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/**********************************************************************
*
* mqmscan.h
*
* Copyright (c) 1996-2009 by
* Ritsert C Jansen, Danny Arends, Pjotr Prins and Karl W Broman
*
* initial MQM C code written between 1996-2002 by Ritsert C. Jansen
* improved for the R-language by Danny Arends, Pjotr Prins and Karl W. Broman
*
* Modified by Danny Arends and Pjotr Prins
* last modified September 2009
*
* 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
*
**********************************************************************/
#ifdef __cplusplus
extern "C" {
#endif
double Lnormal(double residual, double variance);
int mqmmod(int a, int b);
double ftruncate3(double n);
void reorg_pheno(int n_ind, int n_mar, double *pheno, double ***Pheno);
void reorg_int(int n_ind, int n_mar, int *pheno, int ***Pheno);
/* analyseF2 - analyse one F2/BC/RIL family */
double analyseF2(int Nind, int *Nmark, cvector *cofactor, MQMMarkerMatrix marker,
vector y, int Backwards, double **QTL,vector
*mapdistance,int **Chromo,int Nrun,int RMLorML, double
windowsize,double stepsize, double stepmin,double stepmax,double
alfa,int em,int out_Naug,int **INDlist,char reestimate, MQMCrossType
crosstype,bool dominance,int verbose);
//R calling interface
void R_mqmscan(int *Nind,int *Nmark,int *Npheno,
int *geno,int *chromo, double *dist, double *pheno,
int *cofactors, int *backwards, int *RMLorML,double *alfa,int *emiter,
double *windowsize,double *steps,
double *stepmi,double *stepma, int *nRun,int *out_Naug,int *indlist, double *qtl,int *reestimate,int *rqtlcrosstype,int *domi,int *verbose);
void mqmscan(int Nind, int Nmark,int Npheno,int **Geno,int **Chromo,
double **Dist, double **Pheno, int **Cofactors, int Backwards, int RMLorML,double Alfa,int Emiter,
double Windowsize,double Steps,
double Stepmi,double Stepma,int NRUN,int out_Naug,int **INDlist, double **QTL, int re_estimate,RqtlCrossType rqtlcrosstype,int domi,int verbose);
#ifdef __cplusplus
}
#endif
/* end of mqmscan.h */
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