birthdeath.h

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#ifndef __BIRTHDEATH_H__
#define __BIRTHDEATH_H__

#include <assert.h>
#include "hashtable.h"
#include "chooseln_cache.h"

struct square_matrix {
    double *values;
    int size;
};
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_resize(struct square_matrix* matrix, int new_size);
void square_matrix_multiply(struct square_matrix* matrix, double *vector, int row_start, int row_end, int col_start, int col_end, double *result);

static inline double square_matrix_get(struct square_matrix *matrix, int x, int y)
{
    assert(x < matrix->size);
    assert(y < matrix->size);
    return matrix->values[x*matrix->size+y];
}



struct BirthDeathCacheKey
{
    int branchlength;
    double lambda;
    double mu;
};

typedef struct
{
    hash_table_t* table;
    int maxFamilysize;
}BirthDeathCacheArray;
typedef BirthDeathCacheArray* pBirthDeathCacheArray;

extern void birthdeath_cache_array_free(pBirthDeathCacheArray pbdc_array);
extern double birthdeath_likelihood_with_s_c(int s, int c, double branchlength, double lambda, double mu, struct chooseln_cache *cache);
extern struct square_matrix* compute_birthdeath_rates( double branchlength, double lambda, double mu, int maxFamilysize );
struct square_matrix* birthdeath_cache_get_matrix(pBirthDeathCacheArray pbdc_array, double branchlength, double lambda, double mu );
extern void thread_run(int numthreads, void* (*run)(void*), void* param, int size );
double birthdeath_rate_with_log_alpha(int s, int c, double log_alpha, double coeff, struct chooseln_cache *cache);
extern void birthdeath_cache_resize(pBirthDeathCacheArray pbdc_array, int remaxFamilysize);
pBirthDeathCacheArray birthdeath_cache_init(int size, struct chooseln_cache *ln_cache);
#endif