#include <Sampler.hh>

Inheritance diagram for SamplerImpl:

Collaboration diagram for SamplerImpl:

Public Member Functions
	SamplerImpl ()

	SamplerImpl (const EnvironmentPtr &env, const OccurrencesPtr &presences, const OccurrencesPtr &absence, bool isNormalized=false)

	~SamplerImpl ()

EnvironmentPtr	getEnvironment ()

ConstEnvironmentPtr	getEnvironment () const

OccurrencesPtr	getPresences ()

ConstOccurrencesPtr	getPresences () const

OccurrencesPtr	getAbsences ()

ConstOccurrencesPtr	getAbsences () const

void	getMinMax (Sample min, Sample max) const

void	normalize (Normalizer *normalizerPtr)

bool	isNormalized () const

void	resetNormalization ()

int	numIndependent () const

int	numDependent () const

int	numPresence () const

int	numAbsence () const

ConstOccurrencePtr	getOneSample () const

ConstOccurrencePtr	getPresence () const

ConstOccurrencePtr	getPresence (int index) const

ConstOccurrencePtr	getAbsence () const

ConstOccurrencePtr	getAbsence (int index) const

OccurrencePtr	generateRandomSample (Scalar abundance=1.0) const

OccurrencePtr	getPseudoAbsence () const

OccurrencePtr	getPseudoPresence () const

OccurrencePtr	getPseudoAbsence (const Model &model, const Scalar threshold) const

OccurrencePtr	getPseudoPresence (const Model &model, const Scalar threshold) const

OccurrencePtr	getPseudoAbsenceOutsideInterval (const Sample minimum, const Sample maximum) const

OccurrencePtr	getPseudoPresenceInsideInterval (const Sample minimum, const Sample maximum) const

OccurrencesPtr	getPseudoAbsences (const int &numPoints, const Model &model, const Scalar threshold=0.5, const bool geoUnique=false, const bool envUnique=false, const int idSequenceStart=1) const

OccurrencesPtr	getPseudoPresences (const int &numPoints, const Model &model, const Scalar threshold=0.5, const bool geoUnique=false, const bool envUnique=false, const int idSequenceStart=1) const

OccurrencesPtr	getPseudoAbsences (const int &numPoints, const Sample minimum, const Sample maximum, const bool geoUnique=false, const bool envUnique=false, const int idSequenceStart=1) const

OccurrencesPtr	getPseudoPresences (const int &numPoints, const Sample minimum, const Sample maximum, const bool geoUnique=false, const bool envUnique=false, const int idSequenceStart=1) const

int	isCategorical (int i)

void	environmentallyUnique ()

bool	isEnvironmentallyUnique (const OccurrencesPtr &occurrences, const OccurrencePtr &point) const

void	spatiallyUnique ()

bool	isSpatiallyUnique (const OccurrencesPtr &occurrences, const OccurrencePtr &point) const

ConfigurationPtr	getConfiguration () const

void	setConfiguration (const ConstConfigurationPtr &)

void	dump () const

Public Member Functions inherited from Configurable
virtual	~Configurable ()

Public Member Functions inherited from Normalizable
virtual	~Normalizable ()

Private Member Functions
ConstOccurrencePtr	getRandomOccurrence (const OccurrencesPtr &occur) const

void	setEnvironmentInOccurrences ()

void	environmentallyUnique (OccurrencesPtr &occurrencesPtr, const char *type)

void	spatiallyUnique (OccurrencesPtr &occurrencesPtr, const char *type)

Private Member Functions inherited from ReferenceCountedObject
	ReferenceCountedObject ()

virtual	~ReferenceCountedObject ()=0

Private Attributes
OccurrencesPtr	_presence

OccurrencesPtr	_absence

EnvironmentPtr	_env

bool	_normalized

Friends
class	ReferenceCountedPointer< SamplerImpl >

class	ReferenceCountedPointer< const SamplerImpl >

Detailed Description

Base class to create samplers of environmental variables and occurrence data. Each derived class can implement different behaviors, such as proportional sampling according to the distribution of occurrence data, disproportional sampling regarding presence and absence data, etc.

