request-for-documentation/27158 "2022-04-15T16:37:47Z")

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Some projects, such as the book R for Data Science, include a “view source code on GitHub button”. I would like to request the Stan documentation includes a similar feature. This would allow users to easily suggest fixe…

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## [New guide to warnings: request for feedback](https://discourse.mc-stan.org/t/new-guide-to-warnings-request-for-feedback/25978)

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**Author:** [@martinmodrak](https://discourse.mc-stan.org/u/martinmodrak)\
**Replies:** 11\
**Last updated:** [March 10, 2022, 11:37pm UTC](https://discourse.mc-stan.org/t/new-guide-to-warnings-request-for-feedback/25978 "2022-03-10T23:37:21Z")

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Some time ago, we had a discussion on updating the text of warnings for divergent transitions, treedepth etc (https://discourse.mc-stan.org/t/text-for-warning-message/), this led me @andrewgelman , @jonah and @avehtari t…

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## [Understanding the transformation underlying unit\_vector\[2\]](https://discourse.mc-stan.org/t/understanding-the-transformation-underlying-unit-vector-2/26145)

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**Author:** [@Jon\_Alm\_Eriksen](https://discourse.mc-stan.org/u/Jon_Alm_Eriksen)\
**Replies:** 1\
**Last updated:** [January 28, 2022, 11:51pm UTC](https://discourse.mc-stan.org/t/understanding-the-transformation-underlying-unit-vector-2/26145 "2022-01-28T23:51:41Z")

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Dear Community, I’m trying to square section 11.3 and 11.4 in the manual but need some help. Section 11.4 11.4 Unit vectors and rotations | Stan User’s Guide tells me to represent the variable as unit\_vector\[2\] and t…

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## [What is the \`ints\` type mentioned in the Stan Functions Reference](https://discourse.mc-stan.org/t/what-is-the-ints-type-mentioned-in-the-stan-functions-reference/25574)

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**Author:** [@andypea](https://discourse.mc-stan.org/u/andypea)\
**Replies:** 1\
**Last updated:** [December 6, 2021, 9:13am UTC](https://discourse.mc-stan.org/t/what-is-the-ints-type-mentioned-in-the-stan-functions-reference/25574 "2021-12-06T09:13:25Z")

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What is the ints type used the example code in the Stan Functions Reference document. One place it appears is: https://mc-stan.org/docs/2\_28/functions-reference/poisson.html I’ve tried using it myself when specifying a…

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## [Stanc3 developer documentation now available](https://discourse.mc-stan.org/t/stanc3-developer-documentation-now-available/25001)

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**Author:** [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Replies:** 0\
**Last updated:** [October 26, 2021, 6:16pm UTC](https://discourse.mc-stan.org/t/stanc3-developer-documentation-now-available/25001 "2021-10-26T18:16:09Z")

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Hi everyone - Stanc3 now has internal developer documentation available at https://mc-stan.org/stanc3/stanc/index.html. This is similar to the stan-math docs at https://mc-stan.org/math/. It contains a cross-linked refe…

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## [Stan documentation's R code](https://discourse.mc-stan.org/t/stan-documentations-r-code/24467)

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**Author:** [@bnicenboim](https://discourse.mc-stan.org/u/bnicenboim)\
**Replies:** 3\
**Last updated:** [September 30, 2021, 8:30am UTC](https://discourse.mc-stan.org/t/stan-documentations-r-code/24467 "2021-09-30T08:30:08Z")

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Hi, I wanted to check how some plots were done in R in Stan documentation, but I found this: After running this for enough iterations so that the effective sample size is larger than M, then thinning to M draws (here…

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## [Help making a short overview of the Stan ecosystem in R?](https://discourse.mc-stan.org/t/help-making-a-short-overview-of-the-stan-ecosystem-in-r/19814)

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**Author:** [@jonah](https://discourse.mc-stan.org/u/jonah)\
**Replies:** 8\
**Last updated:** [January 4, 2021, 3:58pm UTC](https://discourse.mc-stan.org/t/help-making-a-short-overview-of-the-stan-ecosystem-in-r/19814 "2021-01-04T15:58:07Z")

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There are lots of R packages available for Stan users but I think we’re lacking a good overview of what’s available. Would anyone be interested in helping to write a short overview of the Stan ecosystem in R for new user…

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## [Stan needs your help: Writing and fixing documentation](https://discourse.mc-stan.org/t/stan-needs-your-help-writing-and-fixing-documentation/19701)

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**Author:** [@rok\_cesnovar](https://discourse.mc-stan.org/u/rok_cesnovar)\
**Replies:** 2\
**Last updated:** [December 21, 2020, 8:22am UTC](https://discourse.mc-stan.org/t/stan-needs-your-help-writing-and-fixing-documentation/19701 "2020-12-21T08:22:50Z")

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Are you using Stan for your everyday work, study, or fun? Have you wondered how you could help or give back to the open source project? Here is one opportunity if you can spare an hour or two. You are most likely aware …

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## [ODE control parameter documentation: questions and improvements](https://discourse.mc-stan.org/t/ode-control-parameter-documentation-questions-and-improvements/18999)

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**Author:** [@jtimonen](https://discourse.mc-stan.org/u/jtimonen)\
**Replies:** 4\
**Last updated:** [December 14, 2020, 7:59pm UTC](https://discourse.mc-stan.org/t/ode-control-parameter-documentation-questions-and-improvements/18999 "2020-12-14T19:59:07Z")

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Hello, I think the ODE docs (v2.25), particularly Section 13.6, has some parts that could be improved or clarified to give users better information on how to use the solvers. Tolerances Documentation says " relative\_to…

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## [\_lupdf functions - where/how to doc them?](https://discourse.mc-stan.org/t/lupdf-functions-where-how-to-doc-them/18792)

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**Author:** [@rok\_cesnovar](https://discourse.mc-stan.org/u/rok_cesnovar)\
**Replies:** 24\
**Last updated:** [October 22, 2020, 8:22pm UTC](https://discourse.mc-stan.org/t/lupdf-functions-where-how-to-doc-them/18792 "2020-10-22T20:22:38Z")

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We are exposing the unnormalized form of distributions for the 2.25 version (see https://discourse.mc-stan.org/t/stan-2-25-release-candidate/18706/20 for more info). I am writing some basic information on that but need s…

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## [Building docs](https://discourse.mc-stan.org/t/building-docs/17103)

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**Author:** [@anon79882417](https://discourse.mc-stan.org/u/anon79882417)\
**Replies:** 2\
**Last updated:** [July 30, 2020, 2:18pm UTC](https://discourse.mc-stan.org/t/building-docs/17103 "2020-07-30T14:18:55Z")

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Hey quick question, Is there a way to quickly install all of the required .sty files to build the docs? I’m doing it one by one, and it’s taking forever. There has to be a better way.