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

Author: mitzimorris

Jenkinsfile

@@ -9,6 +9,7 @@ pipeline {
     parameters {
         string(defaultValue: '', name: 'major_version', description: "Major version of the docs to be built")
         string(defaultValue: '', name: 'minor_version', description: "Minor version of the docs to be built")
+        string(defaultValue: '', name: 'last_docs_version_dir', description: "Last docs version found in /docs. Example: 2_21")
     }
     environment {
         GITHUB_TOKEN = credentials('6e7c1e8f-ca2c-4b11-a70e-d934d3f6b681')
@@ -48,6 +49,11 @@ pipeline {
                 sh "python add_redirects.py $major_version $minor_version stan-users-guide"
             }
         }
+        stage("Link docs to latest") {
+            steps{
+                sh "add_links.sh $last_docs_version_dir"
+            }
+        }
         stage("Push PR for docs") {
             steps {
                 withCredentials([usernamePassword(credentialsId: 'a630aebc-6861-4e69-b497-fd7f496ec46b',

add_links.sh

@@ -1,9 +1,20 @@
 #!/usr/bin/env bash
 
-mkdir docs/2_20_tmp
-(cd docs/2_20; tar cf - .) | (cd docs/2_20_tmp; tar xvf - )
-python link_to_latest.py docs/2_20_tmp/stan-users-guide "Stan User's Guide"
-python link_to_latest.py docs/2_20_tmp/reference-manual "Stan Reference Manual"
-python link_to_latest.py docs/2_20_tmp/functions-reference "Stan Functions Reference"
-mv docs/2_20 docs/2_20_bak
-mv docs/2_20_tmp/ docs/2_20
+### USAGE
+# add_links.sh last_docs_version_dir
+# add_links.sh 2_21
+
+directory="$1"
+
+mkdir docs/"$directory"_tmp
+
+(cd docs/"$directory"; tar cf - .) | (cd docs/"$directory"_tmp; tar xvf - )
+
+python link_to_latest.py docs/"$directory"_tmp/stan-users-guide "Stan User's Guide"
+python link_to_latest.py docs/"$directory"_tmp/reference-manual "Stan Reference Manual"
+python link_to_latest.py docs/"$directory"_tmp/functions-reference "Stan Functions Reference"
+
+mv docs/"$directory" docs/"$directory"_bak
+mv docs/"$directory"_tmp/ docs/"$directory"
+
+rm -r "$directory"_tmp

src/functions-reference/array_operations.Rmd

@@ -3,10 +3,11 @@
 ```{r results='asis', echo=FALSE}
 if (knitr::is_html_output()) {
 cat(' * <a href="array-reductions.html">Reductions</a>\n')
-cat(' * <a href="array-size-and-dimension-function.html">Array Size and Dimension Function</a>\n')
-cat(' * <a href="array-broadcasting.html">Array Broadcasting</a>\n')
-cat(' * <a href="array-concatenation.html">Array Concatenation</a>\n')
+cat(' * <a href="array-size-and-dimension-function.html">Array size and dimension function</a>\n')
+cat(' * <a href="array-broadcasting.html">Array broadcasting</a>\n')
+cat(' * <a href="array-concatenation.html">Array concatenation</a>\n')
 cat(' * <a href="sorting-functions.html">Sorting functions</a>\n')
+cat(' * <a href="reversing-functions.html">Reversing functions</a>\n')
 }
 ```
 
@@ -178,7 +179,7 @@ The squared Euclidean distance between x and y
 `real` **`squared_distance`**`(row_vector x, row_vector[] y)`<br>\newline
 The Euclidean distance between x and y
 
-## Array Size and Dimension Function
+## Array size and dimension function
 
 The size of an array or matrix can be obtained using the `dims()`
 function.  The `dims()` function is defined to take an argument
@@ -236,7 +237,7 @@ can be any type, but the size is just the size of the top level array,
 not the total number of elements contained. For example, if `x` is of
 type `real[4,3]` then `size(x)` is 4.
 
