Merge branch 'master' into functions-reference/link-to-to_int

Author: WardBrian

.gitattributes

@@ -0,0 +1 @@
+src/functions-reference/functions_index.qmd linguist-generated=true

.github/ISSUE_TEMPLATE.md

@@ -8,6 +8,3 @@ Describe the issue as clearly as possible.
 
 #### Additional Information:
 Provide any additional information here.
-
-#### Current Version:
-v2.18.0

src/bibtex/all.bib

@@ -1845,3 +1845,29 @@ @article{Timonen+etal:2023:ODE-PSIS
   pages = {e614} 
 }
 
+@article{egozcue+etal:2003,
+  title={Isometric logratio transformations for compositional data analysis},
+  author={Egozcue, Juan Jos{\'e} and Pawlowsky-Glahn, Vera and Mateu-Figueras, Gl{\`o}ria and Barcelo-Vidal, Carles},
+  journal={Mathematical Geology},
+  volume={35},
+  number={3},
+  pages={279--300},
+  year={2003}
+}
+
+@book{filzmoser+etal:2018,
+  title={Geometrical properties of compositional data},
+  author={Filzmoser, Peter and Hron, Karel and Templ, Matthias},
+  booktitle={Applied Compositional Data Analysis: With Worked Examples in R},
+  pages={35--68},
+  year={2018},
+  publisher={Springer}
+}
+
+@misc{seyboldt:2024,
+  author="Seyboldt, Adrian",
+  title="Add ZeroSumNormal distribution",
+  note="pyro-ppl GitHub repository issue \#1751",
+  year = "2024",
+  url ="https://github.com/pyro-ppl/numpyro/pull/1751#issuecomment-1980569811"
+}

src/cmdstan-guide/installation.qmd

@@ -27,10 +27,8 @@ Python bindings to CmdStan seamlessly. Additionally, it provides the
 command `cmdstan_model` to activate the CmdStan makefile from anywhere.
 
 _Note_: This requires that conda has been installed already on your machine.
-You can either install [miniconda](https://docs.conda.io/en/latest/miniconda.html), a free, minimal installer for conda
-or you can get the full [Anaconda](https://docs.continuum.io/anaconda/) system
-which provides graphical installer wizards for [MacOS](https://www.anaconda.com/products/distribution#macos)
-and [Windows](https://www.anaconda.com/products/distribution#windows) users.
+We recommend using the [miniforge](https://github.com/conda-forge/miniforge)
+distribution. 
 
 We recommend installing CmdStan in a new conda environment:
 
@@ -353,36 +351,39 @@ or cluster administrator to install these tools for you.
 
 #### MacOS
 
-To install a C++ development
-environment on a Mac, use Apple's Xcode development environment
-https://developer.apple.com/xcode/.
-
-From the [Xcode home page](https://developer.apple.com/xcode/)
-`View in Mac App Store`.
-
-- From the App Store, click `Install`, enter an Apple ID, and wait
-for Xcode to finish installing.
--  Open the Xcode application, click top-level menu `Preferences`,
-click top-row button `Downloads`, click button for
-`Components`, click on the `Install` button to the right of
-the `Command Line Tools` entry, then wait for it to finish
-installing.
-- Click the top-level menu item `Xcode`, then click item `Quit
-Xcode` to quit.
-
-To test, open the Terminal application and enter:
+To check if you already already have an appropriate toolchain
+installed, open the Terminal application and enter:
 ```
 clang++ --version
 make --version
 ```
 
-If you have installed XCode, but don't have `make`, you can install the
-XCode command-line tools via command:
+If either of these commands prints the message 
+`command not found`, you will need to install Xcode's
+command line tools.
+
+Open the Terminal application and enter:
+
 ```
 xcode-select --install
 ```
 
+Select "Install" in the window that opens.
+
+After the installation completes, you can double check that
+installation was successful by reopening the Terminal and 
+running:
+```
+clang++ --version
+make --version
+```
+
+You can read more about Xcode on its site: 
+[https://developer.apple.com/xcode/](https://developer.apple.com/xcode/)
 
+We don't recommend trying to use the GNU C++ compiler, available via Homebrew,
+based on the number of reports of installation difficulties from Mac users on GitHub
+as well as the Stan forums.
 
