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Bioclim Class Reference

#include <bioclim.hh>

Inheritance diagram for Bioclim:
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Collaboration diagram for Bioclim:
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Public Member Functions

 Bioclim ()
 
 ~Bioclim ()
 
int initialize ()
 
int iterate ()
 
int done () 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 ()
 
virtual float getProgress () const
 
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 ()
 

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)
 

Private Member Functions

void computeStats (const OccurrencesPtr &)
 
void logEnvelope ()
 

Private Attributes

bool _done
 
Sample _minimum
 

is true if the algorithm is finished.

More...
 
Sample _maximum
 

Mininum value for each variable.

More...
 
Sample _mean
 

Maximum value for each variable.

More...
 
Sample _std_dev
 

Mean of sampled points.

More...
 

Additional Inherited Members

- Public Types inherited from AlgorithmImpl
typedef std::map< icstring,
std::string > 		ParamSetType
 
- Protected Attributes inherited from AlgorithmImpl
SamplerPtr _samp
 
Normalizer * _normalizerPtr
 
ParamSetType _param
 

Detailed Description

Declaration of Bioclimatic Envelope Algorithm - Nix, 1986.

Author
Mauro Muñoz mauro.nosp@m.@cri.nosp@m.a.org.nosp@m..br
Date
2004-05-05
Id:
bioclim.hh 4916 2009-03-06 18:16:12Z rdg

LICENSE INFORMATION

Copyright(c) 2004 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 Bioclimatic Envelope Algorithm with occurrence probability based on the distance to points' mean value.

Definition at line 41 of file bioclim.hh.

Constructor & Destructor Documentation

Bioclim::Bioclim ( )

Definition at line 157 of file bioclim.cpp.

Bioclim::~Bioclim ( )

Definition at line 170 of file bioclim.cpp.

Member Function Documentation

void Bioclim::_getConfiguration ( ConfigurationPtr &  config) const
protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 352 of file bioclim.cpp.

References _done, _maximum, _mean, _minimum, and _std_dev.

void Bioclim::_setConfiguration ( const ConstConfigurationPtr &  config)
protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 368 of file bioclim.cpp.

References _done, _maximum, _mean, _minimum, and _std_dev.

void Bioclim::computeStats ( const OccurrencesPtr &  occs)
private

compute the statistic member variables based on the data in the OccurrencesPtr

Definition at line 286 of file bioclim.cpp.

References _maximum, _mean, _minimum, _std_dev, Sample::resize(), Sample::size(), and Sample::sqrt().

Referenced by initialize().

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int Bioclim::done ( ) const
virtual

Return != 0 if algorithm finished.

Reimplemented from AlgorithmImpl.

Definition at line 227 of file bioclim.cpp.

References _done.

int Bioclim::getConvergence ( Scalar *const  val) const
virtual

Returns the algorithm's convergence value at the moment

Reimplemented from AlgorithmImpl.

Definition at line 276 of file bioclim.cpp.

Scalar Bioclim::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 237 of file bioclim.cpp.

References _maximum, _mean, _minimum, _std_dev, and Sample::size().

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int Bioclim::initialize ( )
virtual

Initiate a new training.

Implements AlgorithmImpl.

Definition at line 178 of file bioclim.cpp.

References _done, AlgorithmImpl::_samp, _std_dev, computeStats(), CUTOFF_ID, Log::error(), AlgorithmImpl::getParameter(), Log::info(), Log::instance(), and Log::warn().

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int Bioclim::iterate ( )
virtual

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

Reimplemented from AlgorithmImpl.

Definition at line 218 of file bioclim.cpp.

void Bioclim::logEnvelope ( )
private

Log the bioclimatic envelopes information.

Definition at line 388 of file bioclim.cpp.

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

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Member Data Documentation

bool Bioclim::_done
private

Definition at line 70 of file bioclim.hh.

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

Sample Bioclim::_maximum
private

Mininum value for each variable.

Definition at line 73 of file bioclim.hh.

Referenced by _getConfiguration(), _setConfiguration(), computeStats(), getValue(), and logEnvelope().

Sample Bioclim::_mean
private

Maximum value for each variable.

Definition at line 74 of file bioclim.hh.

Referenced by _getConfiguration(), _setConfiguration(), computeStats(), getValue(), and logEnvelope().

Sample Bioclim::_minimum
private

is true if the algorithm is finished.

Definition at line 72 of file bioclim.hh.

Referenced by _getConfiguration(), _setConfiguration(), computeStats(), getValue(), and logEnvelope().

Sample Bioclim::_std_dev
private

Mean of sampled points.

Definition at line 75 of file bioclim.hh.

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

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