legofit/html/branchtab_8h_source.html

#ifndef BRANCHTAB_INCLUDED

#  define BRANCHTAB_INCLUDED


#include "typedefs.h"

#include <stdio.h>


BranchTab    *BranchTab_new(unsigned nsamples);

void          BranchTab_free(BranchTab * self);

long double   BranchTab_get(BranchTab * self, tipId_t tipid);

int           BranchTab_hasSingletons(BranchTab * self);

void          BranchTab_add(BranchTab * self, tipId_t key, long double value);

unsigned      BranchTab_size(BranchTab * self);

void          BranchTab_print(const BranchTab *self, FILE *fp);


void          BranchTab_plusEquals(BranchTab *lhs, BranchTab *rhs);

void          BranchTab_minusEquals(BranchTab *lhs, BranchTab *rhs);

void          BranchTab_toArrays(BranchTab *self, unsigned n, tipId_t key[n],

                                 long double value[n]);

int           BranchTab_divideBy(BranchTab *self, long double denom);

BranchTab    *BranchTab_dup(const BranchTab *old);

int           BranchTab_equals(const BranchTab *lhs, const BranchTab *rhs);

long double   BranchTab_sum(const BranchTab *self);

long double   BranchTab_entropy(const BranchTab *self);

int           BranchTab_normalize(BranchTab *self);

long double   BranchTab_chiSqCost(const BranchTab *obs, const BranchTab *expt,

                             long double u, long nnuc, long double n);

long double   BranchTab_smplChiSqCost(const BranchTab *obs,

                                      const BranchTab *expt,

                                      long double u, long nnuc, long double n);

long double   BranchTab_KLdiverg(const BranchTab *obs, const BranchTab *expt);

long double   BranchTab_negLnL(const BranchTab *obs, const BranchTab *expt);

long double   BranchTab_poissonCost(const BranchTab *obs, const BranchTab *expt,

                                    long double u, long nnuc, long double n);

BranchTab    *BranchTab_collapse(BranchTab *old, tipId_t collapse);

BranchTab    *BranchTab_rmPops(BranchTab *old, tipId_t remove);

void          BranchTab_sanityCheck(BranchTab *self, const char *file,

                                    int line);

BranchTab    *BranchTab_from_StrDblQueue(StrDblQueue *queue, LblNdx *lndx);

void          make_collapse_map(size_t n, tipId_t map[n], tipId_t collapse);

void          make_rm_map(size_t n, tipId_t map[n], tipId_t remove);

tipId_t       remap_bits(size_t n, tipId_t map[n], tipId_t old);

#endif

BranchTab_new
BranchTab * BranchTab_new(unsigned nsamples)
Create a new BranchTab with room for site patterns associated with data in which the number of sample...
Definition: branchtab.c:31

BranchTab_add
void BranchTab_add(BranchTab *self, tipId_t key, long double value)
Add a value to table.
Definition: branchtab.c:110

BranchTab_divideBy
int BranchTab_divideBy(BranchTab *self, long double denom)
Divide all values by denom. Return 0 on success, or 1 on failure.
Definition: branchtab.c:142

BranchTab_hasSingletons
int BranchTab_hasSingletons(BranchTab *self)
Return 1 if BranchTab includes singleton site patterns.
Definition: branchtab.c:94

BranchTab_negLnL
long double BranchTab_negLnL(const BranchTab *obs, const BranchTab *expt)
Negative log likelihood.
Definition: branchtab.c:334

BranchTab_equals
int BranchTab_equals(const BranchTab *lhs, const BranchTab *rhs)
Return 1 if two BranchTab objects are equal; 0 otherwise.
Definition: branchtab.c:70

BranchTab_KLdiverg
long double BranchTab_KLdiverg(const BranchTab *obs, const BranchTab *expt)
Calculate KL divergence from two BranchTab objects, which should be normalized before entering this f...
Definition: branchtab.c:304

BranchTab_rmPops
BranchTab * BranchTab_rmPops(BranchTab *old, tipId_t remove)
Return pointer to newly-allocated BranchTab, which is like old, except that it lacks the populations ...
Definition: branchtab.c:215

BranchTab_print
void BranchTab_print(const BranchTab *self, FILE *fp)
Print a BranchTab to standard output.
Definition: branchtab.c:156

make_collapse_map
void make_collapse_map(size_t n, tipId_t map[n], tipId_t collapse)
Make map, an array whose i'th entry is an unsigned integer with one bit on and the rest off.
Definition: branchtab.c:368

BranchTab_minusEquals
void BranchTab_minusEquals(BranchTab *lhs, BranchTab *rhs)
Subtract each entry in table rhs from table lhs.
Definition: branchtab.c:170

BranchTab_sum
long double BranchTab_sum(const BranchTab *self)
Return sum of values in BranchTab.
Definition: branchtab.c:236

BranchTab_entropy
long double BranchTab_entropy(const BranchTab *self)
Return negative of sum of p*ln(p)
Definition: branchtab.c:246

BranchTab_free
void BranchTab_free(BranchTab *self)
Destructor for BranchTab.
Definition: branchtab.c:88

make_rm_map
void make_rm_map(size_t n, tipId_t map[n], tipId_t remove)
Make map, an array whose i'th entry is an unsigned integer with one bit on and the rest off.
Definition: branchtab.c:401

BranchTab_collapse
BranchTab * BranchTab_collapse(BranchTab *old, tipId_t collapse)
Return a pointer to a newly-allocated BranchTab, which is like "old", except that two or more of the ...
Definition: branchtab.c:193

BranchTab_plusEquals
void BranchTab_plusEquals(BranchTab *lhs, BranchTab *rhs)
Add each entry in table rhs to table lhs.
Definition: branchtab.c:162

BranchTab_toArrays
void BranchTab_toArrays(BranchTab *self, unsigned n, tipId_t key[n], long double value[n])
Fill arrays key and value with values in BranchTab.
Definition: branchtab.c:180

BranchTab_from_StrDblQueue
BranchTab * BranchTab_from_StrDblQueue(StrDblQueue *queue, LblNdx *lndx)
Construct a BranchTab from a StrDblQueue.
Definition: branchtab.c:278

BranchTab_size
unsigned BranchTab_size(BranchTab *self)
Return the number of elements in the BranchTab.
Definition: branchtab.c:125

BranchTab_get
long double BranchTab_get(BranchTab *self, tipId_t key)
Return value corresponding to key.
Definition: branchtab.c:103

BranchTab_normalize
int BranchTab_normalize(BranchTab *self)
Divide all values by their sum.
Definition: branchtab.c:260

BranchTab
Definition: branchtab.c:20

LblNdx
Definition: lblndx.h:8

StrDblQueue
Definition: strdblqueue.h:22