Merge branch 'master' of https://github.com/stan-dev/stan-dev.github.io

Author: mitzimorris

_quarto.yml

@@ -22,7 +22,7 @@ website:
   page-navigation: true
   back-to-top-navigation: true
   open-graph: true
-  
+
   navbar:
     logo: "img/logo_tm.png"
     logo-alt: "Stan logo"
@@ -31,7 +31,7 @@ website:
       - text: "Stan"
         href: index.qmd
       - text: "Getting Started"
-        href: install/
+        href: install/index.qmd
       - text: "Documentation"
         href: "https://mc-stan.org/docs"
       - text: "Learning Resources"
@@ -49,9 +49,9 @@ website:
           - text: "Diagnostics and Warnings"
             href: learn-stan/diagnostics-warnings.qmd
       - text: "Tools"
-        href: tools/
+        href: tools/index.qmd
       - text: "About"
-        href: about/
+        href: about/index.qmd
     tools:
       - icon: github
         url: https://github.com/stan-dev

about/index.qmd

@@ -13,7 +13,7 @@ Stan is freedom-respecting, open-source software <span
 class="note">(new BSD core, some interfaces GPLv3)</span>.&nbsp; Stan
 is associated with NumFOCUS, a 501(c)(3) nonprofit supporting open code
 and reproducible science, through which you can [help support
-Stan](#support-stan).
+Stan](#help-fund-stan).
 
 ## Licensing
 

index.css

@@ -0,0 +1,75 @@
+/* custom CSS only for the home page */
+/* all other CSS is shared with docs and in the quarto-config submodule */
+
+
+
+.content-block {
+    padding-top: 20px;
+    padding-bottom: 10px;
+    margin-left: 30px;
+    margin-right: 30px;
+  }
+
+  @media (min-width: 900px) {
+    .content-block {
+      margin-left: 50px;
+      margin-right: 50px;
+    }
+  }
+
+  @media (min-width: 1200px) {
+    .content-block {
+      max-width: 1100px;
+      margin-left: auto;
+      margin-right: auto;
+    }
+  }
+
+  .hero-banner {
+    position: relative;
+    display: flex;
+    justify-content: center;
+    color: var(--stan-hero);
+    background-color: var(--stan-hero-bg);
+    border: 10px solid var(--stan-secondary);
+  }
+
+  .hero-banner h1 {
+    font-size: 2.5rem;
+    margin-top: 1rem;
+    text-align: center;
+  }
+
+  .hero-banner .content-block {
+    padding-top: 0;
+  }
+
+  .hero-code {
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    padding-bottom: 1rem;
+    padding-top: 1rem;
+  }
+
+  .hero-code .sourceCode {
+    border-bottom-left-radius: 5px;
+    border-bottom-right-radius: 5px;
+  }
+
+  .hero-code pre,
+  .hero-code code {
+    color: var(--bs-body-color);
+    padding: 0.25em;
+  }
+
+  .hero-code .code-with-filename-file {
+    border: 1px solid rgba(233, 236, 239, 0.2);
+    border-top-left-radius: 5px;
+    border-top-right-radius: 5px;
+    background-color: var(--stan-secondary);
+  }
+  .hero-code .code-with-filename-file pre {
+    background-color: inherit;
+    color: var(--stan-hero);
+  }

index.qmd

@@ -11,26 +11,19 @@ aliases:
  - events/index.html
  - users/index.html
 
-
+css: index.css
+code-copy: false
 ---
 
 
 ::: {.hero-banner}
-::: {.grid}
-::: {.g-col-1}
-:::
-::: {.g-col-8 }
+:::: {.content-block}
+
 # Stan: Software for Bayesian Data Analysis
-:::
-:::
-:::
 
+::::: {.hero-text .grid}
+:::::: {.g-col-12 .g-col-md-8}
 
-::: {.second-banner}
-::: {.grid}
-::: {.g-col-1}
-:::
-::: {.g-col-8}
 ### Bayesian Modeling
 
