likelihood_ratio.cpp File Reference

#include <vector>
#include "likelihood_ratio.h"
#include "cafe.h"
#include <family.h>

Data Structures
struct	LRT2LParam

Functions
void	likelihood_ratio_report (pCafeFamily pfamily, pCafeTree pcafe, const std::vector< double > &pvalues, const std::vector< int > &plambda, const std::vector< double * > &lambda_cache, FILE *fout)
void	update_branchlength (pCafeTree pcafe, pTree lambda_tree, double bl_augment, int *old_branchlength, int *t)
double	__cafe_lhr_get_likelihood_for_diff_lambdas (pCafeParam param, int idx, int t, std::vector< double * > &lambda_cache, std::vector< pBirthDeathCacheArray > &PBDC)
void *	__cafe_lhr_for_diff_lambdas_i (pCafeParam param, std::vector< int > &lambda, std::vector< double > &pvalues, enum OPTIMIZER_INIT_TYPE lfunc, pTree lambda_tree, int num_lambdas, std::vector< double * > &lambda_cache, std::vector< pBirthDeathCacheArray > &PBDC)
void	cafe_lhr_for_diff_lambdas (pCafeParam param, pTree lambda_tree2, int num_lambdas, enum OPTIMIZER_INIT_TYPE lfunc)

Variables
pBirthDeathCacheArray	probability_cache
const double	bl_augment = 0.5

Function Documentation

void* __cafe_lhr_for_diff_lambdas_i	(	pCafeParam	param,
		std::vector< int > &	lambda,
		std::vector< double > &	pvalues,
		enum OPTIMIZER_INIT_TYPE	lfunc,
		pTree	lambda_tree,
		int	num_lambdas,
		std::vector< double * > &	lambda_cache,
		std::vector< pBirthDeathCacheArray > &	PBDC
	)

double __cafe_lhr_get_likelihood_for_diff_lambdas	(	pCafeParam	param,
		int	idx,
		int	t,
		std::vector< double * > &	lambda_cache,
		std::vector< pBirthDeathCacheArray > &	PBDC
	)

void cafe_lhr_for_diff_lambdas	(	pCafeParam	param,
		pTree	lambda_tree2,
		int	num_lambdas,
		enum OPTIMIZER_INIT_TYPE	lfunc
	)

void likelihood_ratio_report	(	pCafeFamily	pfamily,
		pCafeTree	pcafe,
		const std::vector< double > &	pvalues,
		const std::vector< int > &	plambda,
		const std::vector< double * > &	lambda_cache,
		FILE *	fout
	)

void update_branchlength	(	pCafeTree	pcafe,
		pTree	lambda_tree,
		double	bl_augment,
		int *	old_branchlength,
		int *	t
	)

Variable Documentation

const double bl_augment = 0.5

pBirthDeathCacheArray probability_cache

The variable cafe_param is a global singleton that holds general program state. cafe_param holds pcafe, a CafeTree, and pfamily, a CafeFamily . These are set by the user via the commands "tree" and "load" respectively. When the user calls the command "lambda" calculations are performed on the pcafe and pfamily variables.