-## Array Broadcasting {#array-broadcasting}
+## Array broadcasting {#array-broadcasting}
 
 The following operations create arrays by repeating elements to fill
 an array of a specified size.  These operations work for all input
@@ -312,7 +313,7 @@ After the assignment to `b`, the value for `b[j,k,m,n]` is equal to
 `a[m,n]` where it is defined, for `j` in `1:3`, `k` in `1:4`, `m` in
 `1:5`, and `n` in `1:6`.
 
-## Array Concatenation {#array-concatenation}
+## Array concatenation {#array-concatenation}
 
 <!-- T; append_array; (T x, T y); -->
 \index{{\tt \bfseries append\_array }!{\tt (T x, T y): T}|hyperpage}
@@ -409,3 +410,16 @@ Number of components of v less than v[s]
 `int` **`rank`**`(int[] v, int s)`<br>\newline
 Number of components of v less than v[s]
 
+## Reversing functions {#reversing-functions}
+
+Stan provides functions to create a new array by reversing the order of
+elements in an existing array. For example, if `v` is declared as a real
+array of size 3, with values
+\[ \text{v} = (1,\, -10.3,\, 20.987), \] then
+\[ \mathrm{reverse(v)} = (20.987,\, -10.3,\, 1). \]
+
+<!-- T[]; reverse; (T[] v); -->
+\index{{\tt \bfseries reverse }!{\tt (T[] v): T[]}|hyperpage}
+
+`T[]` **`reverse`**`(T[] v)`<br>\newline
+Return a new array containing the elements of the argument in reverse order.

src/functions-reference/higher-order_functions.Rmd

@@ -329,16 +329,16 @@ integrator separates parameter values, `theta`, from data values, `x_r`.
 
 ### Call to the 1D Integrator
 
-<!-- vector; integrate_1d; (function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i); -->
-\index{{\tt \bfseries integrate\_1d }!{\tt (function integrand, real a, real b, real[] theta, real[] x\_r, int[] x\_i): vector}|hyperpage}
+<!-- real; integrate_1d; (function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i); -->
+\index{{\tt \bfseries integrate\_1d }!{\tt (function integrand, real a, real b, real[] theta, real[] x\_r, int[] x\_i): real}|hyperpage}
 
-`vector` **`integrate_1d`** `(function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i)`<br>\newline
+`real` **`integrate_1d`** `(function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i)`<br>\newline
 Integrates the integrand from a to b.
 
-<!-- vector; integrate_1d; (function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i), real relative_tolerance); -->
-\index{{\tt \bfseries integrate\_1d }!{\tt (function integrand, real a, real b, real[] theta, real[] x\_r, int[] x\_i, real relative\_tolerance): vector}|hyperpage}
+<!-- real; integrate_1d; (function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i), real relative_tolerance); -->
+\index{{\tt \bfseries integrate\_1d }!{\tt (function integrand, real a, real b, real[] theta, real[] x\_r, int[] x\_i, real relative\_tolerance): real}|hyperpage}
 
-`vector` **`integrate_1d`** `(function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i, real relative_tolerance)`<br>\newline
+`real` **`integrate_1d`** `(function integrand, real a, real b, real[] theta, real[] x_r, int[] x_i, real relative_tolerance)`<br>\newline
 Integrates the integrand from a to b with the given relative tolerance.
 
 

