openModeller  Version 1.4.0
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes
VirtualNicheGenerator Class Reference

#include <virtual_niche.hh>

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List of all members.

Public Member Functions

 VirtualNicheGenerator ()
 ~VirtualNicheGenerator ()
int initialize ()
int iterate ()
int done () const
Scalar getValue (const Sample &x) const
int getConvergence (Scalar *const val) const

Protected Member Functions

virtual void _getConfiguration (ConfigurationPtr &) const
virtual void _setConfiguration (const ConstConfigurationPtr &)

Private Member Functions

void dump ()
Scalar pdf (Scalar avg, Scalar std, Scalar val) const

Private Attributes

bool _done
OccurrencesPtr _background
 > true if the algorithm is finished.
int _num_background
Sample _minimum
Sample _maximum
 > Mininum value for each variable.
Sample _mean
 > Maximum value for each variable.
Sample _std
 > Average for the normal distribution.
Sample _scale
 > Standard deviation for the normal distribution.
Scalar _threshold
 > Factors to multiply the PDF values.

Detailed Description

Declaration of Virtual Niche Generator.

Author:
Renato De Giovanni <renato at cria.org.br>
Id:
virtual_niche.hh 5526 2012-05-24 19:41:05Z rdg

LICENSE INFORMATION

Copyright(c) 2012 by CRIA - Centro de Referência em Informação Ambiental

http://www.cria.org.br

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 Virtual Niche Generator algorithm

Definition at line 39 of file virtual_niche.hh.

Constructor & Destructor Documentation

VirtualNicheGenerator::VirtualNicheGenerator ( )

Definition at line 175 of file virtual_niche.cpp.

VirtualNicheGenerator::~VirtualNicheGenerator ( )

Definition at line 190 of file virtual_niche.cpp.

Member Function Documentation

void VirtualNicheGenerator::_getConfiguration ( ConfigurationPtr &  config) const [protected, virtual]

Reimplemented from AlgorithmImpl.

Definition at line 398 of file virtual_niche.cpp.

References _done, _maximum, _mean, _minimum, _scale, _std, and _threshold.

void VirtualNicheGenerator::_setConfiguration ( const ConstConfigurationPtr &  config) [protected, virtual]

Reimplemented from AlgorithmImpl.

Definition at line 415 of file virtual_niche.cpp.

References _done, _maximum, _mean, _minimum, _scale, _std, and _threshold.

int VirtualNicheGenerator::done ( ) const [virtual]

Return != 0 if algorithm finished.

Reimplemented from AlgorithmImpl.

Definition at line 355 of file virtual_niche.cpp.

References _done.

void VirtualNicheGenerator::dump ( ) [private]

Definition at line 437 of file virtual_niche.cpp.

References _maximum, _mean, _minimum, _std, Log::info(), Log::instance(), and Sample::size().

Referenced by iterate().

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int VirtualNicheGenerator::getConvergence ( Scalar *const  val) const [virtual]

Returns the algorithm's convergence value at the moment

Reimplemented from AlgorithmImpl.

Definition at line 388 of file virtual_niche.cpp.

Scalar VirtualNicheGenerator::getValue ( const Sample &  x) const [virtual]

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

Parameters:
xEnvironmental conditions.
Returns:
The occurrence probability in the range [0,1].

Implements AlgorithmImpl.

Definition at line 365 of file virtual_niche.cpp.

References _mean, _scale, _std, _threshold, pdf(), and Sample::size().

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int VirtualNicheGenerator::initialize ( ) [virtual]

Initiate a new training.

Implements AlgorithmImpl.

Definition at line 198 of file virtual_niche.cpp.

References _background, _num_background, AlgorithmImpl::_samp, _threshold, BACKGROUND_ID, AlgorithmImpl::getParameter(), Log::info(), Log::instance(), THRESHOLD_ID, USE_ABSENCES_ID, and Log::warn().

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int VirtualNicheGenerator::iterate ( ) [virtual]

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

Reimplemented from AlgorithmImpl.

Definition at line 279 of file virtual_niche.cpp.

References _background, _done, _maximum, _mean, _minimum, _num_background, AlgorithmImpl::_samp, _scale, _std, dump(), Log::info(), Log::instance(), pdf(), Sample::size(), and Sample::sqrt().

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Scalar VirtualNicheGenerator::pdf ( Scalar  avg,
Scalar  std,
Scalar  val 
) const [private]

Definition at line 454 of file virtual_niche.cpp.

References PI.

Referenced by getValue(), and iterate().

Member Data Documentation

OccurrencesPtr VirtualNicheGenerator::_background [private]

> true if the algorithm is finished.

Definition at line 66 of file virtual_niche.hh.

Referenced by initialize(), and iterate().

bool VirtualNicheGenerator::_done [private]

Definition at line 64 of file virtual_niche.hh.

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

Sample VirtualNicheGenerator::_maximum [private]

> Mininum value for each variable.

Definition at line 70 of file virtual_niche.hh.

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

Sample VirtualNicheGenerator::_mean [private]

> Maximum value for each variable.

Definition at line 71 of file virtual_niche.hh.

Referenced by _getConfiguration(), _setConfiguration(), dump(), getValue(), and iterate().

Sample VirtualNicheGenerator::_minimum [private]

Definition at line 69 of file virtual_niche.hh.

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

int VirtualNicheGenerator::_num_background [private]

Definition at line 67 of file virtual_niche.hh.

Referenced by initialize(), and iterate().

Sample VirtualNicheGenerator::_scale [private]

> Standard deviation for the normal distribution.

Definition at line 73 of file virtual_niche.hh.

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

Sample VirtualNicheGenerator::_std [private]

> Average for the normal distribution.

Definition at line 72 of file virtual_niche.hh.

Referenced by _getConfiguration(), _setConfiguration(), dump(), getValue(), and iterate().

Scalar VirtualNicheGenerator::_threshold [private]

> Factors to multiply the PDF values.

Definition at line 74 of file virtual_niche.hh.

Referenced by _getConfiguration(), _setConfiguration(), getValue(), and initialize().

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