 #### Windows {#windows}
 

src/functions-reference/functions_index.qmd

@@ -1630,11 +1630,27 @@ proportion theta, defined by \begin{eqnarray*}
 \lambda_1, \ \log(1 - \theta) + \lambda_2\right). \end{eqnarray*}
 {{< since 2.6 >}}
 
-<!-- R; log_mix; (T1 theta, T2 lp1, T3 lp2); -->
-\index{{\tt \bfseries log\_mix }!{\tt (T1 theta, T2 lp1, T3 lp2): real}|hyperpage}
+<!-- R; log_mix; (T1 thetas, T2 lps); -->
+\index{{\tt \bfseries log\_mix }!{\tt (T1 thetas, T2 lps): real}|hyperpage}
+
+`R` **`log_mix`**`(T1 thetas, T2 lps)`<br>\newline
+
+Calculates the log mixture density given `thetas`,
+mixing proportions which should be between 0 and 1 and sum to 1,
+and `lps`, log densities.
+The `lps` variable must be either a 1-d container of the same
+length as `thetas`, or an array of such.
+
+\begin{eqnarray*}
+\mathrm{log\_mix}(\theta, \lambda)
+& = & \log \!\left( \sum_{n=1}^N \theta_n * \exp(\lambda_n) \right) \\[3pt]
+& = & \mathrm{log\_sum\_exp}\!\left(\log(\theta) + \lambda\right).
+\end{eqnarray*}
+
+This is a generalization of the above signature of three arguments to
+more than two densities.
+For example, `log_mix(lambda, lp1, lp2) == log_mix({lambda, 1 - lambda}, {lp1, lp2})`.
 
-`R` **`log_mix`**`(T1 theta, T2 lp1, T3 lp2)`<br>\newline
-Vectorized implementation of the `log_mix` function
 {{< since 2.26 >}}
 
 <!-- R; log_sum_exp; (T1 x, T2 y); -->

src/functions-reference/real-valued_basic_functions.qmd

@@ -586,3 +586,36 @@ The log Poisson probability mass of `y` given the log-rate `alpha + x * beta`.
 The log Poisson probability mass of `y` given the log-rate `alpha + x * beta`
 dropping constant additive terms.
 {{< since 2.25 >}}
+
+## Beta negative binomial distribution {#beta-neg-binomial}
+
+### Probability mass function
+
+If $r \in \mathbb{R}^+$, $\alpha \in \mathbb{R}^+$, and $\beta \in \mathbb{R}^+$, then for $n \in \mathbb{N}$, \begin{equation*}
+\text{BetaNegBinomial}(n|r,\alpha,\beta) = \frac {\Gamma (n+r )}{n!\;\Gamma (r )}
+\frac {\mathrm {B} (\beta+n,\alpha +r )}{\mathrm {B} (\beta,\alpha )}. \end{equation*}
+
+### Distribution statement
+
+`n ~ ` **`beta_neg_binomial`**`(r,alpha,beta)`
+
+Increment target log probability density with `beta_neg_binomial_lupmf(n | r, alpha, beta)`.
+{{< since 2.36 >}}
+<!-- real; beta_neg_binomial ~; -->
+\index{{\tt \bfseries beta\_neg\_binomial }!sampling statement|hyperpage}
+
+### Stan functions
+
+<!-- real; beta_neg_binomial_lpmf; (ints n | reals r, reals alpha, reals beta); -->
+\index{{\tt \bfseries beta\_neg\_binomial\_lpmf }!{\tt (ints n \textbar\ reals r, reals alpha, reals beta): real}|hyperpage}
+
+`real` **`beta_neg_binomial_lpmf`**`(ints n | reals r, reals alpha, reals beta)`<br>\newline
+The log beta negative binomial probability mass of `n` given parameters `r`, `alpha` and `beta`.
+{{< since 2.36 >}}
+
+<!-- real; beta_neg_binomial_lupmf; (ints n | reals r, reals alpha, reals beta); -->
+\index{{\tt \bfseries beta\_neg\_binomial\_lupmf }!{\tt (ints n \textbar\ reals r, reals alpha, reals beta): real}|hyperpage}
+
+`real` **`beta_neg_binomial_lupmf`**`(ints n | reals r, reals alpha, reals beta)`<br>\newline
+The log beta negative binomial probability mass of `n` given parameters `r`, `alpha` and `beta` dropping constant additive terms.
+{{< since 2.36 >}}

src/functions-reference/unbounded_discrete_distributions.qmd

@@ -149,9 +149,9 @@ any of the following.
 
 ```
 int, real, complex, vector, simplex, unit_vector,
-ordered, positive_ordered, row_vector, matrix,
-cholesky_factor_corr, cholesky_factor_cov,
-corr_matrix, cov_matrix, array
+sum_to_zero_vector, ordered, positive_ordered,
+row_vector, matrix, cholesky_factor_corr,
+cholesky_factor_cov, corr_matrix, cov_matrix, array
 ```
 
