Fix various spelling mistakes

src/doxygen/doxygen-footer.html

@@ -1,5 +1,5 @@
 <hr/>
-<div class="conents" style="font-size:80%;">
+<div class="contents" style="font-size:80%;">
   <span style="float:left; margin=0 1em 0 1em;">
   &nbsp;&nbsp;&nbsp;&nbsp;
   [ <a href="http://mc-stan.org/">Stan Home Page</a> ]

src/doxygen/doxygen.cfg

@@ -1076,7 +1076,7 @@ HTML_STYLESHEET        =
 # cascading style sheets that are included after the standard style sheets
 # created by doxygen. Using this option one can overrule certain style aspects.
 # This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefor more robust against future updates.
+# standard style sheet and is therefore more robust against future updates.
 # Doxygen will copy the style sheet files to the output directory.
 # Note: The order of the extra stylesheet files is of importance (e.g. the last
 # stylesheet in the list overrules the setting of the previous ones in the
@@ -1619,8 +1619,8 @@ EXTRA_PACKAGES         = amsmath
 # Note: Only use a user-defined header if you know what you are doing! The
 # following commands have a special meaning inside the header: $title,
 # $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
-# for the replacement values of the other commands the user is refered to
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty string,
+# for the replacement values of the other commands the user is referred to
 # HTML_HEADER.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 

src/stan/io/json/json_data.hpp

@@ -28,7 +28,7 @@ namespace json {
  * <p>The dimensions and values of variables are accessed by variable name.
  * The values of a variable are stored as a vector of values and
  * a vector of array dimensions, where a scalar value consists of
- * a single value and an emtpy vector for the dimensionality.
+ * a single value and an empty vector for the dimensionality.
  * Multidimensional arrays are stored in column-major order,
  * meaning the first index changes the most quickly.
  * If all the values of an array are int values, the array will be
@@ -121,7 +121,7 @@ class json_data : public stan::io::var_context {
   }
 
   /**
-   * Read out the complex values for the variable with the specifed
+   * Read out the complex values for the variable with the specified
    * name and return a flat vector of complex values.
    *
    * @param name Name of Variable of type string.

src/stan/io/json/json_data_handler.hpp

@@ -552,7 +552,7 @@ class json_data_handler : public stan::json::json_handler {
 
   /** For a start array ("[") event we first check that we're not currently
    *  processing the values in an array.  We need to do this because JSON
-   *  doesn't distinguish lists of heterogenous elements and arrays.
+   *  doesn't distinguish lists of heterogeneous elements and arrays.
    *  Then we add or update the dimensions of the array variable.
    */
   void start_array() {

src/stan/mcmc/hmc/nuts/base_nuts.hpp

@@ -194,7 +194,7 @@ class base_nuts : public base_hmc<Model, Hamiltonian, Integrator, BaseRNG> {
 
     this->n_leapfrog_ = n_leapfrog;
 
-    // Compute average acceptance probabilty across entire trajectory,
+    // Compute average acceptance probability across entire trajectory,
     // even over subtrees that may have been rejected
     double accept_prob = sum_metro_prob / static_cast<double>(n_leapfrog);
 

src/stan/mcmc/hmc/xhmc/base_xhmc.hpp

@@ -115,7 +115,7 @@ class base_xhmc : public base_hmc<Model, Hamiltonian, Integrator, BaseRNG> {
 
     this->n_leapfrog_ = n_leapfrog;
 
-    // Compute average acceptance probabilty across entire trajectory,
+    // Compute average acceptance probability across entire trajectory,
     // even over subtrees that may have been rejected
     double accept_prob = sum_metro_prob / static_cast<double>(n_leapfrog + 1);
 

