COPASI API
4.16.103
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#include <COptMethodSRES.h>
Public Member Functions | |
COptMethodSRES (const COptMethodSRES &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | optimise () |
virtual | ~COptMethodSRES () |
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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 () |
COptMethodSRES (const CCopasiContainer *pParent=NULL) | |
bool | creation (size_t first) |
bool | evaluate (const CVector< C_FLOAT64 > &individual) |
size_t | fittest () |
virtual bool | initialize () |
void | initObjects () |
bool | mutate () |
C_FLOAT64 | phi (size_t indvNum) |
bool | replicate () |
void | select () |
bool | swap (size_t from, size_t to) |
Private Attributes | |
C_FLOAT64 | mBestValue |
C_FLOAT64 | mEvaluationValue |
unsigned C_INT32 | mGeneration |
unsigned C_INT32 | mGenerations |
size_t | mhGenerations |
std::vector< CVector < C_FLOAT64 > * > | mIndividual |
CVector< C_FLOAT64 > | mMaxVariance |
C_FLOAT64 | mPf |
CVector< C_FLOAT64 > | mPhi |
unsigned C_INT32 | mPopulationSize |
CRandom * | mpRandom |
double | mTau |
double | mTauPrime |
CVector< C_FLOAT64 > | mValue |
size_t | mVariableSize |
std::vector< CVector < C_FLOAT64 > * > | mVariance |
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 |
COptMethodSRES class
Definition at line 27 of file COptMethodSRES.h.
COptMethodSRES::COptMethodSRES | ( | const COptMethodSRES & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy Constructor
const | COptMethodSRES & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 57 of file COptMethodSRES.cpp.
References initObjects().
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Default Constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 35 of file COptMethodSRES.cpp.
References CCopasiParameterGroup::addParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.
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Cleanup arrays and pointers.
Reimplemented from COptMethod.
Definition at line 586 of file COptMethodSRES.cpp.
References mIndividual, mpRandom, mVariance, and pdelete.
Referenced by initialize(), optimise(), and ~COptMethodSRES().
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Initialise the population
size_t | first |
Definition at line 293 of file COptMethodSRES.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, COptItem::checkConstraint(), COptItem::checkLowerBound(), COptItem::checkUpperBound(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), CRandom::getRandomNormal(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), max, mEvaluationValue, min, mIndividual, mMaxVariance, mPhi, mPopulationSize, mpRandom, mValue, mVariableSize, mVariance, and phi().
Referenced by optimise().
Evaluate the fitness of one individual
const | CVector< C_FLOAT64 > & individual |
Definition at line 75 of file COptMethodSRES.cpp.
References COptProblem::calculate(), 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 277 of file COptMethodSRES.cpp.
References C_FLOAT64, C_INVALID_INDEX, max, mPhi, mPopulationSize, and mValue.
Referenced by optimise().
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Initialize arrays and pointer.
Reimplemented from COptMethod.
Definition at line 498 of file COptMethodSRES.cpp.
References CProcessReport::addItem(), C_FLOAT64, childrate, cleanup(), CRandom::createGenerator(), COptItem::getLowerBoundValue(), COptItem::getUpperBoundValue(), CCopasiParameter::getValue(), COptMethod::initialize(), mBestValue, mGeneration, mGenerations, mhGenerations, mIndividual, mMaxVariance, CCopasiMethod::mpCallBack, mPf, mPhi, COptMethod::mpOptItem, mPopulationSize, mpRandom, mTau, mTauPrime, mValue, mVariableSize, mVariance, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, CVector< CType >::resize(), and CCopasiParameterGroup::setValue().
Referenced by optimise().
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Initialize contained objects.
Definition at line 493 of file COptMethodSRES.cpp.
References CCopasiContainer::addObjectReference(), mGeneration, and CCopasiObject::ValueInt.
Referenced by COptMethodSRES().
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Mutate the new generation
Definition at line 161 of file COptMethodSRES.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomNormal01(), COptItem::getUpperBoundValue(), mEvaluationValue, min, mIndividual, mMaxVariance, mPhi, mPopulationSize, mpRandom, mTau, mTauPrime, mValue, mVariableSize, mVariance, and phi().
