birthdeath.c File Reference

#include "../config.h"
#include <assert.h>
#include "birthdeath.h"
#include <utils.h>
#include <stdlib.h>
#include <stdio.h>
#include <family.h>
#include <float.h>
#include <mathfunc.h>
#include "chooseln_cache.h"

Functions
double	birthdeath_rate_with_log_alpha_beta (int s, int c, double log_alpha, double log_beta, double log_coeff, struct chooseln_cache *cache)
double	birthdeath_rate_with_log_alpha (int s, int c, double log_alpha, double coeff, struct chooseln_cache *cc)
double	birthdeath_likelihood_with_s_c (int root_family_size, int family_size, double branchlength, double lambda, double mu, struct chooseln_cache *cache)
	Calculates the probability of transitioning from root_family_size to family_size. More...
void	square_matrix_init (struct square_matrix *matrix, int sz)
void	square_matrix_set (struct square_matrix *matrix, int x, int y, double val)
void	square_matrix_delete (struct square_matrix *matrix)
void	square_matrix_resize (struct square_matrix *matrix, int new_size)
void	square_matrix_print (struct square_matrix *matrix)
void	square_matrix_multiply (struct square_matrix *matrix, double *vector, int row_start, int row_end, int col_start, int col_end, double *result)
void	init_zero_matrix (struct square_matrix *matrix)
void	init_identity_matrix (struct square_matrix *matrix)
void	init_matrix (struct square_matrix *matrix, double coeff)
struct square_matrix *	compute_birthdeath_rates (double branchlength, double lambda, double mu, int maxFamilysize)
void	birthdeath_cache_matrix_resize (struct square_matrix *matrix, int remaxFamilysize, double branchlength, double lambda, double mu)
void	birthdeath_cache_resize (pBirthDeathCacheArray pbdc_array, int remaxFamilysize)
pBirthDeathCacheArray	birthdeath_cache_init (int size, struct chooseln_cache *ln_cache)
void	birthdeath_cache_array_free (pBirthDeathCacheArray pbdc_array)
struct square_matrix *	birthdeath_cache_get_matrix (pBirthDeathCacheArray pbdc_array, double branchlength, double lambda, double mu)

Variables
struct chooseln_cache	cache = { 0,0 }
	A cache of values of chooseln. More...

Function Documentation

void birthdeath_cache_array_free

(

pBirthDeathCacheArray

pbdc_array

)

struct square_matrix* birthdeath_cache_get_matrix	(	pBirthDeathCacheArray	pbdc_array,
		double	branchlength,
		double	lambda,
		double	mu
	)

Returns square matrix of doubles, rows and columns representing the transition probability in birthdeath rate in a change of one family size to another, with the given values of branch length, lambda, and mu

pBirthDeathCacheArray birthdeath_cache_init	(	int	size,
		struct chooseln_cache *	ln_cache
	)

void birthdeath_cache_matrix_resize	(	struct square_matrix *	matrix,
		int	remaxFamilysize,
		double	branchlength,
		double	lambda,
		double	mu
	)

void birthdeath_cache_resize	(	pBirthDeathCacheArray	pbdc_array,
		int	remaxFamilysize
	)

double birthdeath_likelihood_with_s_c	(	int	root_family_size,
		int	family_size,
		double	branchlength,
		double	lambda,
		double	mu,
		struct chooseln_cache *	cache
	)

Calculates the probability of transitioning from root_family_size to family_size.

Given the branch length and the expected change rate lammbda

double birthdeath_rate_with_log_alpha	(	int	s,
		int	c,
		double	log_alpha,
		double	coeff,
		struct chooseln_cache *	cc
	)

double birthdeath_rate_with_log_alpha_beta	(	int	s,
		int	c,
		double	log_alpha,
		double	log_beta,
		double	log_coeff,
		struct chooseln_cache *	cache
	)

struct square_matrix* compute_birthdeath_rates	(	double	branchlength,
		double	lambda,
		double	mu,
		int	maxFamilysize
	)

returns a structure representing a matrix of precalculated transition probabilites from one family size to another, given the specified values of branch length, lambda, and mu. Values are calculated from 0 to the given maxFamilySize. All relevant values are stored in the structure.

lambda is the probability of both gene gain and loss per gene per unit time in the phylogeny [CAFE assumes that gene birth and death are equally probable, see Hahn et al. (2005)]. If mu is provided, lambda and mu represent the probability of gene birth and gene death, respectively.

void init_identity_matrix

(

struct square_matrix *

matrix

)

void init_matrix	(	struct square_matrix *	matrix,
		double	coeff
	)

void init_zero_matrix

(

struct square_matrix *

matrix

)

void square_matrix_delete

(

struct square_matrix *

matrix

)

void square_matrix_init	(	struct square_matrix *	matrix,
		int	sz
	)

void square_matrix_multiply	(	struct square_matrix *	matrix,
		double *	vector,
		int	row_start,
		int	row_end,
		int	col_start,
		int	col_end,
		double *	result
	)

void square_matrix_print

(

struct square_matrix *

matrix

)

void square_matrix_resize	(	struct square_matrix *	matrix,
		int	new_size
	)

void square_matrix_set	(	struct square_matrix *	matrix,
		int	x,
		int	y,
		double	val
	)

Variable Documentation

struct chooseln_cache cache = { 0,0 }

A cache of values of chooseln.

Chooseln evaluates the natural logarithm of Gamma(n+1)/(Gamma(k+1)*Gamma(n-k+1)) The cache holds values for integer values of n and k. It does not appear to be threadsafe.

P(X(t) = c | X(0) = s) = {j=0}^{(s,c)} {s}{j}{s+c-j-1}{s-1} ^{s+c-2j}(1-2)^j