src/stan/model/indexing/assign_cl.hpp

@@ -52,7 +52,7 @@ inline const char* print_index_type(const stan::math::matrix_cl<int>&) {
  * of the assignment
  * @tparam ExprRhs type of the prim expression on the right hand side of the
  * assignment
- * @tparam RowIndex type of index (a Stan index type or `matrix_cl<int>` instad
+ * @tparam RowIndex type of index (a Stan index type or `matrix_cl<int>` instead
  * of `index_multi`)
  * @param[in,out] expr_lhs expression on the left hand side of the assignment
  * @param expr_rhs expression on the right hand side of the assignment
@@ -86,9 +86,9 @@ inline void assign(ExprLhs&& expr_lhs, ExprRhs&& expr_rhs, const char* name,
  * @tparam ExprRhs type of the prim expression on the right hand side of the
  * assignment
  * @tparam RowIndex type of row index (a Stan index type or `matrix_cl<int>`
- * instad of `index_multi`)
+ * instead of `index_multi`)
  * @tparam ColIndex type of column index (a Stan index type or `matrix_cl<int>`
- * instad of `index_multi`)
+ * instead of `index_multi`)
  * @param[in,out] expr_lhs expression on the left hand side of the assignment
  * @param expr_rhs expression on the right hand side of the assignment
  * @param name Name of lvalue variable
@@ -155,7 +155,7 @@ inline void assign(ExprLhs&& expr_lhs, const ScalRhs& scal_rhs,
  * @param expr_rhs expression on the right hand side of the assignment
  * @param name Name of lvalue variable
  * @param row_index index used for indexing `expr_lhs` (a Stan index type or
- * `matrix_cl<int>` instad of `index_multi`)
+ * `matrix_cl<int>` instead of `index_multi`)
  * @throw std::out_of_range If the index is out of bounds.
  * @throw std::invalid_argument If the right hand side size isn't the same as
  * the indexed left hand side size.
@@ -205,9 +205,9 @@ inline void assign(math::var_value<math::matrix_cl<double>>& expr_lhs,
  * @tparam ExprRhs type of the prim or rev expression on the right hand side of
  * the assignment
  * @tparam RowIndex type of row index (a Stan index type or `matrix_cl<int>`
- * instad of `index_multi`)
+ * instead of `index_multi`)
  * @tparam ColIndex type of column index (a Stan index type or `matrix_cl<int>`
- * instad of `index_multi`)
+ * instead of `index_multi`)
  * @param[in,out] expr_lhs expression on the left hand side of the assignment
  * @param expr_rhs expression on the right hand side of the assignment
  * @param name Name of lvalue variable

src/stan/model/indexing/rvalue.hpp

@@ -514,7 +514,7 @@ inline plain_type_t<EigMat> rvalue(EigMat&& x, const char* name,
 }
 
 /**
- * Return a column of a matrix with the range of the column specificed
+ * Return a column of a matrix with the range of the column specified
  *  by another index.
  *
  * Types:  matrix[Idx, uni] = vector

src/stan/model/prob_grad.hpp

@@ -75,7 +75,7 @@ class prob_grad {
   inline std::pair<int, int> param_range_i(size_t idx) const {
     if (idx <= param_ranges_i__.size()) {
       std::stringstream ss;
-      ss << "param_range_i(): No integer paramter at index " << idx;
+      ss << "param_range_i(): No integer parameter at index " << idx;
       std::string msg = ss.str();
       throw std::out_of_range(msg);
     }

src/stan/services/pathfinder/psis.hpp

@@ -234,7 +234,7 @@ template <typename EigArray, typename Logger>
 inline Eigen::Array<double, Eigen::Dynamic, 1> psis_weights(
     const EigArray& log_ratios, Eigen::Index tail_len, Logger& logger) {
   const auto S = log_ratios.size();
-  // shift log ratios for safer exponentation
+  // shift log ratios for safer exponentiation
   const double max_log_ratio = log_ratios.maxCoeff();
   Eigen::Array<double, Eigen::Dynamic, 1> llr_weights
       = log_ratios.array() - max_log_ratio;

src/stan/services/pathfinder/single.hpp

@@ -76,9 +76,9 @@ struct taylor_approx_t {
   Eigen::VectorXd x_center;  // Mean estimate
   double logdetcholHk;       // Log deteriminant of the cholesky
   Eigen::MatrixXd L_approx;  // Approximate choleskly
-  Eigen::MatrixXd Qk;  // Q of the QR decompositon. Only used for sparse approx
+  Eigen::MatrixXd Qk;  // Q of the QR decomposition. Only used for sparse approx
   Eigen::VectorXd alpha;  // diagonal of the initial inv hessian
-  bool use_full;  // boolean indicationg if full or sparse approx was used.
+  bool use_full;  // boolean indicating if full or sparse approx was used.
 };
 
 /**
@@ -829,7 +829,7 @@ inline auto pathfinder_lbfgs_single(
     if (refresh != 0) {
       logger.info(path_num + "Best Iter: [" + std::to_string(best_iteration)
                   + "] ELBO (" + std::to_string(elbo_best.elbo) + ")"
-                  + " evalutions: (" + std::to_string(num_evals) + ")");
+                  + " evaluations: (" + std::to_string(num_evals) + ")");
     }
   }
   Eigen::Array<double, Eigen::Dynamic, Eigen::Dynamic> constrained_draws_mat;