 Stan enables sophisticated statistical modeling using Bayesian inference, allowing for more accurate and interpretable results in complex data scenarios.
@@ -44,45 +37,52 @@ Stan's probabilistic programming language is suitable for a wide range of applic
 Interfaces for Python, Julia, R, and the Unix shell make it easy to use Stan in any programming environment,
 on  laptops, clusters, or in the cloud.  A rich ecosystem of tools for validation and visualization support
 decision-making and communication.
-
-::: {.hero-buttons style="position: relative; display: flex; justify-content: center;"}
+::::::
+
+:::::: {.g-col-12 .g-col-md-4 .hero-code}
+
+```{.stan filename="bernoulli.stan"}
+data {
+  int<lower=0> N;
+  array[N] int<lower=0, upper=1> y;
+}
+parameters {
+  real<lower=0, upper=1> theta;
+}
+model {
+  // uniform prior on interval 0,1
+  theta ~ beta(1, 1);
+  y ~ bernoulli(theta);
+}
+```
+
+::::::
+
+:::::
+::::: {.hero-buttons style="position: relative; display: flex; justify-content: center;"}
 [Get Started](install/){.btn-action-primary .btn-action .btn .btn-success .btn-lg role="button"}
+:::::
+::::
 :::
 
-:::
-:::
-:::
 
 
+::: {.content-block}
 
-::: {.second-banner}
-::: {.grid}
-::: {.g-col-1}
-:::
-::: {.g-col-8}
-## Community Resources
+### Community Resources
 * The Stan [forums](https://discourse.mc-stan.org) provide support for all user levels and topics, from installing software, to writing Stan programs, to advanced Bayesian modeling techniques and methodology.
 
 * Stan's [documentation](https://mc-stan.org/docs), [tutorials](learn-stan/tutorials.qmd), and [case studies](learn-stan/case-studies.qmd) help users learn and use Stan effectively in their own projects.
 The [Prior Choice Recommendations](https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations) wiki page provides guidance on appropriate priors for use with Stan.
-:::
-:::
-:::
 
-::: {.second-banner}
-::: {.grid}
-::: {.g-col-1}
-:::
+---
 
-::: {.g-col-8}
-## Developer Resources
+### Developer Resources
 * The [Stan Developer Wiki](https://github.com/stan-dev/stan/wiki)
 
 * The [Stan Forums Developers category](https://discourse.mc-stan.org/c/stan-dev/10)
 
 * The Stan slack channel [mc-stan.slack.com](https://join.slack.com/t/mc-stan/shared_invite/zt-1le4ebi4m-UMtiOkJb4gcS16qz2wIYCw)
 is for informal developer discussions.
-:::
-:::
-:::
 
+:::

learn-stan/case-studies.qmd

@@ -8,6 +8,35 @@ aliases:
 
 The case studies on this page are intended to reflect best practices in Bayesian methodology and Stan programming. We aim to keep them current with the latest version of the Stan language, but there may be times when case studies need updating to reflect the latest Stan features and syntax.
 
+
+## Volume 11 (2025)
+
+### The Sum-to-Zero Constraint in Stan
+
+The [`sum_to_zero_vector`](https://mc-stan.org/docs/reference-manual/transforms.html#zero-sum-vector)
+constrained parameter type was introduced in the [Stan 2.36 release](https://github.com/stan-dev/cmdstan/releases/tag/v2.36.0).
+This case study demonstrates the efficiency and robustness of this constrained type; how to adjust the marginal variances for a normal prior, and how to implement the sum-to-zero constraining transform as a Stan function, to extend its use beyond a simple vector.
+
+<a href="case-studies/sum_to_zero_vector.html" target="_blank" rel="noopener noreferrer">View HTML</a>
+*(link opens in new tab)*
+
+Author
+: Mitzi Morris
+
+Keywords
+: sum-to-zero, group-level categorical predictors, spatial models
+
+Source Repository
+: [example-models/jupyter/sum-to-zero](https://github.com/stan-dev/example-models/tree/master/jupyter/sum-to-zero){target="_blank"}
+(GitHub)
+
+Dependencies
+: `cmdstanpy`, `numpy`, `pandas`, `geopandas`, `libpysal`, `plotnine`
+
+License
+:  BSD (3 clause), CC-BY
+
+
 ## Volume 10 (2023)
 
