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/**********************************************************************
*
* scanone_em.h
*
* copyright (c) 2001-2010, Karl W Broman
*
* last modified Jul, 2010
* first written Nov, 2001
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License,
* version 3, as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be useful,
* but without any warranty; without even the implied warranty of
* merchantability or fitness for a particular purpose. See the GNU
* General Public License, version 3, for more details.
*
* A copy of the GNU General Public License, version 3, is available
* at http://www.r-project.org/Licenses/GPL-3
*
* C functions for the R/qtl package
*
* These functions are for performing a genome scan with a
* single QTL model by interval mapping (the EM algorithm).
*
* Contains: R_scanone_em, scanone_em
*
**********************************************************************/
/**********************************************************************
*
* R_scanone_em
*
* Wrapper for call from R; reorganizes genotype prob and result matrix
* and calls scanone_em.
*
**********************************************************************/
void R_scanone_em(int *n_ind, int *n_pos, int *n_gen,
double *genoprob, double *addcov, int *n_addcov,
double *intcov, int *n_intcov, double *pheno,
double *weights,
double *result, int *std_start, double *start,
int *maxit, double *tol, int *verbose,
int *ind_noqtl);
/**********************************************************************
*
* scanone_em
*
* Performs genome scan using interval mapping. (The multipoint
* genotype probabilities have already been calculated in
* calc.genoprob)
*
* n_ind Number of individuals
*
* n_pos Number of marker positions
*
* n_gen Number of different genotypes
*
* Genoprob Array of conditional genotype probabilities
*
* pheno Phenotype data, as a vector
*
* weights Vector of positive weights, of length n_ind
*
* result Upon exit, the LOD scores
*
* std_start If 1, use the usual starting points [initial weights as
* Pr(QTL geno | marker genotypes)]
* If -1, use iid Bernoulli(1/2) for initial weights.
* If 0, use the specified values for the means and SD as
* the starting point.
*
* start If std_start = 0, use these as initial estimates of the
* genotype-specific means and the residual SD.
*
* maxit Maximum number of iterations in the EM algorithm
*
* tol Tolerance for determining convergence in EM
*
* work Workspace of dimension 4 x n_gen
*
* means Space for the phenotype means at each genotype
*
**********************************************************************/
void scanone_em(int n_ind, int n_pos, int n_gen, double ***Genoprob,
double *pheno, double *weights, double *result,
int std_start, double *start,
int maxit, double tol, double **work, double *means);
/* end of scanone_em.h */
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