helma / lazar-core

DEPRECATED (use the pure ruby implementation in conjunction with libfminer in opentox-algorithm and opentox-model), C++ implementation of various lazar algorithms

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lazar-core / rutils.h
100644 44 lines (38 sloc) 1.499 kb
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#ifndef RPCA_H
#define RPCA_H
 
#include <iostream>
#include <iomanip>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>
#include <R.h>
#include <Rinternals.h>
#include <Rembedded.h>
#include <Rdefines.h>
#include <stdio.h>
#include <string>
 
#include "utils.h"
 
using namespace std;
 
void init_R(int argc, char **argv);
void end_R();
SEXP R_exec4 (const char* command, SEXP structure1, SEXP structure2, SEXP structure3);
SEXP R_exec3 (const char* command, SEXP structure1, SEXP structure2);
SEXP R_exec (const char* command, SEXP structure);
SEXP get_list_element(SEXP list, char *str);
void print_matrix(gsl_matrix* m);
void print_vector(gsl_vector* v);
void matrix_gsl2R(SEXP* mr, gsl_matrix* m);
void vector_gsl2R(SEXP* vr, gsl_vector* v);
void vector_gsl2R_str(SEXP* vr, gsl_vector* v);
void matrix_R2gsl(gsl_matrix* m, SEXP* mr);
void vector_R2gsl(gsl_vector* v, SEXP* vr);
float getVectorMean(gsl_vector* v);
void transposeMatrix(gsl_matrix* m, gsl_matrix* mt);
void cov(gsl_matrix* m, gsl_matrix* covm);
void get_mean(gsl_matrix* m, gsl_vector* mean);
float mahal(gsl_vector* x, gsl_matrix* m, gsl_matrix* covm);
gsl_matrix* pca_cols(gsl_matrix* feature_matrix, gsl_vector* means, unsigned int no_c);
gsl_matrix* pca(gsl_matrix* feature_matrix, gsl_vector* means, float sig_limit);
gsl_matrix* transformData (gsl_matrix* data_c, gsl_matrix* rot, gsl_vector* means);
gsl_matrix* reconstructData (gsl_matrix* t_data, gsl_matrix* rot, gsl_vector* means);
 
#endif