 ### Instrumental Variables Analysis of Randomized Experiments with One-Sided Noncompliance
@@ -466,7 +495,7 @@ Keywords
 equations, posterior predictive checks
 
 Source Repository
-: [stan-dev/example-models/knitr/lotka-volterra](){target="_blank"}
+: [stan-dev/example-models/knitr/lotka-volterra](https://github.com/stan-dev/example-models/tree/master/knitr/lotka-volterra){target="_blank"}
 (GitHub)
 
 R Package Dependencies

learn-stan/case-studies/sum_to_zero_vector.html

@@ -1,5 +1,5 @@
 ---
-title: StanCon Talks
+title: StanCon
 page-layout: full
 toc-location: right
 
@@ -15,30 +15,43 @@ aliases:
 * Location & Date: Oxford University, England -- September 9-13, 2024
 * [Program](stancon/StanCon2024-program.pdf){target="_blank"}
 * Recorded Talks: [YouTube playlist](https://www.youtube.com/playlist?list=PLCrWEzJgSUqzNzh6mjWsWUu-lSK59VXP6)
+* Keynotes:
+  + The Pragmatic Probabilistic Programmer -- Mitzi Morris
+  + Applied modeling for drug development -- Sebastian Weber
+  + From the Depths to the Stars: How Modeling Shark Movements Illuminates Star Behavior -- Vianey Leos Barajas
+  + Bayesian multilevel causal modelling of the frequency and implications of having two HIV infections -- Chris Wymant
 * Tutorials  (not recorded)
   + Introduction to Stan -- Richard McElreath
   + Model selection -- Aki Vehtari, Noa Kallioinen, and Teemu Säilynoja
   + Bayesian hierarchical models in Stan -- Sean Pinkney
   + Bayesian optmization with Stan -- Anna Riha and Elizaveta Semenova
   + Biodiversity modeling and forecasting -- Will Pearse
   + Infectious disease modeling in Stan -- Juliette Unwin
-* Organizers: Charles Margossian, Will Pearse, 
+* Organizers: Michael Collyer, Ellen Mobbs, Joss Wright, Richard McElreath, Elizaveta Semenova, Ben Lambert, Seth Flaxman, Charles Margossian, Juliette Unwin, Will Pearse, Makkunda Sharma
+* Sponsors: Daiichi-Sankyo, Metrum Research Group, Generable, Jumping Rivers, Taylor and Francis, NumFocus, the Oxford Internet Institute, and the Max Planck Institute for Evolutionary Anthropology
+* [Archived event page](https://github.com/stan-dev/stan-dev.github.io/blob/df6b188d6e1057863dddf110c109c1b8bc51b36e/events/stancon2024/index.md)
 
