Fixing some spacing issues

stan/math/fwd/scal/fun/inc_beta.hpp

@@ -25,10 +25,10 @@ namespace stan {
       T d_a; T d_b; T d_x;
 
       grad_reg_inc_beta(d_a, d_b, a.val_, b.val_, x.val_,
-                    digamma(a.val_), digamma(b.val_),
-                    digamma(a.val_+b.val_),
-                    exp(lbeta(a.val_, b.val_)));
-      d_x = pow((1-x.val_), b.val_-1)*pow(x.val_, a.val_-1)
+                        digamma(a.val_), digamma(b.val_),
+                        digamma(a.val_ + b.val_),
+                        exp(lbeta(a.val_, b.val_)));
+      d_x = pow((1 - x.val_), b.val_-1) * pow(x.val_, a.val_ - 1)
         / exp(lbeta(a.val_, b.val_));
       return fvar<T>(inc_beta(a.val_, b.val_, x.val_),
                      a.d_ * d_a + b.d_ * d_b + x.d_ * d_x);

stan/math/memory/stack_alloc.hpp

@@ -37,7 +37,8 @@ namespace stan {
       // big fun to inline, but only called twice
       inline char* eight_byte_aligned_malloc(size_t size) {
         char* ptr = static_cast<char*>(malloc(size));
-        if (!ptr) return ptr;  // malloc failed to alloc
+        if (!ptr)
+          return ptr;  // malloc failed to alloc
         if (!is_aligned(ptr, 8U)) {
           std::stringstream s;
           s << "invalid alignment to 8 bytes, ptr="

stan/math/prim/arr/err/check_ordered.hpp

@@ -30,15 +30,15 @@ namespace stan {
                        const std::string& name,
                        const std::vector<T_y>& y) {
       for (size_t n = 1; n < y.size(); n++) {
-        if (!(y[n] > y[n-1])) {
+        if (!(y[n] > y[n - 1])) {
           std::ostringstream msg1;
           msg1 << "is not a valid ordered vector."
                << " The element at " << stan::error_index::value + n
                << " is ";
           std::string msg1_str(msg1.str());
           std::ostringstream msg2;
           msg2 << ", but should be greater than the previous element, "
-               << y[n-1];
+               << y[n - 1];
           std::string msg2_str(msg2.str());
           domain_error(function, name, y[n],
                        msg1_str.c_str(), msg2_str.c_str());

stan/math/prim/arr/fun/sum.hpp

@@ -16,7 +16,8 @@ namespace stan {
      */
     template <typename T>
     inline T sum(const std::vector<T>& xs) {
-      if (xs.size() == 0) return 0;
+      if (xs.size() == 0)
+        return 0;
       T sum(xs[0]);
       for (size_t i = 1; i < xs.size(); ++i)
         sum += xs[i];

stan/math/prim/arr/functor/integrate_ode_rk45.hpp

@@ -111,7 +111,7 @@ namespace stan {
       std::vector<double> ts_vec(ts.size() + 1);
       ts_vec[0] = t0;
       for (size_t n = 0; n < ts.size(); n++)
-        ts_vec[n+1] = ts[n];
+        ts_vec[n + 1] = ts[n];
 
       std::vector<std::vector<double> > y_coupled(ts_vec.size());
       coupled_ode_observer observer(y_coupled);

stan/math/prim/mat/err/check_ordered.hpp

@@ -36,15 +36,15 @@ namespace stan {
       typedef typename index_type<Matrix<T_y, Dynamic, 1> >::type size_t;
 
       for (size_t n = 1; n < y.size(); n++) {
-        if (!(y[n] > y[n-1])) {
+        if (!(y[n] > y[n - 1])) {
           std::ostringstream msg1;
           msg1 << "is not a valid ordered vector."
                << " The element at " << stan::error_index::value + n
                << " is ";
           std::string msg1_str(msg1.str());
           std::ostringstream msg2;
           msg2 << ", but should be greater than the previous element, "
-               << y[n-1];
+               << y[n - 1];
           std::string msg2_str(msg2.str());
           domain_error(function, name, y[n],
                        msg1_str.c_str(), msg2_str.c_str());

stan/math/prim/mat/fun/autocorrelation.hpp

@@ -15,7 +15,8 @@ namespace stan {
        * a minimum number of zeros are padded.
        */
       size_t fft_next_good_size(size_t N) {
-        if (N <= 2) return 2;
+        if (N <= 2)
+          return 2;
         while (true) {
           size_t m = N;
           while ((m % 2) == 0) m /= 2;

stan/math/prim/mat/fun/autocovariance.hpp

@@ -34,7 +34,7 @@ namespace stan {
                         Eigen::FFT<T>& fft) {
       autocorrelation(y, acov, fft);
 
