Manages a collection of elemental profiles (samples) for source fingerprinting analysis. More...

#include <elemental_profile_set.h>

Inheritance diagram for Elemental_Profile_Set:

Collaboration diagram for Elemental_Profile_Set:

Public Member Functions
	Elemental_Profile_Set ()

	Elemental_Profile_Set (const Elemental_Profile_Set &other)

Elemental_Profile_Set &	operator= (const Elemental_Profile_Set &other)

Elemental_Profile *	AppendProfile (const string &name, const Elemental_Profile &profile=Elemental_Profile(), map< string, element_information > *elementinfo=nullptr)
	Add a new sample profile to the set.

void	AppendProfiles (const Elemental_Profile_Set &profiles, map< string, element_information > *elementinfo)
	Add multiple profiles from another set.

void	UpdateElementDistributions ()
	Rebuild element distributions from all profiles.

Elemental_Profile *	GetProfile (const string &name)
	Get profile by sample name (mutable)

Elemental_Profile	GetProfile (const string &name) const
	Get profile by sample name (const)

Elemental_Profile *	GetProfile (unsigned int index)
	Get profile by index (mutable)

Elemental_Profile	GetProfile (unsigned int index) const
	Get profile by index (const)

vector< string >	GetSampleNames () const
	Get all sample names in the set.

vector< string >	GetElementNames () const
	Get all element names (from first profile)

vector< double >	GetAllConcentrationsFor (const string &element_name)
	Get all concentration values for a specific element across samples.

vector< double >	GetConcentrationsForSample (const string &sample_name) const
	Get all element concentrations for a specific sample.

bool	ContainsElement (const string &element_name) const
	Check if an element exists in ALL profiles.

Elemental_Profile_Set	ExtractElements (const vector< string > &element_list) const
	Create subset with only specified elements.

Elemental_Profile_Set	ExtractChemicalElements (const map< string, element_information > *elementinfo, bool isotopes) const
	Create subset with only chemical elements (and optionally isotopes)

Elemental_Profile_Set	CreateCorrectedSet (bool exclude_samples, bool exclude_elements, bool omnsizecorrect, const vector< double > &om_size, const map< string, element_information > *elementinfo=nullptr) const
	Create corrected and filtered subset.

Elemental_Profile_Set	CopyIncludedInAnalysis (bool applyomsizecorrection, const vector< double > &om_size, map< string, element_information > *elementinfo=nullptr)
	Copy only samples marked for inclusion in analysis.

Elemental_Profile_Set	EliminateSamples (vector< string > samples_to_eliminate, map< string, element_information > *elementinfo) const
	Create subset excluding specified samples.

ConcentrationSet *	GetElementDistribution (const string &element_name)
	Get distribution for a specific element (mutable)

ConcentrationSet	GetElementDistribution (const string &element_name) const
	Get distribution for a specific element (const)

distribution_type	GetAssignedDistribution (const string &element_name) const
	Get assigned distribution type for an element.

CVector	CalculateElementMeans (const vector< string > &element_order=vector< string >()) const
	Calculate mean concentration for each element.

CMBMatrix	CalculateCovarianceMatrix ()
	Calculate covariance matrix across elements.

CMBMatrix	CalculateCorrelationMatrix ()
	Calculate correlation matrix across elements.

CMBVector	CalculateKolmogorovSmirnovStatistics (distribution_type dist_type)
	Calculate Kolmogorov-Smirnov statistics for all elements.

double	GetMaximum () const
	Get maximum concentration across all elements and samples.

double	GetMinimum () const
	Get minimum concentration across all elements and samples.

double	GetEstimatedMu (const string &element) const
	Get estimated mu parameter for an element.

double	GetEstimatedSigma (const string &element) const
	Get estimated sigma parameter for an element.

bool	SetEstimatedMu (const string &element, const double &value)
	Set estimated mu parameter for an element.

bool	SetEstimatedSigma (const string &element, const double &value)
	Set estimated sigma parameter for an element.

Distribution *	GetEstimatedDistribution (const string &element_name)
	Get estimated distribution for an element (for MCMC optimization)

Distribution *	GetFittedDistribution (const string &element_name)
	Get fitted distribution for an element (from data, for likelihood)

MultipleLinearRegressionSet	BuildRegressionModels (const string &om, const string &d, regression_form form=regression_form::linear, const double &p_value_threshold=0.05)
	Build MLR models for all elements vs OM and particle size.

