COPASI API
4.16.103
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#include <COptMethodEP.h>
Public Member Functions | |
COptMethodEP (const COptMethodEP &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | optimise () |
virtual | ~COptMethodEP () |
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COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL) | |
bool | isBounded (void) |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
void | setProblem (COptProblem *problem) |
virtual | ~COptMethod () |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
virtual bool | elevateChildren () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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virtual bool | add (CCopasiObject *pObject, const bool &adopt=true) |
CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | |
CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | |
virtual std::string | getChildObjectUnits (const CCopasiObject *pObject) const |
virtual const objectMap & | getObjects () const |
virtual std::string | getUnits () const |
virtual const CCopasiObject * | getValueObject () const |
virtual bool | remove (CCopasiObject *pObject) |
virtual | ~CCopasiContainer () |
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void | addDirectDependency (const CCopasiObject *pObject) |
CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | |
void | clearDirectDependencies () |
void | clearRefresh () |
bool | dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const |
void | getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
const std::string & | getObjectName () const |
CCopasiContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const |
virtual Refresh * | getRefresh () const |
UpdateMethod * | getUpdateMethod () const |
bool | hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const |
bool | hasUpdateMethod () const |
bool | isArray () const |
bool | isContainer () const |
bool | isDataModel () const |
bool | isMatrix () const |
bool | isNameVector () const |
bool | isNonUniqueName () const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const |
bool | isReference () const |
bool | isRoot () const |
bool | isSeparator () const |
bool | isStaticString () const |
bool | isValueBool () const |
bool | isValueDbl () const |
bool | isValueInt () const |
bool | isValueInt64 () const |
bool | isValueString () const |
bool | isVector () const |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
void | removeDirectDependency (const CCopasiObject *pObject) |
void | setDirectDependencies (const DataObjectSet &directDependencies) |
bool | setObjectName (const std::string &name) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
void | setObjectValue (const C_FLOAT64 &value) |
void | setObjectValue (const C_INT32 &value) |
void | setObjectValue (const bool &value) |
template<class CType > | |
void | setRefresh (CType *pType, void(CType::*method)(void)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const bool &)) |
virtual | ~CCopasiObject () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Member Functions | |
virtual bool | cleanup () |
COptMethodEP (const CCopasiContainer *pParent=NULL) | |
bool | creation () |
bool | evaluate (const CVector< C_FLOAT64 > &individual) |
size_t | fittest () |
virtual bool | initialize () |
void | initObjects () |
bool | mutate (size_t i) |
bool | replicate () |
bool | select () |
bool | swap (size_t from, size_t to) |
Private Attributes | |
size_t | mBestIndex |
C_FLOAT64 | mBestValue |
unsigned C_INT32 | mCurrentIteration |
C_FLOAT64 | mEvaluationValue |
unsigned C_INT32 | mGeneration |
unsigned C_INT32 | mGenerations |
size_t | mhGenerations |
std::vector< CVector < C_FLOAT64 > * > | mIndividual |
CVector< size_t > | mLosses |
CVector< size_t > | mPivot |
unsigned C_INT32 | mPopulationSize |
CRandom * | mpRandom |
CVector< C_FLOAT64 > | mValue |
size_t | mVariableSize |
std::vector< CVector < C_FLOAT64 > * > | mVariance |
double | tau1 |
double | tau2 |
Friends | |
COptMethod * | COptMethod::createMethod (CCopasiMethod::SubType subType) |
Additional Inherited Members | |
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enum | SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static COptMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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enum | Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 } |
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COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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template<class CType > | |
CCopasiObject * | addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
void | initObjects () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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const bool | mBounds |
const std::vector< COptItem * > * | mpOptContraints |
const std::vector< COptItem * > * | mpOptItem |
COptProblem * | mpOptProblem |
COptTask * | mpParentTask |
const std::vector < UpdateMethod * > * | mpSetCalculateVariable |
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CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 27 of file COptMethodEP.h.
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Default Constructor
Definition at line 28 of file COptMethodEP.cpp.
References CCopasiParameterGroup::addParameter(), C_INT32, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.
COptMethodEP::COptMethodEP | ( | const COptMethodEP & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy Constructor
const | COptMethodEP & src |
Definition at line 51 of file COptMethodEP.cpp.
References initObjects().
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Cleanup arrays and pointers.
Reimplemented from COptMethod.
Definition at line 145 of file COptMethodEP.cpp.
References mIndividual, mpRandom, mVariance, and pdelete.
Referenced by initialize(), optimise(), and ~COptMethodEP().
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Initialise the population
size_t | first |
size_t | last (default: population size) |
Definition at line 233 of file COptMethodEP.cpp.
References C_FLOAT64, COptItem::checkConstraint(), COptItem::checkLowerBound(), COptItem::checkUpperBound(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), CRandom::getRandomNormal(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), max, mEvaluationValue, min, mIndividual, mPopulationSize, mpRandom, mValue, mVariableSize, and mVariance.
Referenced by optimise().
Evaluate the objective function for the current parameters
Definition at line 209 of file COptMethodEP.cpp.