 
 ## StanCon 2023 St. Louis
 
 * Location & Date: Washington University, USA -- June 20-23, 2023
 * [Program](stancon/StanCon2023-program.pdf){target="_blank"}
 * GitHub repository of slides and course materials from StanCon 2023: [https://github.com/stan-dev/stancon2023](https://github.com/stan-dev/stancon2023){target="_blank"}
+* Keynotes
+    + The efficient frontier: Bayes, neural nets, and the future of Stan -- Bob Carpenter
+    + We all can benefit from Bayesian analysis reporting guidelines if we use them -- John Kruschke
+    + Statistical Significance Makes our Mission: Impossible -- Mariel Finucane
+    + Regression Under Endogeneity: Bernstein-von Mises Theory and Bayes Factors Testing -- Siddhartha Chib
 * Tutorials
     + Fundamentals of Stan -- Charles Margossian
     + Bayesian workflow illustrated using BRMS -- Mitzi Morris
     + Hierarchical models in Stan: varieties, optimizations & nuances -- Mike Lawrence
     + Building a GPT in Stan -- Daniel Lee
     + Cognitive diagnostic models in R and Stan -- Jake Thompson
     + Advances of model assessment, selection, and inference after model selection --  Andrew Johnson
-* Organizers: Charles Margossian, Debashis Mondal, Yi Zhang, Eric Ward
-
+* Organizers: Charles Margossian, Debashis Mondal, Eric Ward, Vianey Leos Barajas, Yi Zhang
+* Sponsors: Washington University in St Louis, Metrum Research Group, NumFocus, Sage Therapeutics, Jumping Rivers
+* [Archived event page](https://github.com/stan-dev/stan-dev.github.io/blob/df6b188d6e1057863dddf110c109c1b8bc51b36e/events/stancon2023/index.md)
 
 ## StanCon 2020 Global
 

learn-stan/stancon-talks.qmd

@@ -2,7 +2,7 @@
 https://mc-stan.org/shop/index.html https://mc-stan.org/about/#shop-for-stan-swag
 https://mc-stan.org/about/team/index.html https://mc-stan.org/about/#stan-development-team
 https://mc-stan.org/about/developers/index.html https://mc-stan.org/about/#stan-development-team
-https://mc-stan.org/support/index.html https://mc-stan.org/about/#support-stan
+https://mc-stan.org/support/index.html https://mc-stan.org/about/#help-fund-stan
 https://mc-stan.org/events/stanconnect_Ecology1/index.html https://mc-stan.org/learn-stan/field-guides.html#stanconnect-sessions
 https://mc-stan.org/events/stanconnect_CogNeuro/index.html https://mc-stan.org/learn-stan/field-guides.html#stanconnect-sessions
 https://mc-stan.org/events/stanconnect_Biomedical/index.html https://mc-stan.org/learn-stan/field-guides.html#stanconnect-sessions

quarto-config

@@ -110,16 +110,18 @@ For detailed installation instructions see [Getting Started](../install/).
 
