Bioclim Class Reference

#include <bioclim.hh>

Inheritance diagram for Bioclim:

Collaboration diagram for Bioclim:

List of all members.

Public Member Functions
	Bioclim ()
	~Bioclim ()
int	initialize ()
int	iterate ()
int	done () const
Scalar	getValue (const Sample &x) const
int	getConvergence (Scalar *const val) const
Protected Member Functions
void	_getConfiguration (ConfigurationPtr &) const
void	_setConfiguration (const ConstConfigurationPtr &)
Private Member Functions
void	computeStats (const OccurrencesPtr &)
void	logEnvelope ()
Private Attributes
bool	_done
Sample	_minimum
	> is true if the algorithm is finished.
Sample	_maximum
	> Mininum value for each variable.
Sample	_mean
	> Maximum value for each variable.
Sample	_std_dev
	> Mean of sampled points.

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Detailed Description

Declaration of Bioclimatic Envelope Algorithm - Nix, 1986.

Author:

Mauro Muñoz <mauro@cria.org.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.

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Constructor & Destructor Documentation

Bioclim::Bioclim

(

)

Definition at line 157 of file bioclim.cpp.

Bioclim::~Bioclim

(

)

Definition at line 170 of file bioclim.cpp.

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Member Function Documentation

void Bioclim::_getConfiguration

(

ConfigurationPtr &

config

)

const [protected, virtual]

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

)

[protected, virtual]

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:

x	Environmental 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().

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

• bioclim.hh
• bioclim.cpp