Definition at line 81 of file Sampler.hh.

Constructor & Destructor Documentation

SamplerImpl::SamplerImpl ( )

Definition at line 69 of file Sampler.cpp.

References Log::debug(), and Log::instance().

Here is the call graph for this function:

SamplerImpl::SamplerImpl	(	const EnvironmentPtr &	env,
		const OccurrencesPtr &	presences,
		const OccurrencesPtr &	absence,
		bool	isNormalized = `false`
	)

Definition at line 81 of file Sampler.cpp.

References Log::debug(), Log::instance(), and setEnvironmentInOccurrences().

Here is the call graph for this function:

SamplerImpl::~SamplerImpl ( )

Definition at line 100 of file Sampler.cpp.

References Log::debug(), and Log::instance().

Here is the call graph for this function:

Member Function Documentation

void SamplerImpl::dump ( ) const

Definition at line 1156 of file Sampler.cpp.

References _absence, and _presence.

void SamplerImpl::environmentallyUnique ( )

Remove sample duplicates accross the environment (presences and absences are treated separately). After erasing a point, the remaining one increases the abundance by one.

Definition at line 927 of file Sampler.cpp.

References _absence, _presence, Log::info(), and Log::instance().

Here is the call graph for this function:

void SamplerImpl::environmentallyUnique	(	OccurrencesPtr &	occurrencesPtr,
		const char *	type
	)

private

Definition at line 942 of file Sampler.cpp.

References _env, Sample::equals(), Log::info(), and Log::instance().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::generateRandomSample ( Scalar abundance = 1.0 ) const

Generate a random sample

Definition at line 387 of file Sampler.cpp.

References _env, Log::error(), Log::instance(), and numDependent().

Referenced by getPseudoAbsence(), and getPseudoPresence().

Here is the call graph for this function:

ConstOccurrencePtr SamplerImpl::getAbsence ( ) const

inline

Get a random absence point

Definition at line 162 of file Sampler.hh.

Referenced by getOneSample().

ConstOccurrencePtr SamplerImpl::getAbsence ( int index ) const

inline

Get a specific absence point by index

Definition at line 168 of file Sampler.hh.

OccurrencesPtr SamplerImpl::getAbsences ( )

inline

Definition at line 101 of file Sampler.hh.

ConstOccurrencesPtr SamplerImpl::getAbsences ( ) const

inline

Definition at line 102 of file Sampler.hh.

ConfigurationPtr SamplerImpl::getConfiguration ( ) const

virtual

Implements Configurable.

Definition at line 127 of file Sampler.cpp.

References _absence, _env, and _presence.

EnvironmentPtr SamplerImpl::getEnvironment ( )

inline

Definition at line 95 of file Sampler.hh.

ConstEnvironmentPtr SamplerImpl::getEnvironment ( ) const

inline

Definition at line 96 of file Sampler.hh.

void SamplerImpl::getMinMax	(	Sample *	min,
		Sample *	max
	)		const

virtual

Indicate that all non categorical variable layers must be normalized according to the interval [min, max]. Returns through offsets, scales the normalization parameters.

Implements Normalizable.

Definition at line 209 of file Sampler.cpp.

References _absence, and _presence.

ConstOccurrencePtr SamplerImpl::getOneSample ( ) const

Samples one presence, absence or pseudo-absence point in a uniform way. There is 50% of chance to get a presence point and 50% of get an absence or pseudo-absence point. If there are real absence points (user input) then only absences are sampled. If there are not real absence, samples pseudo-absence points.

Returns: Zero if got an absence or pseudo-absence point and not zero if got a presence point.

Definition at line 346 of file Sampler.cpp.

References _absence, _presence, Log::error(), getAbsence(), getPresence(), getPseudoAbsence(), and Log::instance().

Here is the call graph for this function:

ConstOccurrencePtr SamplerImpl::getPresence ( ) const

inline

Get a random presence point

Definition at line 150 of file Sampler.hh.

Referenced by getOneSample().

