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/**********************************************************************
*
* hmm_ri8sib.h
*
* copyright (c) 2005-9, Karl W Broman
*
* last modified Apr, 2009
* first written Mar, 2005
*
* 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
*
* Contains: init_ri8sib, emit_ri8sib, step_ri8sib, step_special_ri8sib,
* calc_genoprob_ri8sib, calc_genoprob_special_ri8sib,
* argmax_geno_ri8sib, sim_geno_ri8sib,
* est_map_ri8sib, nrec2_ri8sib, logprec_ri8sib, est_rf_ri8sib,
* marker_loglik_ri8sib, calc_pairprob_ri8sib,
* errorlod_ri8sib, calc_errorlod_ri8sib
*
* These are the init, emit, and step functions plus
* all of the hmm wrappers for 8-way RIL by sib mating
* (i.e., the Collaborative Cross).
*
* Genotype codes: 1-8
* "Phenotype" codes: 0=missing; otherwise binary 1-255, with bit i
* indicating SNP compatible with parent i
*
**********************************************************************/
double init_ri8sib(int true_gen, int *cross_scheme);
double emit_ri8sib(int obs_gen, int true_gen, double error_prob, int *cross_scheme);
double step_ri8sib(int gen1, int gen2, double rf, double junk, int *cross_scheme);
double step_special_ri8sib(int gen1, int gen2, double rf, double junk, int *cross_scheme);
void calc_genoprob_ri8sib(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob, double *genoprob);
void calc_genoprob_special_ri8sib(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob, double *genoprob);
void argmax_geno_ri8sib(int *n_ind, int *n_pos, int *geno,
double *rf, double *error_prob, int *argmax);
void sim_geno_ri8sib(int *n_ind, int *n_pos, int *n_draws, int *geno,
double *rf, double *error_prob, int *draws);
void est_map_ri8sib(int *n_ind, int *n_mar, int *geno, double *rf,
double *error_prob, double *loglik, int *maxit,
double *tol, int *verbose);
/* expected no. recombinants */
double nrec2_ri8sib(int obs1, int obs2, double rf, int *cross_scheme);
/* log [joint probability * 8] */
double logprec_ri8sib(int obs1, int obs2, double rf, int *cross_scheme);
void est_rf_ri8sib(int *n_ind, int *n_mar, int *geno, double *rf,
int *maxit, double *tol);
void marker_loglik_ri8sib(int *n_ind, int *geno,
double *error_prob, double *loglik);
void calc_pairprob_ri8sib(int *n_ind, int *n_mar, int *geno,
double *rf, double *error_prob,
double *genoprob, double *pairprob);
double errorlod_ri8sib(int obs, double *prob, double error_prob);
void calc_errorlod_ri8sib(int *n_ind, int *n_mar, int *geno,
double *error_prob, double *genoprob,
double *errlod);
/* end of hmm_ri8sib.h */
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