MultipleLinearRegression	BuildRegressionModel (const string &element, const string &om, const string &d, regression_form form=regression_form::linear, const double &p_value_threshold=0.05)
	Build MLR model for single element vs OM and particle size.

void	SetRegressionModels (const string &om, const string &d, regression_form form=regression_form::linear, const double &p_value_threshold=0.05)
	Set regression models (build new)

void	SetRegressionModels (const MultipleLinearRegressionSet *mlrset)
	Set regression models (copy existing)

MultipleLinearRegressionSet *	GetRegressionModels ()
	Get internal regression model set.

ResultItem	GetRegressionsAsResult ()
	Get regressions wrapped in ResultItem for display.

Elemental_Profile_Set	ApplyOrganicMatterAndSizeCorrections (const vector< double > &om_size, map< string, element_information > *elementinfo=nullptr)
	Apply OM and particle size corrections to all profiles.

CMBVector	CalculateBoxCoxParameters ()
	Calculate optimal Box-Cox lambda for each element.

Elemental_Profile_Set	ApplyBoxCoxTransform (CMBVector *lambda_vals=nullptr)
	Apply Box-Cox transformation to all profiles.

CMBMatrix	DetectOutliers (const double &lowerlimit=0, const double &upperlimit=0)
	Detect outliers using Box-Cox transformation and standardization.

bool	OutlierAnalysisDone () const
	Check if outlier analysis has been performed.

vector< string >	CheckForNegativeValues (const vector< string > &element_names) const
	Check for elements with negative values.

bool	SetContribution (const double &value)
	Set contribution value for this source.

double	GetContribution () const
	Get contribution value.

bool	SetContributionSoftmax (const double &value)
	Set softmax-transformed contribution.

double	GetContributionSoftmax () const
	Get softmax-transformed contribution.

Elemental_Profile	SelectTopElementsAggregate (int n) const
	Select top N elements across all samples (aggregate minimum)

CMBVector	CalculateDotProduct (const CVector &v) const
	Calculate dot product of each profile with weight vector.

CMBMatrix	ToMatrix () const
	Convert to matrix format (samples � elements)

gsl_matrix *	CopyToGSLMatrix () const
	Convert to GSL matrix for statistical functions.

string	ToString () const override
	Convert object to string representation.

QTableWidget *	ToTable () override
	Create a Qt table widget representation of the data.

bool	writetofile (QFile *file) override
	Write object data to a file.

QJsonObject	toJsonObject () const override
	Serialize object to JSON format.

bool	ReadFromJsonObject (const QJsonObject &jsonobject) override
	Deserialize object from JSON format.

bool	Read (const QStringList &strlist) override
	Parse object data from a string list.

Public Member Functions inherited from Interface
	Interface ()
	Default constructor.

	Interface (const Interface &intf)
	Copy constructor.

Interface &	operator= (const Interface &intf)
	Assignment operator.

string	GetNotes () const
	Get the notes/annotations associated with this object.

void	SetNotes (const string &note)
	Set the notes for this object, replacing any existing notes.

void	AppendtoNotes (const string &note)
	Append a note to existing notes.

void	ClearNotes ()
	Clear all notes associated with this object.

void	SetLimit (_range lowhigh, const double &value)
	Set upper or lower limit for value highlighting.

void	SetOption (options_key opt, bool val)
	Set a configuration option.

bool	Option (options_key opt)
	Get the current value of a configuration option.

options &	GetOptions ()
	Get reference to the options structure.

QString	XAxisLabel () const
	Get the X-axis label.

QString	YAxisLabel () const
	Get the Y-axis label.

bool	SetXAxisLabel (const QString &label)
	Set the X-axis label.

bool	SetYAxisLabel (const QString &label)
	Set the Y-axis label.

Private Attributes
map< string, ConcentrationSet >	element_distributions_
	Concentration distributions for each element.

MultipleLinearRegressionSet	mlr_vs_om_size_
	MLR models for OM/size corrections.

double	contribution_ = 0.0
	Source contribution (for CMB)

double	contribution_softmax_ = 0.0
	Softmax-transformed contribution.

bool	outlierdone_ = false
	Flag indicating outlier analysis performed.

Additional Inherited Members
Public Attributes inherited from Interface
double	lowlimit
	Lower threshold for value highlighting (when enabled)

double	highlimit
	Upper threshold for value highlighting (when enabled)

bool	highlightoutsideoflimit = false
	Flag indicating whether to highlight values outside defined limits.

Detailed Description

Manages a collection of elemental profiles (samples) for source fingerprinting analysis.

This class stores multiple Elemental_Profile objects (one per sample) and provides:

Statistical analysis across samples (distributions, covariance, correlation)
Data extraction and filtering operations
Organic matter and particle size corrections via multiple linear regression
Box-Cox transformations and outlier detection
Source contribution tracking for CMB (Chemical Mass Balance) analysis

Definition at line 27 of file elemental_profile_set.h.

Constructor & Destructor Documentation

◆ Elemental_Profile_Set() [1/2]

Elemental_Profile_Set::Elemental_Profile_Set ( )

Definition at line 8 of file elemental_profile_set.cpp.

References string.

◆ Elemental_Profile_Set() [2/2]

Elemental_Profile_Set::Elemental_Profile_Set ( const Elemental_Profile_Set & other )

Definition at line 19 of file elemental_profile_set.cpp.

References string.

Member Function Documentation

◆ AppendProfile()

Elemental_Profile * Elemental_Profile_Set::AppendProfile	(	const string &	name,
		const Elemental_Profile &	profile = `Elemental_Profile()`,
		map< string, element_information > *	elementinfo = `nullptr`
	)

Add a new sample profile to the set.

Parameters

name	Sample identifier
profile	Elemental profile data
elementinfo	Optional element metadata for filtering

Returns: Pointer to the added profile, or nullptr if name already exists

Definition at line 179 of file elemental_profile_set.cpp.

References Elemental_Profile::CreateAnalysisProfile(), element_information::do_not_include, element_distributions_, name, element_information::organic_carbon, and element_information::particle_size.

◆ AppendProfiles()

void Elemental_Profile_Set::AppendProfiles	(	const Elemental_Profile_Set &	profiles,
		map< string, element_information > *	elementinfo
	)

Add multiple profiles from another set.

Parameters

profiles	Source profile set
elementinfo	Optional element metadata for filtering

Definition at line 221 of file elemental_profile_set.cpp.

References AppendProfile(), and UpdateElementDistributions().

Referenced by SourceSinkData::LumpAllProfileSets().

◆ ApplyBoxCoxTransform()

Elemental_Profile_Set Elemental_Profile_Set::ApplyBoxCoxTransform ( CMBVector * lambda_vals = nullptr )

Apply Box-Cox transformation to all profiles.

Definition at line 876 of file elemental_profile_set.cpp.

References ConcentrationSet::ApplyBoxCoxTransform(), CalculateBoxCoxParameters(), distribution, and element_distributions_.

◆ ApplyOrganicMatterAndSizeCorrections()

Elemental_Profile_Set Elemental_Profile_Set::ApplyOrganicMatterAndSizeCorrections	(	const vector< double > &	om_size,
		map< string, element_information > *	elementinfo = `nullptr`
	)

Apply OM and particle size corrections to all profiles.

Definition at line 772 of file elemental_profile_set.cpp.

References AppendProfile(), Elemental_Profile::ApplyOrganicMatterAndSizeCorrections(), and mlr_vs_om_size_.

Referenced by CopyIncludedInAnalysis().

◆ BuildRegressionModel()

MultipleLinearRegression Elemental_Profile_Set::BuildRegressionModel	(	const string &	element,
		const string &	om,
		const string &	d,
		regression_form	form = `regression_form::linear`,
		const double &	p_value_threshold = `0.05`
	)

Build MLR model for single element vs OM and particle size.

Definition at line 512 of file elemental_profile_set.cpp.

References GetAllConcentrationsFor(), MultipleLinearRegression::Regress(), MultipleLinearRegression::SetDependentVariableName(), MultipleLinearRegression::SetEquation(), and MultipleLinearRegression::SetPValueThreshold().

Referenced by BuildRegressionModels().

◆ BuildRegressionModels()

MultipleLinearRegressionSet Elemental_Profile_Set::BuildRegressionModels	(	const string &	om,
		const string &	d,
		regression_form	form = `regression_form::linear`,
		const double &	p_value_threshold = `0.05`
	)

Build MLR models for all elements vs OM and particle size.

Definition at line 494 of file elemental_profile_set.cpp.

References BuildRegressionModel(), and GetElementNames().

Referenced by SetRegressionModels().

◆ CalculateBoxCoxParameters()

CMBVector Elemental_Profile_Set::CalculateBoxCoxParameters ( )

Calculate optimal Box-Cox lambda for each element.

Definition at line 794 of file elemental_profile_set.cpp.

References distribution, element_distributions_, and CMBVector::SetLabel().

Referenced by ApplyBoxCoxTransform(), and DetectOutliers().

◆ CalculateCorrelationMatrix()

CMBMatrix Elemental_Profile_Set::CalculateCorrelationMatrix ( )

Calculate correlation matrix across elements.

Definition at line 621 of file elemental_profile_set.cpp.

References CopyToGSLMatrix(), GetElementNames(), CMBMatrix::SetColumnLabel(), and CMBMatrix::SetRowLabel().

◆ CalculateCovarianceMatrix()

CMBMatrix Elemental_Profile_Set::CalculateCovarianceMatrix ( )

Calculate covariance matrix across elements.

Definition at line 578 of file elemental_profile_set.cpp.

References CopyToGSLMatrix(), GetElementNames(), CMBMatrix::SetColumnLabel(), and CMBMatrix::SetRowLabel().

◆ CalculateDotProduct()

CMBVector Elemental_Profile_Set::CalculateDotProduct ( const CVector & v ) const

Calculate dot product of each profile with weight vector.

Definition at line 984 of file elemental_profile_set.cpp.

References CMBVector::SetLabel().

◆ CalculateElementMeans()

CVector Elemental_Profile_Set::CalculateElementMeans ( const vector< string > & element_order = vector<string>() ) const

Calculate mean concentration for each element.

Definition at line 700 of file elemental_profile_set.cpp.

References element_distributions_, and GetElementNames().

◆ CalculateKolmogorovSmirnovStatistics()

CMBVector Elemental_Profile_Set::CalculateKolmogorovSmirnovStatistics ( distribution_type dist_type )

Calculate Kolmogorov-Smirnov statistics for all elements.

Definition at line 684 of file elemental_profile_set.cpp.

References GetElementDistribution(), GetElementNames(), and CMBVector::SetLabels().

◆ CheckForNegativeValues()

vector< string > Elemental_Profile_Set::CheckForNegativeValues ( const vector< string > & element_names ) const

Check for elements with negative values.

Definition at line 936 of file elemental_profile_set.cpp.

References GetElementDistribution(), and ConcentrationSet::GetMinimum().

◆ ContainsElement()

bool Elemental_Profile_Set::ContainsElement ( const string & element_name ) const

Check if an element exists in ALL profiles.

Definition at line 339 of file elemental_profile_set.cpp.

◆ CopyIncludedInAnalysis()

Elemental_Profile_Set Elemental_Profile_Set::CopyIncludedInAnalysis	(	bool	applyomsizecorrection,
		const vector< double > &	om_size,
		map< string, element_information > *	elementinfo = `nullptr`
	)

Copy only samples marked for inclusion in analysis.

Definition at line 114 of file elemental_profile_set.cpp.

References AppendProfile(), ApplyOrganicMatterAndSizeCorrections(), mlr_vs_om_size_, and SetRegressionModels().

◆ CopyToGSLMatrix()

gsl_matrix * Elemental_Profile_Set::CopyToGSLMatrix ( ) const

Convert to GSL matrix for statistical functions.

Definition at line 660 of file elemental_profile_set.cpp.

References GetElementNames(), and matrix.

Referenced by CalculateCorrelationMatrix(), and CalculateCovarianceMatrix().

◆ CreateCorrectedSet()

Elemental_Profile_Set Elemental_Profile_Set::CreateCorrectedSet	(	bool	exclude_samples,
		bool	exclude_elements,
		bool	omnsizecorrect,
		const vector< double > &	om_size,
		const map< string, element_information > *	elementinfo = `nullptr`
	)		const

Create corrected and filtered subset.

Parameters

exclude_samples	If true, exclude samples marked as excluded
exclude_elements	If true, exclude elements marked as excluded
omnsizecorrect	If true, apply organic matter and size corrections
om_size	Target OM and size values for correction
elementinfo	Element metadata for filtering

Definition at line 52 of file elemental_profile_set.cpp.

References AppendProfile(), mlr_vs_om_size_, and SetRegressionModels().

◆ DetectOutliers()

CMBMatrix Elemental_Profile_Set::DetectOutliers	(	const double &	lowerlimit = `0`,
		const double &	upperlimit = `0`
	)

Detect outliers using Box-Cox transformation and standardization.

Parameters

lowerlimit	Lower threshold for standardized values
upperlimit	Upper threshold for standardized values

Returns: Matrix of outlier magnitudes

Definition at line 810 of file elemental_profile_set.cpp.

References Interface::AppendtoNotes(), ConcentrationSet::ApplyBoxCoxTransform(), CalculateBoxCoxParameters(), ConcentrationSet::CalculateMean(), ConcentrationSet::CalculateStdDev(), distribution, element_distributions_, outlierdone_, CMBMatrix::SetColumnLabel(), and CMBMatrix::SetRowLabel().

◆ EliminateSamples()

Elemental_Profile_Set Elemental_Profile_Set::EliminateSamples	(	vector< string >	samples_to_eliminate,
		map< string, element_information > *	elementinfo
	)		const

Create subset excluding specified samples.

Definition at line 141 of file elemental_profile_set.cpp.

References AppendProfile(), mlr_vs_om_size_, and SetRegressionModels().

◆ ExtractChemicalElements()

Elemental_Profile_Set Elemental_Profile_Set::ExtractChemicalElements	(	const map< string, element_information > *	elementinfo,
		bool	isotopes
	)		const

Create subset with only chemical elements (and optionally isotopes)

Parameters

elementinfo	Element metadata for classification
isotopes	Whether to include isotopes

Definition at line 87 of file elemental_profile_set.cpp.

References AppendProfile().

◆ ExtractElements()

Elemental_Profile_Set Elemental_Profile_Set::ExtractElements ( const vector< string > & element_list ) const

Create subset with only specified elements.

Definition at line 101 of file elemental_profile_set.cpp.

References AppendProfile().

◆ GetAllConcentrationsFor()

vector< double > Elemental_Profile_Set::GetAllConcentrationsFor ( const string & element_name )

Get all concentration values for a specific element across samples.

Definition at line 425 of file elemental_profile_set.cpp.

Referenced by BuildRegressionModel().

◆ GetAssignedDistribution()

distribution_type Elemental_Profile_Set::GetAssignedDistribution ( const string & element_name ) const

Get assigned distribution type for an element.

◆ GetConcentrationsForSample()

vector< double > Elemental_Profile_Set::GetConcentrationsForSample ( const string & sample_name ) const

Get all element concentrations for a specific sample.

Definition at line 444 of file elemental_profile_set.cpp.

Referenced by SourceSinkData::ExtractConcentrationData().

◆ GetContribution()

double Elemental_Profile_Set::GetContribution ( ) const

inline

Get contribution value.

Definition at line 346 of file elemental_profile_set.h.

References contribution_.

Referenced by SourceSinkData::GetContributionVector().

◆ GetContributionSoftmax()

double Elemental_Profile_Set::GetContributionSoftmax ( ) const

inline

Get softmax-transformed contribution.

Definition at line 356 of file elemental_profile_set.h.

References contribution_softmax_.

Referenced by SourceSinkData::GetContributionVectorSoftmax().

◆ GetElementDistribution() [1/2]

ConcentrationSet * Elemental_Profile_Set::GetElementDistribution ( const string & element_name )

Get distribution for a specific element (mutable)

Definition at line 1001 of file elemental_profile_set.cpp.

References element_distributions_.

Referenced by SourceSinkData::ANOVA(), CalculateKolmogorovSmirnovStatistics(), CheckForNegativeValues(), SourceSinkData::GetElementDistribution(), SourceSinkData::LogLikelihoodSourceElementalDistributions(), and MainWindow::showdistributionsforelements().

◆ GetElementDistribution() [2/2]

ConcentrationSet Elemental_Profile_Set::GetElementDistribution ( const string & element_name ) const

Get distribution for a specific element (const)

Definition at line 1009 of file elemental_profile_set.cpp.

References element_distributions_.

◆ GetElementNames()

vector< string > Elemental_Profile_Set::GetElementNames ( ) const

Get all element names (from first profile)

Definition at line 356 of file elemental_profile_set.cpp.

Referenced by BuildRegressionModels(), CalculateCorrelationMatrix(), CalculateCovarianceMatrix(), CalculateElementMeans(), CalculateKolmogorovSmirnovStatistics(), CopyToGSLMatrix(), GeneralChart::PlotProfileSet(), ToMatrix(), ToString(), and ToTable().

◆ GetEstimatedDistribution()

Distribution * Elemental_Profile_Set::GetEstimatedDistribution ( const string & element_name )

Get estimated distribution for an element (for MCMC optimization)

Definition at line 1020 of file elemental_profile_set.cpp.

References element_distributions_.

Referenced by SourceSinkData::BuildSourceMeanMatrix(), and SourceSinkData::BuildSourceMeanMatrix_Isotopes().

◆ GetEstimatedMu()

double Elemental_Profile_Set::GetEstimatedMu ( const string & element ) const

Get estimated mu parameter for an element.

◆ GetEstimatedSigma()

double Elemental_Profile_Set::GetEstimatedSigma ( const string & element ) const

Get estimated sigma parameter for an element.

◆ GetFittedDistribution()

Distribution * Elemental_Profile_Set::GetFittedDistribution ( const string & element_name )

Get fitted distribution for an element (from data, for likelihood)

Definition at line 1028 of file elemental_profile_set.cpp.

References element_distributions_.

◆ GetMaximum()

double Elemental_Profile_Set::GetMaximum ( ) const

Get maximum concentration across all elements and samples.

Definition at line 455 of file elemental_profile_set.cpp.

Referenced by GeneralChart::PlotProfileSet().

◆ GetMinimum()

double Elemental_Profile_Set::GetMinimum ( ) const

Get minimum concentration across all elements and samples.

Definition at line 474 of file elemental_profile_set.cpp.

Referenced by GeneralChart::PlotProfileSet().

◆ GetProfile() [1/4]

Elemental_Profile * Elemental_Profile_Set::GetProfile ( const string & name )

Get profile by sample name (mutable)

Returns: Pointer to profile, or nullptr if not found

Definition at line 375 of file elemental_profile_set.cpp.

References name.

Referenced by SourceSinkData::ObservedDataforSelectedSample(), SourceSinkData::ObservedDataforSelectedSample_Isotope(), and SourceSinkData::ObservedDataforSelectedSample_Isotope_delta().

◆ GetProfile() [2/4]

Elemental_Profile Elemental_Profile_Set::GetProfile ( const string & name ) const

Get profile by sample name (const)

Returns: Copy of profile, or empty profile if not found

Definition at line 399 of file elemental_profile_set.cpp.

References name.

◆ GetProfile() [3/4]

Elemental_Profile * Elemental_Profile_Set::GetProfile ( unsigned int index )

Get profile by index (mutable)

Returns: Pointer to profile, or nullptr if index out of range

Definition at line 386 of file elemental_profile_set.cpp.

◆ GetProfile() [4/4]

Elemental_Profile Elemental_Profile_Set::GetProfile ( unsigned int index ) const

Get profile by index (const)

Returns: Copy of profile, or empty profile if index out of range

Definition at line 410 of file elemental_profile_set.cpp.

◆ GetRegressionModels()

MultipleLinearRegressionSet * Elemental_Profile_Set::GetRegressionModels ( )

Get internal regression model set.

Definition at line 571 of file elemental_profile_set.cpp.

References mlr_vs_om_size_.

◆ GetRegressionsAsResult()

ResultItem Elemental_Profile_Set::GetRegressionsAsResult ( )

Get regressions wrapped in ResultItem for display.

Definition at line 563 of file elemental_profile_set.cpp.

References mlr_vs_om_size_, mlrset, ResultItem::SetResult(), and ResultItem::SetType().

◆ GetSampleNames()

vector< string > Elemental_Profile_Set::GetSampleNames ( ) const

Get all sample names in the set.

Definition at line 235 of file elemental_profile_set.cpp.

Referenced by SourceSinkData::GetSampleNames(), and MainWindow::on_tree_selectionChanged().

◆ operator=()

Elemental_Profile_Set & Elemental_Profile_Set::operator= ( const Elemental_Profile_Set & other )

Definition at line 30 of file elemental_profile_set.cpp.

References contribution_, contribution_softmax_, element_distributions_, mlr_vs_om_size_, Interface::operator=(), and outlierdone_.

◆ OutlierAnalysisDone()

bool Elemental_Profile_Set::OutlierAnalysisDone ( ) const

inline

Check if outlier analysis has been performed.

Definition at line 329 of file elemental_profile_set.h.

References outlierdone_.

◆ Read()

bool Elemental_Profile_Set::Read ( const QStringList & strlist )

overridevirtual

Parse object data from a string list.

Parameters

strlist List of strings containing the data to parse

Returns: true if parsing was successful, false otherwise

Pure virtual method for text-based deserialization. Each string in the list typically represents one line of input data.

Note: Format and parsing rules are determined by the derived class

Reimplemented from Interface.

Definition at line 330 of file elemental_profile_set.cpp.

◆ ReadFromJsonObject()

bool Elemental_Profile_Set::ReadFromJsonObject ( const QJsonObject & jsonobject )

overridevirtual

Deserialize object from JSON format.

Parameters

jsonobject The JSON object to read from

Returns: true if deserialization was successful, false otherwise

Pure virtual method for JSON deserialization. Derived classes must implement this to reconstruct their data structure from a JSON object.

Warning: Implementations should validate JSON structure and handle missing fields gracefully

Reimplemented from Interface.

Definition at line 311 of file elemental_profile_set.cpp.

References AppendProfile(), and Elemental_Profile::ReadFromJsonObject().

Referenced by SourceSinkData::ReadElementDatafromJsonObject(), and Results::ReadFromJson().

◆ SelectTopElementsAggregate()

Elemental_Profile Elemental_Profile_Set::SelectTopElementsAggregate ( int n ) const

Select top N elements across all samples (aggregate minimum)

Definition at line 954 of file elemental_profile_set.cpp.

References Elemental_Profile::AppendElement(), and CMBVector::Label().

Referenced by Conductor::ExecuteAutoSelect().

◆ SetContribution()

bool Elemental_Profile_Set::SetContribution ( const double & value )

Set contribution value for this source.

Definition at line 1036 of file elemental_profile_set.cpp.

References contribution_, and x.

Referenced by SourceSinkData::InitializeContributionsRandomly(), SourceSinkData::InitializeContributionsRandomlySoftmax(), SourceSinkData::SetContribution(), and SourceSinkData::SetParameterValue().

◆ SetContributionSoftmax()

bool Elemental_Profile_Set::SetContributionSoftmax ( const double & value )

Set softmax-transformed contribution.

Definition at line 1014 of file elemental_profile_set.cpp.

References contribution_softmax_, and x.

Referenced by SourceSinkData::SetContributionSoftmax().

◆ SetEstimatedMu()

bool Elemental_Profile_Set::SetEstimatedMu	(	const string &	element,
		const double &	value
	)

Set estimated mu parameter for an element.

◆ SetEstimatedSigma()

bool Elemental_Profile_Set::SetEstimatedSigma	(	const string &	element,
		const double &	value
	)

Set estimated sigma parameter for an element.

◆ SetRegressionModels() [1/2]

void Elemental_Profile_Set::SetRegressionModels ( const MultipleLinearRegressionSet * mlrset )

Set regression models (copy existing)

Definition at line 556 of file elemental_profile_set.cpp.

References mlr_vs_om_size_, and mlrset.

◆ SetRegressionModels() [2/2]

void Elemental_Profile_Set::SetRegressionModels	(	const string &	om,
		const string &	d,
		regression_form	form = `regression_form::linear`,
		const double &	p_value_threshold = `0.05`
	)

Set regression models (build new)

Definition at line 547 of file elemental_profile_set.cpp.

References BuildRegressionModels(), and mlr_vs_om_size_.

Referenced by CopyIncludedInAnalysis(), CreateCorrectedSet(), and EliminateSamples().

◆ toJsonObject()

QJsonObject Elemental_Profile_Set::toJsonObject ( ) const

overridevirtual

Serialize object to JSON format.

Returns: QJsonObject containing the serialized data

Pure virtual method for JSON serialization. Derived classes must implement this to convert their data structure to a JSON object suitable for saving to .json files or transmitting over network.

Note: The JSON structure is determined by the derived class

Reimplemented from Interface.

Definition at line 291 of file elemental_profile_set.cpp.

◆ ToMatrix()

CMBMatrix Elemental_Profile_Set::ToMatrix ( ) const

Convert to matrix format (samples � elements)

Definition at line 907 of file elemental_profile_set.cpp.

References GetElementNames(), and matrix.

◆ ToString()

string Elemental_Profile_Set::ToString ( ) const

overridevirtual

Convert object to string representation.

Returns: String representation of the object's data

Pure virtual method that must be implemented by derived classes to provide a human-readable string representation of their data. Typically used for text file export or debugging.

Note: Format is determined by the derived class implementation

Reimplemented from Interface.

Definition at line 250 of file elemental_profile_set.cpp.

References GetElementNames(), and string.

Referenced by writetofile().

◆ ToTable()

QTableWidget * Elemental_Profile_Set::ToTable ( )

overridevirtual

Create a Qt table widget representation of the data.

Returns: Pointer to a newly allocated QTableWidget displaying the data

Pure virtual method that creates a visual table representation of the object's data suitable for display in the Qt GUI. The returned widget is dynamically allocated and should be managed by Qt's parent-child ownership system.

Note: Caller does not need to delete the returned widget if added to a parent; Highlighting based on limit settings is applied if enabled

Reimplemented from Interface.

Definition at line 719 of file elemental_profile_set.cpp.

References GetElementNames(), Interface::highlightoutsideoflimit, Interface::highlimit, and Interface::lowlimit.

◆ UpdateElementDistributions()

void Elemental_Profile_Set::UpdateElementDistributions ( )

Rebuild element distributions from all profiles.

Call this after adding/modifying profiles to update statistical distributions

Definition at line 162 of file elemental_profile_set.cpp.

References element_distributions_.

Referenced by AppendProfiles(), and SourceSinkData::LumpAllProfileSets().

◆ writetofile()

bool Elemental_Profile_Set::writetofile ( QFile * file )

overridevirtual

Write object data to a file.

