#include <best_subsets.hh>

Inheritance diagram for BestSubsets:

Collaboration diagram for BestSubsets:

Public Member Functions
	BestSubsets (AlgMetadata *metadata)

virtual	~BestSubsets ()

int	initialize ()

int	iterate ()

int	done () const

float	getProgress () const

Scalar	getValue (const Sample &x) const

int	getConvergence (Scalar *const val) const

void	printListOfRuns (string msg, AlgorithmRun **runs, int numOfRuns)

Public Member Functions inherited from AlgorithmImpl
	AlgorithmImpl (AlgMetadata const *metadata)

virtual	~AlgorithmImpl ()

void	setParameters (int nparam, AlgParameter const *param)

void	setParameters (const ParamSetType &)

std::string const	getID () const

AlgMetadata const *	getMetadata () const

AlgorithmPtr	getFreshCopy ()

virtual int	supportsModelProjection () const

Model	createModel (const SamplerPtr &samp, CallbackWrapper *func=0)

void	setSampler (const SamplerPtr &samp)

virtual int	finalize ()

virtual int	needNormalization ()

Normalizer *	getNormalizer () const

void	setNormalization (const SamplerPtr &samp) const

void	setNormalization (const EnvironmentPtr &env) const

virtual Model	getModel () const

ConfigurationPtr	getConfiguration () const

void	setConfiguration (const ConstConfigurationPtr &)

Public Member Functions inherited from Configurable
virtual	~Configurable ()

Public Member Functions inherited from BSAlgorithmFactory
virtual	~BSAlgorithmFactory ()

Protected Member Functions
void	_getConfiguration (ConfigurationPtr &) const

void	_setConfiguration (const ConstConfigurationPtr &)

Protected Member Functions inherited from AlgorithmImpl
int	dimDomain ()

int	getParameter (std::string const &name, std::string *value)

int	getParameter (std::string const &name, double *value)

int	getParameter (std::string const &name, float *value)

int	getParameter (std::string const &name, int *value)

Protected Attributes
int	_nparam

AlgParameter *	_alg_params

Protected Attributes inherited from AlgorithmImpl
SamplerPtr	_samp

Normalizer *	_normalizerPtr

ParamSetType	_param

Private Member Functions
virtual AlgorithmImpl *	getBSAlgorithm ()=0

virtual int	transferParametersToAlgorithm ()=0

int	numActiveThreads ()

int	earlyTerminationConditionMet ()

int	calculateBestSubset ()

void	sortRuns (AlgorithmRun **runList, int nelements, int errorType)

Private Attributes
double	_trainProp

int	_totalRuns

double	_omissionThreshold

int	_modelsUnderOmission

double	_commissionThreshold

int	_commissionSampleSize

int	_maxThreads

bool	_softOmissionThreshold

int	_currentModelsUnderOmissionThreshold

AlgorithmRun **	_finishedRun

AlgorithmRun **	_activeRun

AlgorithmRun **	_bestRun

int	_numFinishedRuns

int	_numActiveRuns

int	_numBestRuns

int	_done

float	_maxProgress

Additional Inherited Members
Public Types inherited from AlgorithmImpl
typedef std::map< icstring, std::string >	ParamSetType

Detailed Description

Implements Best Subset Procedure (Anderson et al. 2003).

It runs "n" Garp models, filter the best ones based on the procedure defined by Anderson et al. 2003 and sum them to obtain a probability map for the species distribution.

Current implementation uses multi-threading to run multiple Garp runs in parallel. Takes advantage of multi-processor servers and workstations.

Definition at line 55 of file best_subsets.hh.

Constructor & Destructor Documentation

BestSubsets::BestSubsets ( AlgMetadata * metadata )

Definition at line 66 of file best_subsets.cpp.

References _activeRun, _alg_params, _bestRun, _commissionSampleSize, _commissionThreshold, _currentModelsUnderOmissionThreshold, _done, _finishedRun, _maxProgress, _modelsUnderOmission, _nparam, _numActiveRuns, _numFinishedRuns, _omissionThreshold, _softOmissionThreshold, _totalRuns, and _trainProp.

BestSubsets::~BestSubsets ( )

virtual

Definition at line 95 of file best_subsets.cpp.

References _activeRun, _alg_params, _bestRun, _finishedRun, and _numFinishedRuns.

Member Function Documentation

void BestSubsets::_getConfiguration ( ConfigurationPtr & config ) const

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 458 of file best_subsets.cpp.

References _bestRun, _done, _numBestRuns, and AlgorithmRun::getAlgorithm().

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void BestSubsets::_setConfiguration ( const ConstConfigurationPtr & config )

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 486 of file best_subsets.cpp.

References _bestRun, _done, _numBestRuns, and AlgorithmFactory::newAlgorithm().

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int BestSubsets::calculateBestSubset ( )

private

Definition at line 313 of file best_subsets.cpp.

References _bestRun, _commissionThreshold, _finishedRun, _modelsUnderOmission, _numBestRuns, _numFinishedRuns, _totalRuns, Log::info(), Log::instance(), printListOfRuns(), and sortRuns().

Referenced by iterate().

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int BestSubsets::done ( ) const

virtual

Check if the model generation is completed (e.g. convergence point has been met.

Returns: Implementation specific but usually 1 for completion.

Reimplemented from AlgorithmImpl.

Definition at line 390 of file best_subsets.cpp.

References _done.

Referenced by getProgress().

int BestSubsets::earlyTerminationConditionMet ( )

private

Definition at line 306 of file best_subsets.cpp.

References _currentModelsUnderOmissionThreshold, _modelsUnderOmission, and _softOmissionThreshold.

Referenced by iterate().

virtual AlgorithmImpl* BestSubsets::getBSAlgorithm ( )

privatepure virtual

Implements BSAlgorithmFactory.

Implemented in GarpBestSubsets, and DgGarpBestSubsets.

int BestSubsets::getConvergence ( Scalar *const val ) const

virtual

Returns a value that represents the convergence of the algorithm expressed as a number between 0 and 1 where 0 represents model completion.

Returns

Parameters

val

Reimplemented from AlgorithmImpl.

Definition at line 450 of file best_subsets.cpp.

float BestSubsets::getProgress ( ) const

virtual

Return progress so far

Reimplemented from AlgorithmImpl.

Definition at line 398 of file best_subsets.cpp.

References _activeRun, _currentModelsUnderOmissionThreshold, _maxProgress, _modelsUnderOmission, _numActiveRuns, _numFinishedRuns, _softOmissionThreshold, _totalRuns, done(), and AlgorithmRun::getProgress().

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Scalar BestSubsets::getValue ( const Sample & x ) const

virtual

This method is used when projecting the model.

Note: This method is inherited from the Algorithm class

Returns

Parameters

x	Pointer to a vector of openModeller Scalar type (currently double). The vector should contain values looked up on the environmental variable layers into which the mode is being projected.

Implements AlgorithmImpl.

Definition at line 433 of file best_subsets.cpp.

References _bestRun, _done, _numBestRuns, and AlgorithmRun::getValue().

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