src/functions-reference/matrix_operations.Rmd

@@ -16,6 +16,7 @@ cat(' * <a href="softmax.html">Special Matrix Functions</a>\n')
 cat(' * <a href="covariance.html">Covariance Functions</a>\n')
 cat(' * <a href="linear-algebra-functions-and-solvers.html">Linear Algebra Functions and Solvers</a>\n')
 cat(' * <a href="sort-functions.html">Sort Functions</a>\n')
+cat(' * <a href="reverse-functions.html">Reverse Functions</a>\n')
 }
 ```
 
@@ -1544,8 +1545,8 @@ The singular values of A in descending order
 
 ## Sort Functions
 
-see section [sorting functions](#sorting-functions) for examples of how the functions
-work.
+See the [sorting functions section](#sorting-functions) for examples of how
+the functions work.
 
 <!-- vector; sort_asc; (vector v); -->
 \index{{\tt \bfseries sort\_asc }!{\tt (vector v): vector}|hyperpage}
@@ -1611,3 +1612,16 @@ Number of components of v less than v[s]
 `int` **`rank`**`(row_vector v, int s)`<br>\newline
 Number of components of v less than v[s]
 
+## Reverse Functions {#reverse-functions}
+
+<!-- vector; reverse; (vector v); -->
+\index{{\tt \bfseries reverse }!{\tt (vector v): vector}|hyperpage}
+
+`vector` **`reverse`**`(vector v)`<br>\newline
+Return a new vector containing the elements of the argument in reverse order.
+
+<!-- row_vector; reverse; (row_vector v); -->
+\index{{\tt \bfseries reverse }!{\tt (row_vector v): row_vector}|hyperpage}
+
+`row_vector` **`reverse`**`(row_vector v)`<br>\newline
+Return a new row vector containing the elements of the argument in reverse order.

src/reference-manual/analysis.Rmd

@@ -85,9 +85,8 @@ $\theta$ and real- and discrete-valued data $y$.^[Using vectors simplifies high
 
 An MCMC *sample* consists of a set of a sequence of $M$ Markov chains,
 each consisting of an ordered sequence of $N$ *draws* from the
-posterior.^[The structure is assumed to be rectangular;  in the
-future, this needs to be generalized to ragged samples.]  The sample
-thus consists of $M \times N$ draws from the posterior.
+posterior.^[The structure is assumed to be rectangular; in the future, this needs to be generalized to ragged samples.]
+The sample thus consists of $M \times N$ draws from the posterior.
 
 
 ### Potential Scale Reduction
@@ -189,10 +188,7 @@ quantities.  The short answer is "no," but this is elaborated
 further in this section.
 
 For example, consider the value `lp__`, which is the log posterior
-density (up to a constant).^[The `lp__` value also represents the
-potential energy in the Hamiltonian system and is rate bounded by the
-randomly supplied kinetic energy each iteration, which follows a
-Chi-square distribution in the number of parameters.]
+density (up to a constant).^[The `lp__` value also represents the potential energy in the Hamiltonian system and is rate bounded by the randomly supplied kinetic energy each iteration, which follows a Chi-square distribution in the number of parameters.]
 
 It is thus a mistake to declare convergence in any practical sense if
 `lp__` has not converged, because different chains are really in

src/reference-manual/statements.Rmd

@@ -800,11 +800,7 @@ Such reassignment is not permitted in BUGS.  In BUGS, for loops are
 declarative, defining plates in directed graphical model notation,
 which can be thought of as repeated substructures in the graphical
 model.  Therefore, it is illegal in BUGS or JAGS to have a for loop
-that repeatedly reassigns a value to a variable.^[A programming idiom
-in BUGS code simulates a local variable by replacing `theta` in the
-above example with `theta[n]`, effectively creating `N` different
-variables, `theta[1]`, ..., `theta[N]`.  Of course, this is not a hack
-if the value of `theta[n]` is required for all `n`.]
+that repeatedly reassigns a value to a variable.^[A programming idiom in BUGS code simulates a local variable by replacing `theta` in the above example with `theta[n]`, effectively creating `N` different variables, `theta[1]`, ..., `theta[N]`.  Of course, this is not a hack if the value of `theta[n]` is required for all `n`.]
 
 In Stan, assignments are executed in the order they are encountered.
 As a consequence, the following Stan program has a very different
@@ -987,8 +983,8 @@ for (n in 1:N) {
 }
 ```
 
-The open curly bracket (`\{`) is the first character of the block
-and the close curly bracket (`\`}) is the last character.
+The open curly bracket (`{`) is the first character of the block
+and the close curly bracket (`}`) is the last character.
 
 Because whitespace is ignored in Stan, the following program will
 not compile.