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. @ return success;
Reimplemented from COptMethod.
Definition at line 641 of file COptMethodSRES.cpp.
References C_INVALID_INDEX, cleanup(), creation(), COutputInterface::DURING, CProcessReport::finishItem(), fittest(), initialize(), mBestValue, mGeneration, mGenerations, mhGenerations, mIndividual, CCopasiMethod::mpCallBack, COptMethod::mpOptProblem, mPopulationSize, COptMethod::mpParentTask, mValue, CCopasiTask::output(), CProcessReport::progressItem(), replicate(), select(), and COptProblem::setSolution().
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For Stochastic Ranking, evaluate the distance ofparameters to boundaries
Definition at line 602 of file COptMethodSRES.cpp.
References C_FLOAT64, mIndividual, COptMethod::mpOptContraints, and COptMethod::mpOptItem.
Referenced by creation(), and mutate().
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Replicate the individuals with crossover
Definition at line 114 of file COptMethodSRES.cpp.
References C_FLOAT64, childrate, CRandom::getRandomU(), mIndividual, mPopulationSize, mpRandom, mutate(), mVariableSize, and mVariance.
Referenced by optimise().
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Select surviving population
Definition at line 233 of file COptMethodSRES.cpp.
References CRandom::getRandomOO(), mIndividual, mPf, mPhi, mpRandom, mValue, and swap().
Referenced by optimise().
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Swap individuals from and to
size_t | from |
size_t | to |
Definition at line 93 of file COptMethodSRES.cpp.
References C_FLOAT64, mIndividual, mPhi, mValue, and mVariance.
Referenced by select().
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Definition at line 191 of file COptMethodSRES.h.
Referenced by initialize(), and optimise().
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The value of the last evaluation.
Definition at line 184 of file COptMethodSRES.h.
Referenced by creation(), evaluate(), and mutate().
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Definition at line 193 of file COptMethodSRES.h.
Referenced by initialize(), initObjects(), and optimise().
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number of generations
Definition at line 134 of file COptMethodSRES.h.
Referenced by initialize(), and optimise().
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Handle to the process report item "Current Generation"
Definition at line 139 of file COptMethodSRES.h.
Referenced by initialize(), and optimise().
for array of individuals w/ candidate values for the parameters
Definition at line 164 of file COptMethodSRES.h.
Referenced by cleanup(), creation(), initialize(), mutate(), optimise(), phi(), replicate(), select(), and swap().
A vector of maximal variances
Definition at line 179 of file COptMethodSRES.h.
Referenced by creation(), initialize(), and mutate().
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Probability value used for SR ****
Definition at line 154 of file COptMethodSRES.h.
Referenced by initialize(), and select().
For Stochastic Ranking. Used for array of Phi values for the individuals
Definition at line 169 of file COptMethodSRES.h.
Referenced by creation(), fittest(), initialize(), mutate(), select(), and swap().
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size of the population
Definition at line 144 of file COptMethodSRES.h.
Referenced by creation(), fittest(), initialize(), mutate(), optimise(), and replicate().
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a pointer to the randomnumber generator.
Definition at line 149 of file COptMethodSRES.h.
Referenced by cleanup(), creation(), initialize(), mutate(), replicate(), and select().
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Definition at line 195 of file COptMethodSRES.h.
Referenced by initialize(), and mutate().
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Definition at line 197 of file COptMethodSRES.h.
Referenced by initialize(), and mutate().
array of values of objective function f/ individuals
Definition at line 189 of file COptMethodSRES.h.
Referenced by creation(), fittest(), initialize(), mutate(), optimise(), select(), and swap().
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number of parameters
Definition at line 159 of file COptMethodSRES.h.
Referenced by creation(), initialize(), mutate(), and replicate().
for array of variances w/ variance values for the parameters
Definition at line 174 of file COptMethodSRES.h.
Referenced by cleanup(), creation(), initialize(), mutate(), replicate(), and swap().