NicheMosaic Class Reference

#include <niche_mosaic.hh>

Inheritance diagram for NicheMosaic:

Collaboration diagram for NicheMosaic:

List of all members.

Public Member Functions
	NicheMosaic ()
	~NicheMosaic ()
int	initialize ()
int	iterate ()
int	done () const
float	getProgress () const
Scalar	getValue (const Sample &x) const
int	setMinMaxDelta ()
void	createModel (std::vector< ScalarVector > &_model_min, std::vector< ScalarVector > &_model_max, const std::vector< Scalar > &delta)
void	editModel (std::vector< ScalarVector > &model_min, std::vector< ScalarVector > &model_max, const std::vector< Scalar > &delta, size_t i_layer)
size_t	calculateCostPres (const std::vector< ScalarVector > &_model_min, const std::vector< ScalarVector > &_model_max)
size_t	calculateCostAus (const std::vector< ScalarVector > &_model_min, const std::vector< ScalarVector > &_model_max)
size_t	getRandomLayerNumber ()
Scalar	getRandomPercent (const std::vector< Scalar > &delta, const size_t i_layer, size_t &cost1)
void	renewTabuDegree (std::vector< size_t > &tabuDegree)
void	saveBestModel (const std::vector< ScalarVector > &model_min, const std::vector< ScalarVector > &model_max)
void	improveModel (const std::vector< Scalar > &deltaBest)
void	findSolution (size_t &costBest, std::vector< Scalar > &deltaBest, int &bestIter, size_t &bestCost2)
OccurrencesPtr	cleanOccurrences (const OccurrencesPtr &occurrences)
void	computeMeanDeviation (const OccurrencesPtr &occs, Sample &mean, Sample &deviation)
Protected Member Functions
void	_getConfiguration (ConfigurationPtr &) const
void	_setConfiguration (const ConstConfigurationPtr &)
Private Attributes
int	_num_iterations
int	_num_points
size_t	_num_points_test
size_t	_num_points_absence_test
int	_num_layers
Sample	_minimum
Sample	_maximum
Sample	_delta
OccurrencesPtr	_my_presences
OccurrencesPtr	_my_presences_test
OccurrencesPtr	_my_absence_test
Scalar	_bestCost
bool	_done
float	_progress
SamplerPtr	_sampp
std::vector< ScalarVector >	_model_min_best
std::vector< ScalarVector >	_model_max_best

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Detailed Description

Definition at line 35 of file niche_mosaic.hh.

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Constructor & Destructor Documentation

NicheMosaic::NicheMosaic

(

)

Definition at line 120 of file niche_mosaic.cpp.

NicheMosaic::~NicheMosaic

(

)

Definition at line 139 of file niche_mosaic.cpp.

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Member Function Documentation

void NicheMosaic::_getConfiguration

(

ConfigurationPtr &

config

)

const [protected, virtual]

Reimplemented from AlgorithmImpl.

Definition at line 633 of file niche_mosaic.cpp.

References _done, _model_max_best, _model_min_best, _num_layers, and _num_points.

void NicheMosaic::_setConfiguration

(

const ConstConfigurationPtr &

config

)

[protected, virtual]

Reimplemented from AlgorithmImpl.

Definition at line 660 of file niche_mosaic.cpp.

References _done, _model_max_best, _model_min_best, _num_layers, and _num_points.

size_t NicheMosaic::calculateCostAus	(	const std::vector< ScalarVector > &	_model_min,
		const std::vector< ScalarVector > &	_model_max
	)

Definition at line 426 of file niche_mosaic.cpp.

References _my_absence_test, _num_layers, and _num_points.

Referenced by findSolution().

size_t NicheMosaic::calculateCostPres	(	const std::vector< ScalarVector > &	_model_min,
		const std::vector< ScalarVector > &	_model_max
	)

Definition at line 391 of file niche_mosaic.cpp.

References _my_presences_test, _num_layers, and _num_points.

Referenced by findSolution().

OccurrencesPtr NicheMosaic::cleanOccurrences

(

const OccurrencesPtr &

occurrences

)

Definition at line 697 of file niche_mosaic.cpp.

References AlgorithmImpl::_samp, computeMeanDeviation(), createSampler(), and Sample::size().