 The following built in functions are also reserved and
@@ -810,9 +810,9 @@ In addition to single integer indexes, as described in
 [the language indexing section](#language-indexing.section), Stan supports multiple indexing.
 Multiple indexes can be integer arrays of indexes, lower
 bounds, upper bounds, lower and upper bounds, or simply shorthand for
-all of the indexes.  If the upper bound is smaller than the lower bound, 
-the range is empty (unlike, e.g., in R). The upper bound and lower bound can be 
-expressions that evaluate to integer. A complete list of index types is 
+all of the indexes.  If the upper bound is smaller than the lower bound,
+the range is empty (unlike, e.g., in R). The upper bound and lower bound can be
+expressions that evaluate to integer. A complete list of index types is
 given in the following table.
 
 ##### Indexing Options Table {- #index-types-table}
@@ -1078,6 +1078,7 @@ the following table shows the mapping from types to their primitive types.
    | `vector`               | `vector`             |
    | `simplex`              | `vector`             |
    | `unit_vector`          | `vector`             |
+   | `sum_to_zero_vector`   | `vector`             |
    | `ordered`              | `vector`             |
    | `positive_ordered`     | `vector`             |
    | `row_vector`           | `row_vector`         |
@@ -1378,7 +1379,7 @@ model {
 }
 ```
 
-Algebraically, 
+Algebraically,
 [the distribution statement](statements.qmd#distribution-statements.section)
 in the model could be reduced to
 

src/reference-manual/expressions.qmd

@@ -24,6 +24,7 @@
 
 <identifier> ::= IDENTIFIER
                | TRUNCATE
+               | JACOBIAN
 
 <decl_identifier> ::= <identifier>
                     | <reserved_word>
@@ -57,10 +58,13 @@
                   | POSITIVEORDERED
                   | SIMPLEX
                   | UNITVECTOR
+                  | SUMTOZERO
                   | CHOLESKYFACTORCORR
                   | CHOLESKYFACTORCOV
                   | CORRMATRIX
                   | COVMATRIX
+                  | STOCHASTICCOLUMNMATRIX
+                  | STOCHASTICROWMATRIX
                   | PRINT
                   | REJECT
                   | FATAL_ERROR
@@ -165,11 +169,16 @@
                  | POSITIVEORDERED LBRACK <expression> RBRACK
                  | SIMPLEX LBRACK <expression> RBRACK
                  | UNITVECTOR LBRACK <expression> RBRACK
+                 | SUMTOZERO LBRACK <expression> RBRACK
                  | CHOLESKYFACTORCORR LBRACK <expression> RBRACK
                  | CHOLESKYFACTORCOV LBRACK <expression> [COMMA <expression>]
                    RBRACK
                  | CORRMATRIX LBRACK <expression> RBRACK
                  | COVMATRIX LBRACK <expression> RBRACK
+                 | STOCHASTICCOLUMNMATRIX LBRACK <expression> COMMA
+                   <expression> RBRACK
+                 | STOCHASTICROWMATRIX LBRACK <expression> COMMA <expression>
+                   RBRACK
 
 <type_constraint> ::= [LABRACK <range> RABRACK]
                     | LABRACK <offset_mult> RABRACK

src/reference-manual/grammar.txt

@@ -113,6 +113,7 @@ The raw output is available [here](https://raw.githubusercontent.com/stan-dev/do
 ```
 <identifier> ::= IDENTIFIER
                | TRUNCATE
+               | JACOBIAN
 
 <decl_identifier> ::= <identifier>
 
@@ -175,11 +176,16 @@ The raw output is available [here](https://raw.githubusercontent.com/stan-dev/do
                  | POSITIVEORDERED LBRACK <expression> RBRACK
                  | SIMPLEX LBRACK <expression> RBRACK
                  | UNITVECTOR LBRACK <expression> RBRACK
+                 | SUMTOZERO LBRACK <expression> RBRACK
                  | CHOLESKYFACTORCORR LBRACK <expression> RBRACK
                  | CHOLESKYFACTORCOV LBRACK <expression> [COMMA <expression>]
                    RBRACK
                  | CORRMATRIX LBRACK <expression> RBRACK
                  | COVMATRIX LBRACK <expression> RBRACK
+                 | STOCHASTICCOLUMNMATRIX LBRACK <expression> COMMA
+                   <expression> RBRACK
+                 | STOCHASTICROWMATRIX LBRACK <expression> COMMA <expression>
+                   RBRACK
 
 <type_constraint> ::= [LABRACK <range> RABRACK]
                     | LABRACK <offset_mult> RABRACK