 | **Editor/IDE**         | **Tool** | **Description** |
 |------------------------|----------|-----------------|
-| **RStudio**            | **Built-in Support** | RStudio 1.2+ includes Stan syntax highlighting and code snippets.  [(Source code)](https://github.com/rstudio/rstudio/blob/main/src/gwt/acesupport/acemode/stan_highlight_rules.js){target="_blank"} |
-| **Visual Studio Code** | [**Stan VSCode Extension**](https://marketplace.visualstudio.com/items?itemName=ivan-bocharov.stan-vscode){target="_blank"} | Stan language support with syntax highlighting, autocompletion, and snippets. |
-| **Emacs**              | [**stan-mode**](https://github.com/stan-dev/stan-mode){target="_blank"} | Major mode for Stan with syntax highlighting and indentation. |
-| **Vim**                | [**stan-vim**](https://github.com/eigenfoo/stan-vim){target="_blank"} | Syntax highlighting, indentation, and code folding for Stan in Vim. |
-| **Atom**               | [**language-stan**](https://github.com/stan-dev/atom-language-stan){target="_blank"} | Stan language support in Atom editor. |
-| **Sublime Text**       | [**SublimeStan**](https://github.com/djsutherland/sublime-stan){target="_blank"} | Syntax highlighting for Stan in Sublime Text. |
-| **JupyterLab**         | [**jupyterlab-stan-highlight**](https://www.npmjs.com/package/jupyterlab-stan-highlight){target="_blank"} | Syntax highlighting for Stan code blocks in JupyterLab. |
-| **Javascript**         | [**Prism**](https://prismjs.com/){target="_blank"} </br> [**Highlight.js**](https://github.com/highlightjs/highlight.js){target="_blank"} | Lightweight syntax highlighting library - [(Source code)](https://github.com/PrismJS/prism/blob/master/components/prism-stan.js){target="_blank"}. </br> Syntax highlighter written in javascript - [(Source code)](https://github.com/highlightjs/highlight.js/blob/main/src/languages/stan.js){target="_blank"} |
- **Markdown Editors**   | [**Pandoc**](https://pandoc.org/){target="_blank"} </br> [**Pygments**](https://pygments.org/){target="_blank"} | Stan syntax highlighting for document formats. [(Source code)](https://invent.kde.org/frameworks/syntax-highlighting/-/blob/master/data/syntax/stan.xml)</br>Python highlighter for Stan code blocks [(Source code)](https://github.com/pygments/pygments/blob/master/pygments/lexers/modeling.py){target="_blank"} |
-| **LaTeX**              | [**lstbayes**](https://github.com/jrnold/lstbayes){target="_blank"} | LaTeX listings for Stan syntax highlighting. |
+| **RStudio**            | **Built-in Support** | RStudio 1.2+ includes Stan syntax highlighting and code snippets  [(Source code)](https://github.com/rstudio/rstudio/blob/main/src/gwt/acesupport/acemode/stan_highlight_rules.js){target="_blank"} |
+| **Visual Studio Code** | [**VSCode Stan Extension**](https://marketplace.visualstudio.com/items?itemName=wardbrian.vscode-stan-extension){target="_blank"} | Stan language support with syntax highlighting, linting, autocompletion, and snippets |
+| **Emacs**              | [**stan-mode**](https://github.com/stan-dev/stan-mode){target="_blank"} <br/> [**stan-ts-mode**](https://github.com/WardBrian/stan-ts-mode){target="_blank"} | Major mode for Stan with syntax highlighting and indentation <br /> Tree-sitter based (Emacs 29+) major mode for Stan. Fewer features than stan-mode, but generally more up to date syntax highlighting. |
+| **Vim**                | [**stan-vim**](https://github.com/eigenfoo/stan-vim){target="_blank"} | Syntax highlighting, indentation, and code folding for Stan in Vim |
+| **JupyterLab**         | [**jupyterlab-stan-highlight**](https://www.npmjs.com/package/jupyterlab-stan-highlight){target="_blank"} | Syntax highlighting for Stan code blocks in JupyterLab |
+| **Javascript**         | [**Prism**](https://prismjs.com/){target="_blank"} </br> [**Highlight.js**](https://github.com/highlightjs/highlight.js){target="_blank"} | Lightweight syntax highlighting library [(Source code)](https://github.com/PrismJS/prism/blob/master/components/prism-stan.js){target="_blank"} </br> Syntax highlighter written in javascript [(Source code)](https://github.com/highlightjs/highlight.js/blob/main/src/languages/stan.js){target="_blank"} |
+ **Markdown**   | [**Pandoc**](https://pandoc.org/){target="_blank"} </br> [**Pygments**](https://pygments.org/){target="_blank"} | Stan syntax highlighting for document formats [(Source code)](https://invent.kde.org/frameworks/syntax-highlighting/-/blob/master/data/syntax/stan.xml)</br>Python highlighter for Stan code blocks [(Source code)](https://github.com/pygments/pygments/blob/master/pygments/lexers/modeling.py){target="_blank"} |
+| **Zed**                | [**zed-stan-extension**](https://github.com/wardbrian/zed-stan-extension){target="_blank"} | Syntax highlighting for Stan in the Zed editor |
+| **LaTeX**              | [**lstbayes**](https://github.com/jrnold/lstbayes){target="_blank"} | LaTeX listings for Stan syntax highlighting |
+| **Sublime Text**       | [**SublimeStan**](https://github.com/djsutherland/sublime-stan){target="_blank"} | Syntax highlighting for Stan in Sublime Text |
+| **Atom**               | [**atom-language-stan**](https://github.com/stan-dev/atom-language-stan){target="_blank"} | Stan language support in Atom editor and GitHub.com |
+
 : {tbl-colwidths="[15, 25, 60]"}
 
 ---