Population process class. More...

#include <popul_proc.h>

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

	popul_proc_t (double t0=0)

	popul_proc_t (raw_t *o)
	constructor from serialized binary form

	popul_proc_t (const popul_proc_t &X)
	copy constructor

popul_proc_t &	operator= (const popul_proc_t &X)
	copy assignment operator

	popul_proc_t (popul_proc_t &&)=delete
	move constructor

popul_proc_t &	operator= (popul_proc_t &&)=delete
	move assignment operator

	~popul_proc_t (void)
	destructor

slate_t	time (void) const
	get current time.

virtual void	valid (void) const

void	update_params (double *, int)
	set parameters

void	update_IVPs (double *, int)
	set initial-value parameters

double	event_rates (double *rate, int n) const
	compute event rates

virtual void	rinit (void)=0
	initialize the state

virtual void	jump (int e)=0
	makes a jump

std::string	yaml (std::string tab) const
	machine/human readable info

void	update_clocks (void)
	updates clock and next event

int	play (double tfin)

Protected Types
typedef STATE	state_t

typedef PARAMETERS	parameters_t

Protected Attributes
slate_t	next

size_t	event

slate_t	current

state_t	state

parameters_t	params

Static Protected Attributes
static const size_t	nevent = NEVENT

static const size_t	ndeme = NDEME

Private Member Functions
void	clean (void)

Friends
raw_t *	operator>> (const popul_proc_t &X, raw_t *o)
	binary serialization

raw_t *	operator>> (raw_t *o, popul_proc_t &X)
	binary deserialization

Detailed Description

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>
class popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >

Population process class.

The class for the simulation of the Markov process.

STATE is a datatype that holds the state of the Markov process.
PARAMETERS is a datatype for the model parameters
NEVENT is the number of event-types
NDEME is the number of demes

Definition at line 20 of file popul_proc.h.

Member Typedef Documentation

◆ parameters_t

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

typedef PARAMETERS popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::parameters_t

protected

Definition at line 25 of file popul_proc.h.

◆ state_t

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

typedef STATE popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::state_t

protected

Definition at line 24 of file popul_proc.h.

Constructor & Destructor Documentation

◆ popul_proc_t() [1/4]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::popul_proc_t ( double t0 = 0 )

inline

basic constructor for popul_proc class t0 = initial time

Definition at line 74 of file popul_proc.h.

                               {
    clean();
    next = current = slate_t(t0);
    event = 0;
  };

◆ popul_proc_t() [2/4]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::popul_proc_t ( raw_t * o )

inline

constructor from serialized binary form

Definition at line 80 of file popul_proc.h.

                          {
    o >> *this;
  };

◆ popul_proc_t() [3/4]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::popul_proc_t ( const popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > & X )

inline

copy constructor

Definition at line 84 of file popul_proc.h.

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

◆ popul_proc_t() [4/4]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::popul_proc_t ( popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > && )

delete

move constructor

◆ ~popul_proc_t()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::~popul_proc_t ( void )

inline

destructor

Definition at line 104 of file popul_proc.h.

                       {
    clean();
  };

Member Function Documentation

◆ bytesize()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

size_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::bytesize ( void ) const

inline

size of serialized binary form

Definition at line 45 of file popul_proc.h.

                               {
    return 2*sizeof(slate_t) + sizeof(size_t)
      + sizeof(state_t) + sizeof(parameters_t);
  };

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◆ clean()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::clean ( void )

inlineprivate

Definition at line 39 of file popul_proc.h.

39{}; // memory cleanup

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◆ event_rates()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

double popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::event_rates	(	double *	rate,
		int	n ) const

compute event rates

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◆ jump()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

virtual void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::jump ( int e )

pure virtual

makes a jump

Implemented in master_t< lbdp_proc_t, 1 >, master_t< lbdp_proc_t, 1 >, master_t< moran_proc_t, 1 >, master_t< moran_proc_t, 1 >, master_t< s2i2r2_proc_t, 3 >, master_t< s2i2r2_proc_t, 3 >, master_t< seir_proc_t, 2 >, master_t< seir_proc_t, 2 >, master_t< si2r_proc_t, 2 >, master_t< si2r_proc_t, 2 >, master_t< siir_proc_t, 2 >, master_t< siir_proc_t, 2 >, master_t< sir_proc_t, 1 >, master_t< sir_proc_t, 1 >, master_t< twospecies_proc_t, 3 >, and master_t< twospecies_proc_t, 3 >.

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◆ operator=() [1/2]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t & popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::operator= ( const popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > & X )

inline

copy assignment operator

Definition at line 91 of file popul_proc.h.

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

◆ operator=() [2/2]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

popul_proc_t & popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::operator= ( popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > && )

delete

move assignment operator

◆ play()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

int popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::play ( double tfin )

inline

run process to a specified time. return number of events that have occurred.

Definition at line 160 of file popul_proc.h.