Referenced by initialize().

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void NicheMosaic::computeMeanDeviation	(	const OccurrencesPtr &	occs,
		Sample &	mean,
		Sample &	deviation
	)

Definition at line 806 of file niche_mosaic.cpp.

References min(), Sample::resize(), Sample::size(), and Sample::sqrt().

Referenced by cleanOccurrences().

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void NicheMosaic::createModel	(	std::vector< ScalarVector > &	_model_min,
		std::vector< ScalarVector > &	_model_max,
		const std::vector< Scalar > &	delta
	)

Definition at line 353 of file niche_mosaic.cpp.

References _my_presences, and _num_layers.

Referenced by findSolution().

int NicheMosaic::done

(

)

const [inline, virtual]

Return != 0 if algorithm finished.

Reimplemented from AlgorithmImpl.

Definition at line 69 of file niche_mosaic.hh.

References _done.

Referenced by getProgress().

void NicheMosaic::editModel	(	std::vector< ScalarVector > &	model_min,
		std::vector< ScalarVector > &	model_max,
		const std::vector< Scalar > &	delta,
		size_t	i_layer
	)

Definition at line 373 of file niche_mosaic.cpp.

References _my_presences.

Referenced by findSolution().

void NicheMosaic::findSolution	(	size_t &	costBest,
		std::vector< Scalar > &	deltaBest,
		int &	bestIter,
		size_t &	bestCost2
	)

Definition at line 556 of file niche_mosaic.cpp.

References _bestCost, _delta, _num_iterations, _num_layers, _num_points, _num_points_absence_test, _num_points_test, _progress, calculateCostAus(), calculateCostPres(), createModel(), editModel(), getRandomLayerNumber(), getRandomPercent(), renewTabuDegree(), and saveBestModel().

Referenced by iterate().

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float NicheMosaic::getProgress

(

)

const [virtual]

Returns progress so far (between 0.0 and 1.0)

Reimplemented from AlgorithmImpl.

Definition at line 277 of file niche_mosaic.cpp.

References _progress, and done().

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size_t NicheMosaic::getRandomLayerNumber

(

)

Definition at line 462 of file niche_mosaic.cpp.

References _num_layers.

Referenced by findSolution().

Scalar NicheMosaic::getRandomPercent	(	const std::vector< Scalar > &	delta,
		const size_t	i_layer,
		size_t &	cost1
	)

Definition at line 470 of file niche_mosaic.cpp.

References _num_points_test.

Referenced by findSolution().

Scalar NicheMosaic::getValue

(

const Sample &

x

)

const [virtual]

The algorithm must return the occurrence probability at the given environment conditions.

Parameters:

x	Environmental conditions.

Returns:

The occurrence probability in the range [0,1].

Implements AlgorithmImpl.

Definition at line 292 of file niche_mosaic.cpp.

References _model_max_best, _model_min_best, _num_layers, and _num_points.

void NicheMosaic::improveModel

(

const std::vector< Scalar > &

deltaBest

)

Definition at line 513 of file niche_mosaic.cpp.

References _model_max_best, _model_min_best, _my_presences_test, _num_layers, and _num_points.

Referenced by iterate().

int NicheMosaic::initialize

(

)

[virtual]

Initiate a new training.

Implements AlgorithmImpl.

Definition at line 146 of file niche_mosaic.cpp.

References _my_absence_test, _my_presences, _my_presences_test, _num_iterations, _num_layers, _num_points_absence_test, AlgorithmImpl::_samp, _sampp, cleanOccurrences(), createSampler(), Log::error(), AlgorithmImpl::getParameter(), Log::instance(), NUMITERATIONS_ID, and Log::warn().

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int NicheMosaic::iterate

(

)

[virtual]

One step further on the training. Return 0 if something wrong happened.

Reimplemented from AlgorithmImpl.

Definition at line 214 of file niche_mosaic.cpp.

References _done, _model_max_best, _model_min_best, _my_absence_test, _my_presences, _my_presences_test, _num_iterations, _num_layers, _num_points, _num_points_absence_test, _num_points_test, _sampp, findSolution(), improveModel(), setMinMaxDelta(), and splitOccurrences().

