#include <AbstractBestSubsets.hh>

Inheritance diagram for AbstractBestSubsets:

Collaboration diagram for AbstractBestSubsets:

Public Member Functions
	AbstractBestSubsets (AlgMetadata const *)

virtual	~AbstractBestSubsets ()=0

int	needNormalization ()

int	initialize ()

int	iterate ()

int	done () const

float	getProgress () const

Scalar	getValue (const Sample &x) const

int	getConvergence (Scalar *const val) const

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 ()

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 ()

Protected Member Functions
virtual void	_getConfiguration (ConfigurationPtr &) const

virtual 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
std::string	_subAlgorithm

Protected Attributes inherited from AlgorithmImpl
SamplerPtr	_samp

Normalizer *	_normalizerPtr

ParamSetType	_param

Private Member Functions
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

Declaration of Best Subsets Procedure base class

Author: Ricardo Scachetti Pereira (rpere.nosp@m.ira@.nosp@m.ku.ed.nosp@m.u)

Date: 2004-12-10

Id:: AbstractBestSubsets.hh 5932 2014-03-17 22:51:58Z rdg

LICENSE INFORMATION

Copyright(c), The Center for Research, University of Kansas, 2385 Irving Hill Road, Lawrence, KS 66044-4755, USA.

http://www.nhm.ku.edu

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details:

http://www.gnu.org/copyleft/gpl.html 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 53 of file AbstractBestSubsets.hh.

Constructor & Destructor Documentation

AbstractBestSubsets::AbstractBestSubsets ( AlgMetadata const * metadata_bs )

Definition at line 64 of file AbstractBestSubsets.cpp.

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

AbstractBestSubsets::~AbstractBestSubsets ( )

pure virtual

Definition at line 91 of file AbstractBestSubsets.cpp.

References _activeRun, _bestRun, _finishedRun, and _numFinishedRuns.

Member Function Documentation

void AbstractBestSubsets::_getConfiguration ( ConfigurationPtr & config ) const

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 114 of file AbstractBestSubsets.cpp.

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

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void AbstractBestSubsets::_setConfiguration ( const ConstConfigurationPtr & config )

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 141 of file AbstractBestSubsets.cpp.

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

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int AbstractBestSubsets::calculateBestSubset ( )

private

Definition at line 423 of file AbstractBestSubsets.cpp.

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

Referenced by iterate().

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int AbstractBestSubsets::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 500 of file AbstractBestSubsets.cpp.

References _done.

Referenced by getProgress().

int AbstractBestSubsets::earlyTerminationConditionMet ( )

private

Definition at line 416 of file AbstractBestSubsets.cpp.

References _currentModelsUnderOmissionThreshold, _modelsUnderOmission, and _softOmissionThreshold.

Referenced by iterate().

int AbstractBestSubsets::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 560 of file AbstractBestSubsets.cpp.

float AbstractBestSubsets::getProgress ( ) const

virtual

Return progress so far

Reimplemented from AlgorithmImpl.

Definition at line 508 of file AbstractBestSubsets.cpp.

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

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Scalar AbstractBestSubsets::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 543 of file AbstractBestSubsets.cpp.

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

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int AbstractBestSubsets::initialize ( )

virtual

Initialize data structures

Note: This method is inherited from the Algorithm class

Returns: 0 on error

Implements AlgorithmImpl.

Definition at line 228 of file AbstractBestSubsets.cpp.

References _activeRun, _commissionSampleSize, _commissionThreshold, _finishedRun, _maxThreads, _modelsUnderOmission, _omissionThreshold, _softOmissionThreshold, _subAlgorithm, _totalRuns, _trainProp, Log::error(), AlgorithmImpl::getParameter(), Log::instance(), and Log::warn().

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int AbstractBestSubsets::iterate ( )

virtual

Start model execution (build the model). Consists of a single GARP run. It is also the control loop for the threads

Returns: 0 on error

Reimplemented from AlgorithmImpl.

Definition at line 311 of file AbstractBestSubsets.cpp.

References _activeRun, _commissionSampleSize, _done, _maxThreads, _numActiveRuns, _numFinishedRuns, AlgorithmImpl::_param, AlgorithmImpl::_samp, _subAlgorithm, _totalRuns, _trainProp, calculateBestSubset(), earlyTerminationConditionMet(), AlgorithmRun::initialize(), AlgorithmFactory::newAlgorithm(), numActiveThreads(), AlgorithmRun::run(), SLEEP, and splitSampler().

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int AbstractBestSubsets::needNormalization ( )

virtual

This method is used when you want to ensure that all variables in all environmental layers are scaled to the same value range. GARP requires values to be normalized between -1.0 and 1.0.