                         {
    int count = 0;
    if (current > tfin)
      err("cannot simulate backward! (current t=%lg, requested t=%lg)",current,tfin);
    while (next < tfin) {
      current = next;
      jump(event);
      update_clocks();
      count++;
      R_CheckUserInterrupt();
    }
    if (next > tfin) current = tfin; // relies on Markov property
    return count;
  };

◆ rinit()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

virtual void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::rinit ( void )

pure virtual

initialize the state

Implemented in master_t< lbdp_proc_t, 1 >, master_t< lbdp_proc_t, 1 >, master_t< moran_proc_t, 1 >, master_t< moran_proc_t, 1 >, master_t< s2i2r2_proc_t, 3 >, master_t< s2i2r2_proc_t, 3 >, master_t< seir_proc_t, 2 >, master_t< seir_proc_t, 2 >, master_t< si2r_proc_t, 2 >, master_t< si2r_proc_t, 2 >, master_t< siir_proc_t, 2 >, master_t< siir_proc_t, 2 >, master_t< sir_proc_t, 1 >, master_t< sir_proc_t, 1 >, master_t< twospecies_proc_t, 3 >, and master_t< twospecies_proc_t, 3 >.

◆ time()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

slate_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::time ( void ) const

inline

get current time.

Definition at line 112 of file popul_proc.h.

                            {
    return current;
  };

◆ update_clocks()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::update_clocks ( void )

inline

updates clock and next event

Definition at line 138 of file popul_proc.h.

                            {
    double rate[nevent];
    double total_rate = event_rates(rate,nevent);
    if (total_rate > 0) {
      next = current+rexp(1/total_rate);
    } else {
      next = R_PosInf;
    }
    double u = runif(0,total_rate);
    event = 0;
    while (u > rate[event] && event < nevent) {
      if (rate[event] < 0)
        err("in '%s' (%s line %d): invalid negative rate[%zd]=%lg", // #nocov
            __func__,__FILE__,__LINE__,event,rate[event]); // #nocov
      u -= rate[event];
      event++;
    }
    assert(event < nevent);
  };

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◆ update_IVPs()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::update_IVPs	(	double *	,
		int	)

set initial-value parameters

◆ update_params()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::update_params	(	double *	,
		int	)

set parameters

◆ valid()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

virtual void popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::valid ( void ) const

inlinevirtual

Definition at line 118 of file popul_proc.h.

118{};

◆ yaml()

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

std::string popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::yaml ( std::string tab ) const

machine/human readable info

Friends And Related Symbol Documentation

◆ operator>> [1/2]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

raw_t * operator>>	(	const popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > &	X,
		raw_t *	o )

friend

binary serialization

Definition at line 50 of file popul_proc.h.

                                                             {
    slate_t A[2]; A[0] = X.current; A[1] = X.next;
    memcpy(o,A,sizeof(A)); o += sizeof(A);
    memcpy(o,&X.event,sizeof(size_t)); o += sizeof(size_t);
    memcpy(o,&X.state,sizeof(state_t)); o += sizeof(state_t);
    memcpy(o,&X.params,sizeof(parameters_t)); o += sizeof(parameters_t);
    return o;
  };

◆ operator>> [2/2]

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

raw_t * operator>>	(	raw_t *	o,
		popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME > &	X )

friend

binary deserialization

Definition at line 59 of file popul_proc.h.

                                                       {
    X.clean();
    slate_t A[2];
    memcpy(A,o,sizeof(A)); o += sizeof(A);
    X.current = A[0]; X.next = A[1];
    memcpy(&X.event,o,sizeof(size_t)); o += sizeof(size_t);
    memcpy(&X.state,o,sizeof(state_t)); o += sizeof(state_t);
    memcpy(&X.params,o,sizeof(parameters_t)); o += sizeof(parameters_t);
    return o;
  };

Field Documentation

◆ current

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

slate_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::current

protected

Definition at line 33 of file popul_proc.h.

◆ event

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

size_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::event

protected

Definition at line 32 of file popul_proc.h.

◆ ndeme

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

const size_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::ndeme = NDEME

staticprotected

Definition at line 27 of file popul_proc.h.

◆ nevent

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

const size_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::nevent = NEVENT

staticprotected

Definition at line 26 of file popul_proc.h.

◆ next

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

slate_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::next

protected

Definition at line 31 of file popul_proc.h.

◆ params

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

parameters_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::params

protected

Definition at line 35 of file popul_proc.h.

◆ state

template<class STATE, class PARAMETERS, size_t NEVENT, size_t NDEME = 1>

state_t popul_proc_t< STATE, PARAMETERS, NEVENT, NDEME >::state

protected

Definition at line 34 of file popul_proc.h.

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

src/popul_proc.h

Public Member Functions

Protected Types

Protected Attributes

Static Protected Attributes

Private Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ parameters_t

◆ state_t

Constructor & Destructor Documentation

◆ popul_proc_t() [1/4]

◆ popul_proc_t() [2/4]

◆ popul_proc_t() [3/4]

◆ popul_proc_t() [4/4]

◆ ~popul_proc_t()

Member Function Documentation

◆ bytesize()

◆ clean()

◆ event_rates()

◆ jump()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ play()

◆ rinit()

◆ time()

◆ update_clocks()

◆ update_IVPs()

◆ update_params()

◆ valid()

◆ yaml()

Friends And Related Symbol Documentation

◆ operator>> [1/2]

◆ operator>> [2/2]

Field Documentation

◆ current

◆ event

◆ ndeme

◆ nevent

◆ next

◆ params

◆ state