ConstOccurrencePtr SamplerImpl::getPresence ( int index ) const

inline

Get a specific presence point by index

Definition at line 156 of file Sampler.hh.

OccurrencesPtr SamplerImpl::getPresences ( )

inline

Definition at line 98 of file Sampler.hh.

ConstOccurrencesPtr SamplerImpl::getPresences ( ) const

inline

Definition at line 99 of file Sampler.hh.

OccurrencePtr SamplerImpl::getPseudoAbsence ( ) const

Generate a pseudo absence sample

Definition at line 412 of file Sampler.cpp.

References generateRandomSample().

Referenced by getOneSample(), getPseudoAbsence(), getPseudoAbsenceOutsideInterval(), and getPseudoAbsences().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::getPseudoAbsence	(	const Model &	model,
		const Scalar	threshold
	)		const

Generate a pseudo absence sample outside the given model

Definition at line 428 of file Sampler.cpp.

References Log::error(), getPseudoAbsence(), and Log::instance().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::getPseudoAbsenceOutsideInterval	(	const Sample *	minimum,
		const Sample *	maximum
	)		const

Generate a pseudo absence sample outside the minimum and maximum

Definition at line 504 of file Sampler.cpp.

References Log::error(), getPseudoAbsence(), Log::instance(), and Sample::size().

Referenced by getPseudoAbsences().

Here is the call graph for this function:

OccurrencesPtr SamplerImpl::getPseudoAbsences	(	const int &	numPoints,
		const Model &	model,
		const Scalar	threshold = `0.5`,
		const bool	geoUnique = `false`,
		const bool	envUnique = `false`,
		const int	idSequenceStart = `1`
	)		const

Generate pseudo absence samples outside the given model according to the specified threshold

Definition at line 598 of file Sampler.cpp.

References _absence, _presence, getPseudoAbsence(), isEnvironmentallyUnique(), and isSpatiallyUnique().

Here is the call graph for this function:

OccurrencesPtr SamplerImpl::getPseudoAbsences	(	const int &	numPoints,
		const Sample *	minimum,
		const Sample *	maximum,
		const bool	geoUnique = `false`,
		const bool	envUnique = `false`,
		const int	idSequenceStart = `1`
	)		const

Generate pseudo absence samples outside the minimum and maximum

Definition at line 760 of file Sampler.cpp.

References _absence, _presence, getPseudoAbsenceOutsideInterval(), isEnvironmentallyUnique(), and isSpatiallyUnique().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::getPseudoPresence ( ) const

Generate a pseudo presence sample

Definition at line 420 of file Sampler.cpp.

References generateRandomSample().

Referenced by getPseudoPresence(), getPseudoPresenceInsideInterval(), and getPseudoPresences().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::getPseudoPresence	(	const Model &	model,
		const Scalar	threshold
	)		const

Generate a pseudo presence sample inside the given model

Definition at line 466 of file Sampler.cpp.

References Log::error(), getPseudoPresence(), and Log::instance().

Here is the call graph for this function:

OccurrencePtr SamplerImpl::getPseudoPresenceInsideInterval	(	const Sample *	minimum,
		const Sample *	maximum
	)		const

Generate a pseudo presence sample inside the minimum and maximum

Definition at line 551 of file Sampler.cpp.

References Log::error(), getPseudoPresence(), Log::instance(), and Sample::size().

Referenced by getPseudoPresences().

Here is the call graph for this function:

OccurrencesPtr SamplerImpl::getPseudoPresences	(	const int &	numPoints,
		const Model &	model,
		const Scalar	threshold = `0.5`,
		const bool	geoUnique = `false`,
		const bool	envUnique = `false`,
		const int	idSequenceStart = `1`
	)		const

Generate pseudo presence samples inside the given model according to the specified threshold

Definition at line 679 of file Sampler.cpp.

References _absence, _presence, getPseudoPresence(), isEnvironmentallyUnique(), and isSpatiallyUnique().

Here is the call graph for this function:

OccurrencesPtr SamplerImpl::getPseudoPresences	(	const int &	numPoints,
		const Sample *	minimum,
		const Sample *	maximum,
		const bool	geoUnique = `false`,
		const bool	envUnique = `false`,
		const int	idSequenceStart = `1`
	)		const

Generate pseudo presence samples inside the minimum and maximum

Definition at line 834 of file Sampler.cpp.

