lambda.h File Reference

#include <vector>
#include <string>
#include "cafe.h"
#include "family.h"
#include "cafe_shell.h"
#include "gmatrix.h"

Go to the source code of this file.

Data Structures
struct	lambda_range
struct	lambda_arg_base
struct	lambda_args
struct	posterior
struct	poisson_lambda

Enumerations
enum	LAMBDA_TYPE { UNDEFINED_LAMBDA, SINGLE_LAMBDA, MULTIPLE_LAMBDAS }

Functions
int	cafe_cmd_lambda (Globals &globals, std::vector< std::string > tokens)
void	set_all_lambdas (pCafeParam param, double value)
pGMatrix	cafe_lambda_distribution (pCafeParam param, const std::vector< lambda_range > &range)
void	cafe_set_prior_rfsize_poisson_lambda (std::vector< double > &prior_rfsize, int shift, double *lambda)
double	cafe_set_prior_rfsize_empirical (pCafeParam param, std::vector< double > &prior_rfsize)
	set empirical prior on rootsize based on the assumption that rootsize follows leaf size distribution More...
double	get_posterior (pCafeFamily pfamily, pCafeTree pcafe, family_size_range *range, std::vector< double > &ML, std::vector< double > &MAP, std::vector< double > &prior_rfsize, int quiet)
posterior	compute_posterior (pCafeFamilyItem pitem, pCafeTree pcafe, const std::vector< double > &prior_rfsize)
poisson_lambda	find_poisson_lambda (pCafeFamily pfamily)
void	initialize_params_and_k_weights (pCafeParam param, int what)
void	set_parameters (pCafeParam param, lambda_args &params)
void	lambda_set (pCafeParam param, lambda_args &params)
std::vector< int >	collect_leaf_sizes (pCafeFamily pfamily)

Variables
const int	INIT_PARAMS = 1
const int	INIT_KWEIGHTS = 2

Enumeration Type Documentation

enum LAMBDA_TYPE

Enumerator
UNDEFINED_LAMBDA
SINGLE_LAMBDA
MULTIPLE_LAMBDAS

Function Documentation

int cafe_cmd_lambda	(	Globals &	globals,
		std::vector< std::string >	tokens
	)

pGMatrix cafe_lambda_distribution	(	pCafeParam	param,
		const std::vector< lambda_range > &	range
	)

double cafe_set_prior_rfsize_empirical	(	pCafeParam	param,
		std::vector< double > &	prior_rfsize
	)

set empirical prior on rootsize based on the assumption that rootsize follows leaf size distribution

void cafe_set_prior_rfsize_poisson_lambda	(	std::vector< double > &	prior_rfsize,
		int	shift,
		double *	lambda
	)

std::vector<int> collect_leaf_sizes

(

pCafeFamily

pfamily

)

posterior compute_posterior	(	pCafeFamilyItem	pitem,
		pCafeTree	pcafe,
		const std::vector< double > &	prior_rfsize
	)

poisson_lambda find_poisson_lambda

(

pCafeFamily

pfamily

)

double get_posterior	(	pCafeFamily	pfamily,
		pCafeTree	pcafe,
		family_size_range *	range,
		std::vector< double > &	ML,
		std::vector< double > &	MAP,
		std::vector< double > &	prior_rfsize,
		int	quiet
	)

void initialize_params_and_k_weights	(	pCafeParam	param,
		int	what
	)

void lambda_set	(	pCafeParam	param,
		lambda_args &	params
	)

void set_all_lambdas	(	pCafeParam	param,
		double	value
	)

void set_parameters	(	pCafeParam	param,
		lambda_args &	params
	)

Variable Documentation

const int INIT_KWEIGHTS = 2

const int INIT_PARAMS = 1