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void NicheMosaic::renewTabuDegree

(

std::vector< size_t > &

tabuDegree

)

Definition at line 492 of file niche_mosaic.cpp.

References _num_layers.

Referenced by findSolution().

void NicheMosaic::saveBestModel	(	const std::vector< ScalarVector > &	model_min,
		const std::vector< ScalarVector > &	model_max
	)

Definition at line 502 of file niche_mosaic.cpp.

References _model_max_best, _model_min_best, _num_layers, and _num_points.

Referenced by findSolution().

int NicheMosaic::setMinMaxDelta

(

)

Definition at line 322 of file niche_mosaic.cpp.

References _delta, _maximum, _minimum, _my_presences, _num_layers, Log::error(), and Log::instance().

Referenced by iterate().

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Member Data Documentation

Scalar NicheMosaic::_bestCost [private]

Definition at line 50 of file niche_mosaic.hh.

Referenced by findSolution().

Sample NicheMosaic::_delta [private]

Definition at line 46 of file niche_mosaic.hh.

Referenced by findSolution(), and setMinMaxDelta().

bool NicheMosaic::_done [private]

Definition at line 51 of file niche_mosaic.hh.

Referenced by _getConfiguration(), _setConfiguration(), done(), and iterate().

Sample NicheMosaic::_maximum [private]

Definition at line 45 of file niche_mosaic.hh.

Referenced by setMinMaxDelta().

Sample NicheMosaic::_minimum [private]

Definition at line 44 of file niche_mosaic.hh.

Referenced by setMinMaxDelta().

std::vector<ScalarVector> NicheMosaic::_model_max_best [private]

Definition at line 55 of file niche_mosaic.hh.

Referenced by _getConfiguration(), _setConfiguration(), getValue(), improveModel(), iterate(), and saveBestModel().

std::vector<ScalarVector> NicheMosaic::_model_min_best [private]

Definition at line 54 of file niche_mosaic.hh.

Referenced by _getConfiguration(), _setConfiguration(), getValue(), improveModel(), iterate(), and saveBestModel().

OccurrencesPtr NicheMosaic::_my_absence_test [private]

Definition at line 49 of file niche_mosaic.hh.

Referenced by calculateCostAus(), initialize(), and iterate().

OccurrencesPtr NicheMosaic::_my_presences [private]

Definition at line 47 of file niche_mosaic.hh.

Referenced by createModel(), editModel(), initialize(), iterate(), and setMinMaxDelta().

OccurrencesPtr NicheMosaic::_my_presences_test [private]

Definition at line 48 of file niche_mosaic.hh.

Referenced by calculateCostPres(), improveModel(), initialize(), and iterate().

int NicheMosaic::_num_iterations [private]

Definition at line 39 of file niche_mosaic.hh.

Referenced by findSolution(), initialize(), and iterate().

int NicheMosaic::_num_layers [private]

Definition at line 43 of file niche_mosaic.hh.

Referenced by _getConfiguration(), _setConfiguration(), calculateCostAus(), calculateCostPres(), createModel(), findSolution(), getRandomLayerNumber(), getValue(), improveModel(), initialize(), iterate(), renewTabuDegree(), saveBestModel(), and setMinMaxDelta().

int NicheMosaic::_num_points [private]

Definition at line 40 of file niche_mosaic.hh.

Referenced by _getConfiguration(), _setConfiguration(), calculateCostAus(), calculateCostPres(), findSolution(), getValue(), improveModel(), iterate(), and saveBestModel().

size_t NicheMosaic::_num_points_absence_test [private]

Definition at line 42 of file niche_mosaic.hh.

Referenced by findSolution(), initialize(), and iterate().

size_t NicheMosaic::_num_points_test [private]

Definition at line 41 of file niche_mosaic.hh.

Referenced by findSolution(), getRandomPercent(), and iterate().

float NicheMosaic::_progress [private]

Definition at line 52 of file niche_mosaic.hh.

Referenced by findSolution(), and getProgress().

SamplerPtr NicheMosaic::_sampp [private]

Definition at line 53 of file niche_mosaic.hh.

Referenced by initialize(), and iterate().

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The documentation for this class was generated from the following files:

• niche_mosaic.hh
• niche_mosaic.cpp