References _absence, _presence, getPseudoPresenceInsideInterval(), isEnvironmentallyUnique(), and isSpatiallyUnique().

Here is the call graph for this function:

ConstOccurrencePtr SamplerImpl::getRandomOccurrence ( const OccurrencesPtr & occur ) const

private

Definition at line 1141 of file Sampler.cpp.

int SamplerImpl::isCategorical ( int i )

Returns 1 if i-th variable is categorical, otherwise returns 0.

Definition at line 908 of file Sampler.cpp.

References _env.

bool SamplerImpl::isEnvironmentallyUnique	(	const OccurrencesPtr &	occurrences,
		const OccurrencePtr &	point
	)		const

If OccurrencePtr point duplicates accross the environment, return false. Otherwise return true. Missae(set/2008)

Definition at line 1065 of file Sampler.cpp.

References _env, and Sample::equals().

Referenced by getPseudoAbsences(), and getPseudoPresences().

Here is the call graph for this function:

bool SamplerImpl::isNormalized ( ) const

inline

Returns true if "normalized()" was called, false otherwise.

Definition at line 115 of file Sampler.hh.

bool SamplerImpl::isSpatiallyUnique	(	const OccurrencesPtr &	occurrences,
		const OccurrencePtr &	point
	)		const

If OccurrencePtr point duplicates accross geographic space, return false. Otherwise return true. Uniqueness is considered for row/col pairs defined in the input mask. If mask is undefined, use first layer as a mask. Missae(set/2008)

Definition at line 1097 of file Sampler.cpp.

References _env, and Map::getRowColumn().

Referenced by getPseudoAbsences(), and getPseudoPresences().

Here is the call graph for this function:

void SamplerImpl::normalize ( Normalizer * normalizerPtr )

virtual

Normalize sampler data

Implements Normalizable.

Definition at line 233 of file Sampler.cpp.

References _absence, _env, _normalized, _presence, Log::error(), Log::instance(), and setEnvironmentInOccurrences().

Here is the call graph for this function:

int SamplerImpl::numAbsence ( ) const

Number of absences (localities with no occurrence).

Definition at line 337 of file Sampler.cpp.

References _absence.

int SamplerImpl::numDependent ( ) const

Number of dependent variables (attributes of the occurred thing). These are the variables to be modelled.

Definition at line 319 of file Sampler.cpp.

References _absence, and _presence.

Referenced by generateRandomSample().

int SamplerImpl::numIndependent ( ) const

Number of independent variables (environmental variables).

Definition at line 296 of file Sampler.cpp.

References _absence, _env, and _presence.

int SamplerImpl::numPresence ( ) const

Number of presences (occurrence points).

Definition at line 328 of file Sampler.cpp.

References _presence.

void SamplerImpl::resetNormalization ( )

Reset normalization

Definition at line 273 of file Sampler.cpp.

References _absence, _env, _normalized, and _presence.

void SamplerImpl::setConfiguration ( const ConstConfigurationPtr & config )

virtual

Implements Configurable.

Definition at line 156 of file Sampler.cpp.

References _absence, _env, _presence, createEnvironment(), Log::debug(), Log::error(), Log::instance(), and setEnvironmentInOccurrences().

Here is the call graph for this function:

void SamplerImpl::setEnvironmentInOccurrences ( )

private

Definition at line 108 of file Sampler.cpp.

References _absence, _env, and _presence.

Referenced by normalize(), SamplerImpl(), and setConfiguration().

void SamplerImpl::spatiallyUnique ( )

Remove sample duplicates accross geographic space (presences and absences are treated separately). After erasing a point, the remaining one increases the abundance by one. Uniqueness is considered for row/col pairs defined in the input mask. If mask is undefined, use first layer as a mask.

Definition at line 990 of file Sampler.cpp.

References _absence, _presence, Log::info(), and Log::instance().

Here is the call graph for this function: