elemental_profile_set.h

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#ifndef ELEMENTAL_PROFILE_SET_H
#define ELEMENTAL_PROFILE_SET_H
 
#include <elemental_profile.h>
#include <map>
#include <string>
#include <vector>
#include "concentrationset.h"
#include "interface.h"
#include "multiplelinearregressionset.h"
#include "resultitem.h"
#include <gsl/gsl_vector.h>
#include <gsl/gsl_matrix.h>
#include "cmbvector.h"
 
class Elemental_Profile_Set : public map<string, Elemental_Profile>, public Interface
{
public:
    // ========== Construction and Assignment ==========
 
    Elemental_Profile_Set();
    Elemental_Profile_Set(const Elemental_Profile_Set& other);
    Elemental_Profile_Set& operator=(const Elemental_Profile_Set& other);
 
    // ========== Data Management ==========
 
    Elemental_Profile* AppendProfile(
        const string& name,
        const Elemental_Profile& profile = Elemental_Profile(),
        map<string, element_information>* elementinfo = nullptr
    );
 
    void AppendProfiles(
        const Elemental_Profile_Set& profiles,
        map<string, element_information>* elementinfo
    );
 
    void UpdateElementDistributions();
 
    // ========== Data Access ==========
 
    Elemental_Profile* GetProfile(const string& name);
 
    Elemental_Profile GetProfile(const string& name) const;
 
    Elemental_Profile* GetProfile(unsigned int index);
 
    Elemental_Profile GetProfile(unsigned int index) const;
 
    vector<string> GetSampleNames() const;
 
    vector<string> GetElementNames() const;
 
    vector<double> GetAllConcentrationsFor(const string& element_name);
 
    vector<double> GetConcentrationsForSample(const string& sample_name) const; 
 
    bool ContainsElement(const string& element_name) const;
 
    // ========== Data Extraction and Filtering ==========
 
    Elemental_Profile_Set ExtractElements(const vector<string>& element_list) const;
 
    Elemental_Profile_Set ExtractChemicalElements(
        const map<string, element_information>* elementinfo,
        bool isotopes
    ) const;
 
    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;
 
    Elemental_Profile_Set CopyIncludedInAnalysis(
        bool applyomsizecorrection,
        const vector<double>& om_size,
        map<string, element_information>* elementinfo = nullptr
    );
 
    Elemental_Profile_Set EliminateSamples(
        vector<string> samples_to_eliminate,
        map<string, element_information>* elementinfo
    ) const;
 
    // ========== Statistical Analysis ==========
 
    ConcentrationSet* GetElementDistribution(const string& element_name);
 
    ConcentrationSet GetElementDistribution(const string& element_name) const;
 
    distribution_type GetAssignedDistribution(const string& element_name) const;
 
    CVector CalculateElementMeans(const vector<string>& element_order = vector<string>()) const;
 
    CMBMatrix CalculateCovarianceMatrix();
 
    CMBMatrix CalculateCorrelationMatrix();
 
    CMBVector CalculateKolmogorovSmirnovStatistics(distribution_type dist_type);
 
    double GetMaximum() const;
 
    double GetMinimum() const;
 
    // ========== Estimated Distribution Parameters (for MCMC) ==========
 
    double GetEstimatedMu(const string& element) const;
 
    double GetEstimatedSigma(const string& element) const;
 
    bool SetEstimatedMu(const string& element, const double& value);
 
    bool SetEstimatedSigma(const string& element, const double& value);
 
    Distribution* GetEstimatedDistribution(const string& element_name);
 
    Distribution* GetFittedDistribution(const string& element_name);
 
    // ========== Regression Models (OM/Size Corrections) ==========
 
    MultipleLinearRegressionSet BuildRegressionModels(
        const string& om,
        const string& d,
        regression_form form = regression_form::linear,
        const double& p_value_threshold = 0.05
    );
 
    MultipleLinearRegression BuildRegressionModel(
        const string& element,
        const string& om,
        const string& d,
        regression_form form = regression_form::linear,
        const double& p_value_threshold = 0.05
    );
 
    void SetRegressionModels(
        const string& om,
        const string& d,
        regression_form form = regression_form::linear,
        const double& p_value_threshold = 0.05
    );
 
    void SetRegressionModels(const MultipleLinearRegressionSet* mlrset);
 
    MultipleLinearRegressionSet* GetRegressionModels();
 
    ResultItem GetRegressionsAsResult();
 
    Elemental_Profile_Set ApplyOrganicMatterAndSizeCorrections(
        const vector<double>& om_size,
        map<string, element_information>* elementinfo = nullptr
    );
 
    // ========== Box-Cox Transformations ==========
 
    CMBVector CalculateBoxCoxParameters();
 
    Elemental_Profile_Set ApplyBoxCoxTransform(CMBVector* lambda_vals = nullptr);
 
    // ========== Outlier Detection ==========
 
    CMBMatrix DetectOutliers(const double& lowerlimit = 0, const double& upperlimit = 0);
 
    bool OutlierAnalysisDone() const { return outlierdone_; }
 
    vector<string> CheckForNegativeValues(const vector<string>& element_names) const;
 
    // ========== Source Contribution (for CMB) ==========
 
    bool SetContribution(const double& value);
 
    double GetContribution() const { return contribution_; }
 
    bool SetContributionSoftmax(const double& value);
 
    double GetContributionSoftmax() const { return contribution_softmax_; }
 
    // ========== Utility Functions ==========
 
    Elemental_Profile SelectTopElementsAggregate(int n) const;
 
    CMBVector CalculateDotProduct(const CVector& v) const;
 
    CMBMatrix ToMatrix() const;
 
    gsl_matrix* CopyToGSLMatrix() const;
 
    // ========== Serialization ==========
 
    string ToString() const override;
    QTableWidget* ToTable() override;
    bool writetofile(QFile* file) override;
    QJsonObject toJsonObject() const override;
    bool ReadFromJsonObject(const QJsonObject& jsonobject) override;
    bool Read(const QStringList& strlist) override;
 
private:
    map<string, ConcentrationSet> element_distributions_;  
    MultipleLinearRegressionSet mlr_vs_om_size_;          
    double contribution_ = 0.0;                            
    double contribution_softmax_ = 0.0;                    
    bool outlierdone_ = false;                             
};
 
#endif // ELEMENTAL_PROFILE_SET_H