-      T var = variance(y) * (y.size()-1) / y.size();
+      T var = variance(y) * (y.size() - 1) / y.size();
       for (size_t i = 0; i < y.size(); i++) {
         acov[i] *= var;
       }

stan/math/prim/mat/fun/block.hpp

@@ -24,9 +24,9 @@ namespace stan {
     block(const Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>& m,
           size_t i, size_t j, size_t nrows, size_t ncols) {
       check_row_index("block", "i", m, i);
-      check_row_index("block", "i+nrows-1", m, i+nrows-1);
+      check_row_index("block", "i+nrows-1", m, i + nrows - 1);
       check_column_index("block", "j", m, j);
-      check_column_index("block", "j+ncols-1", m, j+ncols-1);
+      check_column_index("block", "j+ncols-1", m, j + ncols - 1);
       return m.block(i - 1, j - 1, nrows, ncols);
     }
 

stan/math/prim/mat/fun/cholesky_corr_constrain.hpp

@@ -26,7 +26,8 @@ namespace stan {
       for (int i = 0; i < k_choose_2; ++i)
         z(i) = corr_constrain(y(i));
       Matrix<T, Dynamic, Dynamic> x(K, K);
-      if (K == 0) return x;
+      if (K == 0)
+        return x;
       T zero(0);
       for (int j = 1; j < K; ++j)
         for (int i = 0; i < j; ++i)
@@ -62,7 +63,8 @@ namespace stan {
       for (int i = 0; i < k_choose_2; ++i)
         z(i) = corr_constrain(y(i), lp);
       Matrix<T, Dynamic, Dynamic> x(K, K);
-      if (K == 0) return x;
+      if (K == 0)
+        return x;
       T zero(0);
       for (int j = 1; j < K; ++j)
         for (int i = 0; i < j; ++i)

stan/math/prim/mat/fun/corr_matrix_free.hpp

@@ -46,7 +46,7 @@ namespace stan {
       typedef typename index_type<Matrix<T, Dynamic, 1> >::type size_type;
 
       size_type k = y.rows();
-      size_type k_choose_2 = (k * (k-1)) / 2;
+      size_type k_choose_2 = (k * (k - 1)) / 2;
       Array<T, Dynamic, 1> x(k_choose_2);
       Array<T, Dynamic, 1> sds(k);
       bool successful = factor_cov_matrix(y, x, sds);

stan/math/prim/mat/fun/cov_matrix_free_lkj.hpp

@@ -40,7 +40,7 @@ namespace stan {
       check_nonzero_size("cov_matrix_free_lkj", "y", y);
       check_square("cov_matrix_free_lkj", "y", y);
       size_type k = y.rows();
-      size_type k_choose_2 = (k * (k-1)) / 2;
+      size_type k_choose_2 = (k * (k - 1)) / 2;
       Array<T, Dynamic, 1> cpcs(k_choose_2);
       Array<T, Dynamic, 1> sds(k);
       bool successful = factor_cov_matrix(y, cpcs, sds);

stan/math/prim/mat/fun/csr_to_dense_matrix.hpp

@@ -15,7 +15,7 @@ namespace stan {
     /** \addtogroup csr_format
      *  @{
      */
-    /** 
+    /**
      * Construct a dense Eigen matrix from the CSR format components.
      *
      * @tparam T Type of matrix entries.
@@ -44,10 +44,10 @@ namespace stan {
 
       check_positive("csr_to_dense_matrix", "m", m);
       check_positive("csr_to_dense_matrix", "n", n);
-      check_size_match("csr_to_dense_matrix", "m", m, "u", u.size()-1);
+      check_size_match("csr_to_dense_matrix", "m", m, "u", u.size() - 1);
       check_size_match("csr_to_dense_matrix", "w", w.size(), "v", v.size());
       check_size_match("csr_to_dense_matrix", "u/z",
-                       u[m-1] + csr_u_to_z(u, m - 1) - 1,
+                       u[m - 1] + csr_u_to_z(u, m - 1) - 1,
                        "v", v.size());
       for (size_t i = 0; i < v.size(); ++i)
         check_range("csr_to_dense_matrix", "v[]", n, v[i]);

stan/math/prim/mat/fun/cumulative_sum.hpp

@@ -26,7 +26,7 @@ namespace stan {
         return result;
       result[0] = x[0];
       for (size_t i = 1; i < result.size(); ++i)
-        result[i] = x[i] + result[i-1];
+        result[i] = x[i] + result[i - 1];
       return result;
     }
 
@@ -52,7 +52,7 @@ namespace stan {
         return result;
       result(0) = m(0);
       for (int i = 1; i < result.size(); ++i)
-        result(i) = m(i) + result(i-1);
+        result(i) = m(i) + result(i - 1);
       return result;
     }
   }

stan/math/prim/mat/fun/factor_U.hpp

@@ -48,7 +48,7 @@ namespace stan {
         CPCs.segment(position, pull) = temp;
         acc.tail(pull) *= 1.0 - temp.square();
       }
-      CPCs = 0.5 * ( (1.0 + CPCs) / (1.0 - CPCs) ).log();  // now unbounded
+      CPCs = 0.5 * ((1.0 + CPCs) / (1.0 - CPCs)).log();  // now unbounded
     }
 
