added source file

Fecundity.hpp

@@ -0,0 +1,112 @@
+/* 
+ * File:   Fecundity.hpp
+ * 
+ * Author: Matthew Supernaw
+ * National Oceanic and Atmospheric Administration
+ * National Marine Fisheries Service 
+ * Sustainable Fisheries Division
+ * St. Petersburg, FL, 33701
+ * 
+ * Created on September 16, 2016, 12:34 PM
+ * 
+ * This File is part of the NOAA, National Marine Fisheries Service 
+ * Metapopulation Assessment System project.
+ * 
+ * This software is a "United States Government Work" under the terms of the
+ * United States Copyright Act.  It was written as part of the author's official
+ * duties as a United States Government employee and thus cannot be copyrighted.
+ * This software is freely available to the public for use. The National Oceanic 
+ * And Atmospheric Administration and the U.S. Government have not placed any 
+ * restriction on its use or reproduction.  Although all reasonable efforts have 
+ * been taken to ensure the accuracy and reliability of the software and data, 
+ * the National Oceanic And Atmospheric Administration and the U.S. Government 
+ * do not and cannot warrant the performance or results that may be obtained by 
+ * using this  software or data. The National Oceanic And Atmospheric
+ * Administration and the U.S. Government disclaim all warranties, express or 
+ * implied, including warranties of performance, merchantability or fitness 
+ * for any particular purpose.
+ *
+ * Please cite the author(s) in any work or product based on this material.
+ *
+ */
+
+#ifndef MAS_FECUNDITY_HPP
+#define MAS_FECUNDITY_HPP
+
+#include "Common.hpp"
+
+namespace mas {
+
+    template<typename REAL_T>
+    struct FecundityBase : mas::ModelObject<REAL_T> {
+
+        typedef typename VariableTrait<REAL_T>::variable variable;
+
+        virtual const variable Evaluate(const int& sex, const variable& age) = 0;
+
+        virtual const std::string Name() {
+            return "FecundityBase";
+        }
+
+    };
+
+
+    template<typename REAL_T>
+    struct LogisticFec : FecundityBase<REAL_T> {
+        typedef typename VariableTrait<REAL_T>::variable variable;
+        variable a50; //age of 50% maturity
+        variable s; //the rate of increase in maturity at a50
+
+        /**
+         * Age based logistic maturity
+         *
+         * @param sex
+         * @param age
+         * @return fraction_mature
+         */
+        virtual const variable Evaluate(const int& sex, const variable& age) {
+            return static_cast<REAL_T> (1.0) / (static_cast<REAL_T> (1.0) + std::exp(-1.0*(age - a50)/s));
+        }
+
+        virtual const std::string Name() {
+            return "Logistic Fecundity";
+        }
+
+    };
+
+    template<typename REAL_T>
+    struct DoubleLogisticFec : FecundityBase<REAL_T> {
+        typedef typename VariableTrait<REAL_T>::variable variable;
+        variable alpha_asc; //ascending alpha
+        variable beta_asc; // ascending beta
+        variable alpha_desc; // descending alpha
+        variable beta_desc; // descending beta
+
+        /**
+         * Age based double logistic maturity
+         *
+         * @param sex
+         * @param age
+         * @return fraction_mature
+         */
+        virtual const variable Evaluate(const int& sex, const variable& age) {
+            return (static_cast<REAL_T> (1.0) /
+                    (static_cast<REAL_T> (1.0) +
+                    std::exp(-beta_asc * (age - alpha_asc)))) *
+                    (static_cast<REAL_T> (1.0) - (static_cast<REAL_T> (1.0) /
+                    (static_cast<REAL_T> (1.0) +
+                    std::exp(-beta_desc * (age - alpha_desc)))));
+        }
+
+        virtual const std::string Name() {
+            return "Double Logistic Fecundity";
+        }
+
+    };
+
+
+}
+
+
+#endif /* MAS_FECUNDITY_HPP */
+