Encodes the master process. More...

#include <master.h>

Inheritance diagram for master_t< POPN, NDEME >:

Collaboration diagram for master_t< POPN, NDEME >:

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Public Types
typedef POPN	popul_t

Public Member Functions
size_t	bytesize (void) const
	size of serialized binary form

	master_t (double t0=0)

	master_t (raw_t *o)
	constructor from serialized binary form

	master_t (SEXP o)
	constructor from RAW SEXP (containing binary serialization)

	master_t (const master_t &A)
	copy constructor

master_t &	operator= (const master_t &A)
	copy assignment operator

	master_t (master_t &&)=default
	move constructor

master_t &	operator= (master_t &&)=default
	move assignment operator

	~master_t (void)
	destructor

slate_t	timezero (void) const
	get zero-time

int	play (double tfin)
	runs the process to time `tfin`

slate_t	time (void) const
	current time

string_t	yaml (string_t tab="") const
	human/machine readable info

string_t	newick (void) const
	tree in Newick format

SEXP	lineage_count (void) const
	lineage count table

SEXP	structure (void) const
	structure in R list format

void	birth (name_t i=1, name_t j=1, int n=1)
	n births into deme j with parent in deme i

void	death (name_t i=1)
	death in deme i

void	graft (name_t i=1, int m=1)
	new root in deme i

void	sample (name_t i=1, int n=1)
	sample in deme i

void	sample_death (name_t i=1, int n=1)
	sample_death in deme i

void	migrate (name_t i=1, name_t j=1)
	migration from deme i to deme j

void	sample_migrate (name_t i=1, name_t j=1)
	sample_migrate in deme i to deme j

void	rinit (void)
	initialize the state

void	jump (int e)
	makes a jump

Data Fields
genealogy_t	geneal

inventory_t< NDEME >	inventory

Static Public Attributes
static const size_t	ndeme = NDEME

Private Member Functions
void	clean (void)

Friends
raw_t *	operator>> (const master_t &A, raw_t *o)
	binary serialization

raw_t *	operator>> (raw_t *o, master_t &A)
	binary deserialization

Detailed Description

template<class POPN, size_t NDEME>
class master_t< POPN, NDEME >

Encodes the master process.

This consists of a population process and a genealogy process.

Definition at line 21 of file master.h.

Member Typedef Documentation

◆ popul_t

template<class POPN, size_t NDEME>

typedef POPN master_t< POPN, NDEME >::popul_t

Definition at line 25 of file master.h.

Constructor & Destructor Documentation

◆ master_t() [1/5]

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::master_t ( double t0 = 0 )

inline

basic constructor t0 = initial time

Definition at line 61 of file master.h.

61: popul_t(t0), geneal(t0,ndeme) {};

master_t

Encodes the master process.

Definition master.h:21

master_t::geneal

genealogy_t geneal

Definition master.h:30

master_t::popul_t

POPN popul_t

Definition master.h:25

master_t::ndeme

static const size_t ndeme

Definition master.h:26

◆ master_t() [2/5]

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::master_t ( raw_t * o )

inline

constructor from serialized binary form

Definition at line 63 of file master.h.

                      {
    o >> *this;
  };

◆ master_t() [3/5]

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::master_t ( SEXP o )

inline

constructor from RAW SEXP (containing binary serialization)

Definition at line 67 of file master.h.

                    {
    if (LENGTH(o)==0)
      err("in %s: cannot deserialize a NULL.",__func__);
    PROTECT(o = AS_RAW(o));
    RAW(o) >> *this;
    UNPROTECT(1);
  };

◆ master_t() [4/5]

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::master_t ( const master_t< POPN, NDEME > & A )

inline

copy constructor

Definition at line 75 of file master.h.

                               {
    raw_t *o = new raw_t[A.bytesize()];
    A >> o;
    o >> *this;
    delete[] o;
  };

◆ master_t() [5/5]

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::master_t ( master_t< POPN, NDEME > && )

default

move constructor

◆ ~master_t()

template<class POPN, size_t NDEME>

master_t< POPN, NDEME >::~master_t ( void )

inline

destructor

Definition at line 95 of file master.h.