Parameters

file	Pointer to an open QFile object for writing

Returns: true if write was successful, false otherwise

Pure virtual method for file output. Derived classes implement this to write their data to an open file stream in their preferred text format.

Precondition: file must be opened in write mode

Note: File is not closed by this method

Reimplemented from Interface.

Definition at line 281 of file elemental_profile_set.cpp.

References ToString().

Member Data Documentation

◆ contribution_

double Elemental_Profile_Set::contribution_ = 0.0

private

Source contribution (for CMB)

Definition at line 392 of file elemental_profile_set.h.

Referenced by GetContribution(), operator=(), and SetContribution().

◆ contribution_softmax_

double Elemental_Profile_Set::contribution_softmax_ = 0.0

private

Softmax-transformed contribution.

Definition at line 393 of file elemental_profile_set.h.

Referenced by GetContributionSoftmax(), operator=(), and SetContributionSoftmax().

◆ element_distributions_

map<string, ConcentrationSet> Elemental_Profile_Set::element_distributions_

private

Concentration distributions for each element.

Definition at line 390 of file elemental_profile_set.h.

Referenced by AppendProfile(), ApplyBoxCoxTransform(), CalculateBoxCoxParameters(), CalculateElementMeans(), DetectOutliers(), GetElementDistribution(), GetElementDistribution(), GetEstimatedDistribution(), GetFittedDistribution(), operator=(), and UpdateElementDistributions().

◆ mlr_vs_om_size_

MultipleLinearRegressionSet Elemental_Profile_Set::mlr_vs_om_size_

private

MLR models for OM/size corrections.

Definition at line 391 of file elemental_profile_set.h.

Referenced by ApplyOrganicMatterAndSizeCorrections(), CopyIncludedInAnalysis(), CreateCorrectedSet(), EliminateSamples(), GetRegressionModels(), GetRegressionsAsResult(), operator=(), SetRegressionModels(), and SetRegressionModels().

◆ outlierdone_

bool Elemental_Profile_Set::outlierdone_ = false

private

Flag indicating outlier analysis performed.

Definition at line 394 of file elemental_profile_set.h.

Referenced by DetectOutliers(), operator=(), and OutlierAnalysisDone().

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Elemental_Profile_Set() [1/2]

◆ Elemental_Profile_Set() [2/2]

Member Function Documentation

◆ AppendProfile()

◆ AppendProfiles()

◆ ApplyBoxCoxTransform()

◆ ApplyOrganicMatterAndSizeCorrections()

◆ BuildRegressionModel()

◆ BuildRegressionModels()

◆ CalculateBoxCoxParameters()

◆ CalculateCorrelationMatrix()

◆ CalculateCovarianceMatrix()

◆ CalculateDotProduct()

◆ CalculateElementMeans()

◆ CalculateKolmogorovSmirnovStatistics()

◆ CheckForNegativeValues()

◆ ContainsElement()

◆ CopyIncludedInAnalysis()

◆ CopyToGSLMatrix()

◆ CreateCorrectedSet()

◆ DetectOutliers()

◆ EliminateSamples()

◆ ExtractChemicalElements()

◆ ExtractElements()

◆ GetAllConcentrationsFor()

◆ GetAssignedDistribution()

◆ GetConcentrationsForSample()

◆ GetContribution()

◆ GetContributionSoftmax()

◆ GetElementDistribution() [1/2]

◆ GetElementDistribution() [2/2]

◆ GetElementNames()

◆ GetEstimatedDistribution()

◆ GetEstimatedMu()

◆ GetEstimatedSigma()

◆ GetFittedDistribution()

◆ GetMaximum()

◆ GetMinimum()

◆ GetProfile() [1/4]

◆ GetProfile() [2/4]

◆ GetProfile() [3/4]

◆ GetProfile() [4/4]

◆ GetRegressionModels()

◆ GetRegressionsAsResult()

◆ GetSampleNames()

◆ operator=()

◆ OutlierAnalysisDone()

◆ Read()

◆ ReadFromJsonObject()

◆ SelectTopElementsAggregate()

◆ SetContribution()

◆ SetContributionSoftmax()

◆ SetEstimatedMu()

◆ SetEstimatedSigma()

◆ SetRegressionModels() [1/2]

◆ SetRegressionModels() [2/2]

◆ toJsonObject()

◆ ToMatrix()

◆ ToString()

◆ ToTable()

◆ UpdateElementDistributions()

◆ writetofile()

Member Data Documentation

◆ contribution_

◆ contribution_softmax_

◆ element_distributions_

◆ mlr_vs_om_size_

◆ outlierdone_