References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::getCalculateValue(), mEvaluationValue, and COptMethod::mpOptProblem.
Referenced by creation(), and mutate().
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Find the best individual at this generation
Definition at line 471 of file COptMethodEP.cpp.
References C_FLOAT64, mLosses, mPopulationSize, and mValue.
Referenced by optimise().
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Initialize arrays and pointer.
Reimplemented from COptMethod.
Definition at line 160 of file COptMethodEP.cpp.
References CProcessReport::addItem(), cleanup(), CRandom::createGenerator(), CCopasiParameter::getValue(), COptMethod::initialize(), mGeneration, mGenerations, mhGenerations, mIndividual, mLosses, CCopasiMethod::mpCallBack, COptMethod::mpOptItem, mPopulationSize, mpRandom, mValue, mVariableSize, mVariance, CCopasiParameter::Value::pUINT, CVector< CType >::resize(), tau1, and tau2.
Referenced by optimise().
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Initialize contained objects.
Definition at line 228 of file COptMethodEP.cpp.
References CCopasiContainer::addObjectReference(), mGeneration, and CCopasiObject::ValueInt.
Referenced by COptMethodEP().
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Mutate one individual
CVector< | C_FLOAT64 > & individual |
Definition at line 511 of file COptMethodEP.cpp.
References C_FLOAT64, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomNormal01(), COptItem::getUpperBoundValue(), max, mEvaluationValue, mIndividual, mpRandom, mValue, mVariableSize, mVariance, tau1, and tau2.
Referenced by replicate().
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Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback.
Reimplemented from COptMethod.
Definition at line 72 of file COptMethodEP.cpp.
References C_INVALID_INDEX, cleanup(), creation(), COutputInterface::DURING, CProcessReport::finishItem(), fittest(), initialize(), mBestIndex, mBestValue, mGeneration, mGenerations, mhGenerations, mIndividual, CCopasiMethod::mpCallBack, COptMethod::mpOptProblem, COptMethod::mpParentTask, mValue, CCopasiTask::output(), CProcessReport::progressItem(), replicate(), select(), and COptProblem::setSolution().
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Replicate the individuals with crossover
Definition at line 486 of file COptMethodEP.cpp.
References mIndividual, mPopulationSize, mutate(), mValue, mVariableSize, and mVariance.
Referenced by optimise().
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Select surviving population
Definition at line 411 of file COptMethodEP.cpp.
References applyPartialPivot(), CVectorCore< CType >::array(), C_INT32, CRandom::getRandomU(), mLosses, mPivot, mPopulationSize, mpRandom, mValue, partialSortWithPivot(), and swap().
Referenced by optimise().
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Swap individuals from and to
size_t | from |
size_t | to |
Definition at line 450 of file COptMethodEP.cpp.
References C_FLOAT64, mIndividual, mLosses, mValue, and mVariance.
Referenced by select().
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Definition at line 151 of file COptMethodEP.h.
Referenced by optimise().
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The best value found so far.
Definition at line 165 of file COptMethodEP.h.
Referenced by optimise().
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The current iteration
Definition at line 195 of file COptMethodEP.h.
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The value of the last evaluation.
Definition at line 170 of file COptMethodEP.h.
Referenced by creation(), evaluate(), and mutate().
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size of the population
Definition at line 134 of file COptMethodEP.h.
Referenced by initialize(), initObjects(), and optimise().
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number of generations
Definition at line 129 of file COptMethodEP.h.
Referenced by initialize(), and optimise().
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Handle to the process report item "Current Generation"
Definition at line 139 of file COptMethodEP.h.
Referenced by initialize(), and optimise().
for array of individuals w/ candidate values for the parameters
Definition at line 185 of file COptMethodEP.h.
Referenced by cleanup(), creation(), initialize(), mutate(), optimise(), replicate(), and swap().
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number of wins of each individual in the tournament
Definition at line 160 of file COptMethodEP.h.
Referenced by fittest(), initialize(), select(), and swap().
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Pivot vector used for sorting
Definition at line 200 of file COptMethodEP.h.
Referenced by select().
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size of the population
Definition at line 144 of file COptMethodEP.h.
Referenced by creation(), fittest(), initialize(), replicate(), and select().
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a pointer to the randomnumber generator.
Definition at line 149 of file COptMethodEP.h.
Referenced by cleanup(), creation(), initialize(), mutate(), and select().
array of values of objective function f/ individuals
Definition at line 175 of file COptMethodEP.h.
Referenced by creation(), fittest(), initialize(), mutate(), optimise(), replicate(), select(), and swap().
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number of parameters
Definition at line 180 of file COptMethodEP.h.
Referenced by creation(), initialize(), mutate(), and replicate().
for array of variances w/ variance values for the parameters
Definition at line 190 of file COptMethodEP.h.
Referenced by cleanup(), creation(), initialize(), mutate(), replicate(), and swap().
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Definition at line 153 of file COptMethodEP.h.
Referenced by initialize(), and mutate().
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Definition at line 155 of file COptMethodEP.h.
Referenced by initialize(), and mutate().