                   {
    clean();
  };

Member Function Documentation

◆ birth()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::birth	(	name_t	i = 1,
		name_t	j = 1,
		int	n = 1 )

inline

n births into deme j with parent in deme i

Definition at line 136 of file master.h.

                                                     {
    ball_t *a = inventory.random_ball(i);
    ball_t *b = geneal.birth(a,time(),j);
    inventory.insert(b);
    while (n > 1) {
      b = geneal.birth(b->holder(),j);
      inventory.insert(b);
      n--;
    }
  };

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◆ bytesize()

template<class POPN, size_t NDEME>

size_t master_t< POPN, NDEME >::bytesize ( void ) const

inline

size of serialized binary form

Definition at line 35 of file master.h.

                               {
    return geneal.bytesize() + popul_t::bytesize();
  };

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◆ clean()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::clean ( void )

inlineprivate

Definition at line 55 of file master.h.

55{ };

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◆ death()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::death ( name_t i = 1 )

inline

death in deme i

Definition at line 147 of file master.h.

                            {
    ball_t *a = inventory.random_ball(i);
    inventory.erase(a);
    geneal.death(a,time());
  };

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◆ graft()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::graft	(	name_t	i = 1,
		int	m = 1 )

inline

new root in deme i

Definition at line 153 of file master.h.

                                       {
    for (int j = 0; j < m; j++) {
      ball_t *a = geneal.graft(time(),i);
      inventory.insert(a);
    }
  };

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◆ jump()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::jump ( int e )

makes a jump

◆ lineage_count()

template<class POPN, size_t NDEME>

SEXP master_t< POPN, NDEME >::lineage_count ( void ) const

inline

lineage count table

Definition at line 126 of file master.h.

                                  {
    return geneal.lineage_count();
  };

◆ migrate()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::migrate	(	name_t	i = 1,
		name_t	j = 1 )

inline

migration from deme i to deme j

Definition at line 179 of file master.h.

                                            {
    ball_t *a = inventory.random_ball(i);
    inventory.erase(a);
    geneal.migrate(a,time(),j);
    inventory.insert(a);
  };

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◆ newick()

template<class POPN, size_t NDEME>

string_t master_t< POPN, NDEME >::newick ( void ) const

inline

tree in Newick format

Definition at line 122 of file master.h.

                               {
    return geneal.newick();
  };

◆ operator=() [1/2]

template<class POPN, size_t NDEME>

master_t & master_t< POPN, NDEME >::operator= ( const master_t< POPN, NDEME > & A )

inline

copy assignment operator

Definition at line 82 of file master.h.

                                           {
    clean();
    raw_t *o = new raw_t[A.bytesize()];
    A >> o;
    o >> *this;
    delete[] o;
    return *this;
  };

◆ operator=() [2/2]

template<class POPN, size_t NDEME>

master_t & master_t< POPN, NDEME >::operator= ( master_t< POPN, NDEME > && )

default

move assignment operator

◆ play()

template<class POPN, size_t NDEME>

int master_t< POPN, NDEME >::play ( double tfin )

inline

runs the process to time tfin

Definition at line 103 of file master.h.

                         {
    int count = popul_t::play(tfin);
    geneal.time() = tfin;
    return count;
  };

◆ rinit()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::rinit ( void )

initialize the state

◆ sample()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::sample	(	name_t	i = 1,
		int	n = 1 )

inline

sample in deme i

Definition at line 160 of file master.h.

                                        {
    pocket_t *p = inventory.random_balls(i,n);
    for (ball_t *a : *p) {
      geneal.sample(a,time());
    }
    p->clear();
    delete p;
  };

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◆ sample_death()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::sample_death	(	name_t	i = 1,
		int	n = 1 )

inline

sample_death in deme i

Definition at line 169 of file master.h.