   }

stan/math/prim/mat/fun/factor_cov_matrix.hpp

@@ -29,7 +29,8 @@ namespace stan {
       size_t K = sds.rows();
 
       sds = Sigma.diagonal().array();
-      if ( (sds <= 0.0).any() ) return false;
+      if ((sds <= 0.0).any())
+        return false;
       sds = sds.sqrt();
 
       Eigen::DiagonalMatrix<T, Eigen::Dynamic> D(K);

stan/math/prim/mat/fun/get_base1.hpp

@@ -58,7 +58,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, error_msg, idx + 1);
     }
 
     /**
@@ -87,7 +87,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, error_msg, idx + 1);
     }
 
     /**
@@ -118,7 +118,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, i4, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, i4, error_msg, idx + 1);
     }
 
     /**
@@ -152,7 +152,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, i4, i5, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, i4, i5, error_msg, idx + 1);
     }
 
     /**
@@ -188,7 +188,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, error_msg, idx + 1);
     }
 
     /**
@@ -226,7 +226,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, i7, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, i7, error_msg, idx + 1);
     }
 
     /**
@@ -267,7 +267,8 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, i7, i8, error_msg, idx+1);
+      return get_base1(x[i1 - 1], i2, i3, i4, i5, i6, i7, i8, error_msg,
+                       idx + 1);
     }
 
     /**
@@ -297,7 +298,7 @@ namespace stan {
               const std::string& error_msg,
               size_t idx) {
       check_range("[]", "rows of x", x.rows(), m, idx, error_msg);
-      return x.block(m-1, 0, 1, x.cols());
+      return x.block(m - 1, 0, 1, x.cols());
     }
 
     /**

stan/math/prim/mat/fun/get_base1_lhs.hpp

@@ -87,7 +87,7 @@ namespace stan {
                      const std::string& error_msg,
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1_lhs(x[i1 - 1], i2, i3, error_msg, idx+1);
+      return get_base1_lhs(x[i1 - 1], i2, i3, error_msg, idx + 1);
     }
 
     /**
@@ -119,7 +119,7 @@ namespace stan {
                      const std::string& error_msg,
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1_lhs(x[i1 - 1], i2, i3, i4, error_msg, idx+1);
+      return get_base1_lhs(x[i1 - 1], i2, i3, i4, error_msg, idx + 1);
     }
 
     /**
@@ -153,7 +153,7 @@ namespace stan {
                      const std::string& error_msg,
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, error_msg, idx+1);
+      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, error_msg, idx + 1);
     }
 
     /**
@@ -189,7 +189,7 @@ namespace stan {
                      const std::string& error_msg,
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, i6, error_msg, idx+1);
+      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, i6, error_msg, idx + 1);
     }
 
     /**
@@ -228,7 +228,8 @@ namespace stan {
                      const std::string& error_msg,
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
-      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, i6, i7, error_msg, idx+1);
+      return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, i6, i7, error_msg,
+                           idx + 1);
     }
 
     /**
@@ -270,7 +271,7 @@ namespace stan {
                      size_t idx) {
       check_range("[]", "x", x.size(), i1, idx, error_msg);
       return get_base1_lhs(x[i1 - 1], i2, i3, i4, i5, i6, i7, i8,
-                           error_msg, idx+1);
+                           error_msg, idx + 1);
     }
 
     /**
@@ -301,7 +302,7 @@ namespace stan {
                   const std::string& error_msg,
                   size_t idx) {
       check_range("[]", "rows of x", x.rows(), m, idx, error_msg);
-      return x.block(m-1, 0, 1, x.cols());
+      return x.block(m - 1, 0, 1, x.cols());
     }
 
     /**

stan/math/prim/mat/fun/ordered_constrain.hpp

@@ -32,7 +32,7 @@ namespace stan {
         return y;
       y[0] = x[0];
       for (size_type i = 1; i < k; ++i)
-        y[i] = y[i-1] + exp(x[i]);
+        y[i] = y[i - 1] + exp(x[i]);
       return y;
     }
 

stan/math/prim/mat/fun/ordered_free.hpp

@@ -37,7 +37,7 @@ namespace stan {
         return x;
       x[0] = y[0];
       for (size_type i = 1; i < k; ++i)
-        x[i] = log(y[i] - y[i-1]);
+        x[i] = log(y[i] - y[i - 1]);
       return x;
     }
   }

stan/math/prim/mat/fun/positive_ordered_constrain.hpp

@@ -31,7 +31,7 @@ namespace stan {
         return y;
       y[0] = exp(x[0]);
       for (size_type i = 1; i < k; ++i)
-        y[i] = y[i-1] + exp(x[i]);
+        y[i] = y[i - 1] + exp(x[i]);
       return y;
     }
 

stan/math/prim/mat/fun/positive_ordered_free.hpp

@@ -38,7 +38,7 @@ namespace stan {
         return x;
       x[0] = log(y[0]);
       for (size_type i = 1; i < k; ++i)
-        x[i] = log(y[i] - y[i-1]);
+        x[i] = log(y[i] - y[i - 1]);
       return x;
     }
   }