Merge commit 'f27abb080e30808b4aa079efdabff712bfe310e9' as 'cmdstan/s…

…tan/lib/stan_math/stan/math/torsten'

cmdstan/stan/lib/stan_math/stan/math/torsten/.gitignore

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+# Ignore all
+# *
+
+# Unignore all dirs
+!*/
+
+# ignore all temp tilder files
+*.*~
+
+# ignore test binaries
+*_test
+
+### Above combination will ignore all files without extension ###
+
+# specific types to ignore
+*.d
+*.o
+*.cpp~
+*.hpp~
+*.xml
+
+# specific folders to ignore
+*.dSYM/

cmdstan/stan/lib/stan_math/stan/math/torsten/LICENSE.txt

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+Copyright (c) 2015--2018, Torsten Developers and their Assignees
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+   * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+   * Neither the name of Columbia University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cmdstan/stan/lib/stan_math/stan/math/torsten/PKModel/ExtractVector.hpp

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+#ifndef STAN_MATH_TORSTEN_PKMODEL_EXTRACTVECTOR_HPP
+#define STAN_MATH_TORSTEN_PKMODEL_EXTRACTVECTOR_HPP
+
+#include <Eigen/Dense>
+#include <iostream>
+#include <string>
+#include <vector>
+
+namespace torsten {
+
+/**
+ * Extracts the nth column or row from a matrix and
+ * returns it as an std::vector. Indexing starts at 0, meaning the
+ * first row or column is found for n = 0.
+ *
+ * @param[in]: matrix from which the row or column will be extracted
+ * @param[in]: n the row or column number
+ * @param[in]: str a string that specifies whether the function extracts
+ *             a column or a row.
+ * @return: output dvector
+ */
+template <typename T>
+std::vector<T> ExtractVector(Eigen::Matrix<T, Eigen::Dynamic, 1>
+  matrix, int n, std::string str) {
+  using std::vector;
+  using std::string;
+  using Eigen::Matrix;
+  using Eigen::Dynamic;
+
+  assert((str == "row") || (str == "col"));
+  int length;
+  vector<T> ExtVec;
+
+  if (str == "col") {  // extract a column.
+    length = matrix.rows();
+    assert(n < matrix.cols());
+    ExtVec.resize(length);
+    for (int i = 0; i < length; i++) ExtVec[i] = matrix(i, n);
+  } else {  // extract a row
+    length = matrix.cols();
+    assert(n < matrix.rows());
+    ExtVec.resize(length);
+    for (int i = 0; i < length; i++) ExtVec[i] = matrix(n, i);
+  }
+  return ExtVec;
+}
+
+}
+#endif