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scantwo_binary_em.h

/**********************************************************************
 * 
 * scantwo_binary_em.h
 *
 * copyright (c) 2004, Karl W Broman, Johns Hopkins University
 *
 * last modified Dec, 2004
 * first written Dec, 2001
 *
 * Licensed under the GNU General Public License version 2 (June, 1991)
 *
 * C functions for the R/qtl package
 *
 * These functions are for performing a 2-dimensional genome scan 
 * with a 2-QTL model by interval mapping.(the EM algorithm).
 *
 * Contains: R_scantwo_1chr_binary_em, scantwo_1chr_binary_em, 
 *           R_scantwo_2chr_binary_em, scantwo_2chr_binary_em,
 *           scantwo_binary_em_estep, scantwo_binary_em_mstep
 *  
 **********************************************************************/

void R_scantwo_1chr_binary_em(int *n_ind, int *n_pos, int *n_gen,
                        double *pairprob, double *addcov, int *n_addcov, 
                        double *intcov, int *n_intcov, int *pheno, 
                        double *start,
                        double *result, int *maxit, double *tol, int *verbose);
void scantwo_1chr_binary_em(int n_ind, int n_pos, int n_gen, 
                      double *****Pairprob, double **Addcov, int n_addcov, 
                      double **Intcov, int n_intcov, int *pheno, double *start,
                      double **Result, int maxit, double tol, int verbose);
void R_scantwo_2chr_binary_em(int *n_ind, int *n_pos1, int *n_pos2, 
                        int *n_gen1, int *n_gen2, double *genoprob1,
                        double *genoprob2, double *addcov, int *n_addcov, 
                        double *intcov, int *n_intcov, 
                        int *pheno, double *start,
                        double *result_full, double *result_int,
                        int *maxit, double *tol, int *verbose);
void scantwo_2chr_binary_em(int n_ind, int n_pos1, int n_pos2, int n_gen1, 
                      int n_gen2, double ***Genoprob1, double ***Genoprob2,
                      double **Addcov, int n_addcov, double **Intcov, 
                      int n_intcov, int *pheno, double *start,
                      double **Result_full, double **Result_int, 
                      int maxit, double tol, int verbose);
void scantwo_binary_em_mstep(int n_ind, int n_gen1, int n_gen2, 
                       double **Addcov, int n_addcov, 
                       double **Intcov, int n_intcov, int *pheno, 
                       double ***Wts12, 
                       double *param, int full_model,
                       int n_col, int *error_flag);
void scantwo_binary_em_estep(int n_ind, int n_gen1, int n_gen2, 
                       double ***Probs, double ***Wts12, 
                       double **Addcov, int n_addcov, double **Intcov,
                       int n_intcov, int *pheno, 
                       double *param, int full_model, int rescale);

double scantwo_binary_em_loglik(int n_ind, int n_gen1, int n_gen2, 
                        double ***Probs, double **Addcov, int n_addcov,
                        double **Intcov, int n_intcov, int *pheno,
                        double *param, int full_model);

/* end of scantwo_binary_em.h */


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