lambda.cpp File Reference

#include <family.h>
#include "cafe_shell.h"
#include "cafe.h"
#include <mathfunc.h>
#include <exception>
#include <string>
#include <stdexcept>
#include <vector>
#include <sstream>
#include <iterator>
#include <algorithm>
#include <iostream>
#include <numeric>
#include <cmath>
#include "lambda.h"
#include "cafe_commands.h"
#include "Globals.h"
#include "log_buffer.h"
#include "gene_family.h"

Functions
void	cafe_shell_set_lambda (pCafeParam param, double *parameters)
int	__cafe_cmd_lambda_tree (pCafeParam param, char *arg1, char *arg2)
double	__cafe_best_lambda_search (double *plambda, void *args)
double	__cafe_cluster_lambda_search (double *parameters, void *args)
bool	is_out (Argument arg)
void	set_all_lambdas (pCafeParam param, double value)
pGMatrix	cafe_lambda_distribution (pCafeParam param, const vector< lambda_range > &range)
void	write_lambda_distribution (pCafeParam param, const std::vector< lambda_range > &range, FILE *fp)
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)
void	lambda_search (pCafeParam param, lambda_args &params)
int	cafe_cmd_lambda (Globals &globals, vector< string > tokens)
	Find lambda values. More...
double *	cafe_best_lambda_by_fminsearch (pCafeParam param, int lambda_len, int k)
posterior	compute_posterior (pCafeFamilyItem pitem, pCafeTree pcafe, const std::vector< double > &prior_rfsize)
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)
double	__lnLPoisson (double *plambda, void *data)
std::vector< int >	collect_leaf_sizes (pCafeFamily pfamily)
poisson_lambda	find_poisson_lambda (pCafeFamily pfamily)
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...

Variables
pCafeParam	cafe_param
	Holds the global program state that user commands act on. More...

Function Documentation

double __cafe_best_lambda_search	(	double *	plambda,
		void *	args
	)

double __cafe_cluster_lambda_search	(	double *	parameters,
		void *	args
	)

int __cafe_cmd_lambda_tree	(	pCafeParam	param,
		char *	arg1,
		char *	arg2
	)

double __lnLPoisson	(	double *	plambda,
		void *	data
	)

double* cafe_best_lambda_by_fminsearch	(	pCafeParam	param,
		int	lambda_len,
		int	k
	)

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

Find lambda values.

Arguments include -s and -t. The -s argument starts a search for lambda values maximizing the log likelihood of data for all values. Subsequent analayses will automatically use the results from the lambda search. -t takes the same Newick tree structure as in the tree command, excluding branch lengths and subsituting integer values from 1 to N taxon names. etc.

pGMatrix cafe_lambda_distribution	(	pCafeParam	param,
		const 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
	)

void cafe_shell_set_lambda	(	pCafeParam	param,
		double *	parameters
	)

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
	)

bool is_out

(

Argument

arg

)

void lambda_search	(	pCafeParam	param,
		lambda_args &	params
	)

void lambda_set	(	pCafeParam	param,
		lambda_args &	params
	)

void set_all_lambdas	(	pCafeParam	param,
		double	value
	)

void set_parameters	(	pCafeParam	param,
		lambda_args &	params
	)

void write_lambda_distribution	(	pCafeParam	param,
		const std::vector< lambda_range > &	range,
		FILE *	fp
	)

Variable Documentation

pCafeParam cafe_param

Holds the global program state that user commands act on.