                                              {
    pocket_t *p = inventory.random_balls(i,n);
    for (ball_t *a : *p) {
      inventory.erase(a);
      geneal.sample_death(a,time());
    }
    p->clear();
    delete p;
  };

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◆ sample_migrate()

template<class POPN, size_t NDEME>

void master_t< POPN, NDEME >::sample_migrate	(	name_t	i = 1,
		name_t	j = 1 )

inline

sample_migrate in deme i to deme j

Definition at line 186 of file master.h.

                                                   {
    ball_t *a = inventory.random_ball(i);
    inventory.erase(a);
    geneal.sample_migrate(a,time(),j);
    inventory.insert(a);
  };

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◆ structure()

template<class POPN, size_t NDEME>

SEXP master_t< POPN, NDEME >::structure ( void ) const

inline

structure in R list format

Definition at line 130 of file master.h.

                              {
    return geneal.structure();
  };

◆ time()

template<class POPN, size_t NDEME>

slate_t master_t< POPN, NDEME >::time ( void ) const

inline

current time

Definition at line 111 of file master.h.

                            {
    return popul_t::time();
  };

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◆ timezero()

template<class POPN, size_t NDEME>

slate_t master_t< POPN, NDEME >::timezero ( void ) const

inline

get zero-time

Definition at line 99 of file master.h.

                                {
    return geneal.timezero();
  };

◆ yaml()

template<class POPN, size_t NDEME>

string_t master_t< POPN, NDEME >::yaml ( string_t tab = "" ) const

inline

human/machine readable info

Definition at line 115 of file master.h.

                                          {
    string_t t = tab + "  ";
    string_t s = popul_t::yaml(tab)
      + "genealogy:\n" + geneal.yaml(t);
    return s;
  };

Friends And Related Symbol Documentation

◆ operator>> [1/2]

template<class POPN, size_t NDEME>

raw_t * operator>>	(	const master_t< POPN, NDEME > &	A,
		raw_t *	o )

friend

binary serialization

Definition at line 39 of file master.h.

                                                         {
    o = (A.geneal >> o);
    o = (reinterpret_cast<const popul_t&>(A) >> o);
    return o;
  }

◆ operator>> [2/2]

template<class POPN, size_t NDEME>

raw_t * operator>>	(	raw_t *	o,
		master_t< POPN, NDEME > &	A )

friend

binary deserialization

Definition at line 45 of file master.h.

                                                   {
    A.clean();
    o = (o >> A.geneal);
    o = (o >> reinterpret_cast<popul_t&>(A));
    A.inventory = A.geneal;
    return o;
  }

Field Documentation

◆ geneal

template<class POPN, size_t NDEME>

genealogy_t master_t< POPN, NDEME >::geneal

Definition at line 30 of file master.h.

◆ inventory

template<class POPN, size_t NDEME>

inventory_t<NDEME> master_t< POPN, NDEME >::inventory

Definition at line 31 of file master.h.

◆ ndeme

template<class POPN, size_t NDEME>

const size_t master_t< POPN, NDEME >::ndeme = NDEME

static

Definition at line 26 of file master.h.

The documentation for this class was generated from the following file:

src/master.h

Public Types

Public Member Functions

Data Fields

Static Public Attributes

Private Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ popul_t

Constructor & Destructor Documentation

◆ master_t() [1/5]

◆ master_t() [2/5]

◆ master_t() [3/5]

◆ master_t() [4/5]

◆ master_t() [5/5]

◆ ~master_t()

Member Function Documentation

◆ birth()

◆ bytesize()

◆ clean()

◆ death()

◆ graft()

◆ jump()

◆ lineage_count()

◆ migrate()

◆ newick()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ play()

◆ rinit()

◆ sample()

◆ sample_death()

◆ sample_migrate()

◆ structure()

◆ time()

◆ timezero()

◆ yaml()

Friends And Related Symbol Documentation

◆ operator>> [1/2]

◆ operator>> [2/2]

Field Documentation

◆ geneal

◆ inventory

◆ ndeme