phylopomp
Phylodynamics for POMPs
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Population process class. More...
#include <popul_proc.h>
Public Member Functions | |
size_t | bytesize (void) const |
size of serialized binary form More... | |
popul_proc_t (double t0=0) | |
popul_proc_t (raw_t *o) | |
constructor from serialized binary form More... | |
popul_proc_t (const popul_proc_t &X) | |
copy constructor More... | |
popul_proc_t & | operator= (const popul_proc_t &X) |
copy assignment operator More... | |
popul_proc_t (popul_proc_t &&)=delete | |
move constructor More... | |
popul_proc_t & | operator= (popul_proc_t &&)=delete |
move assignment operator More... | |
~popul_proc_t (void) | |
destructor More... | |
slate_t | time (void) const |
get current time. More... | |
virtual void | valid (void) const |
void | update_params (double *, int) |
set parameters More... | |
void | update_IVPs (double *, int) |
set initial-value parameters More... | |
double | event_rates (double *rate, int n) const |
compute event rates More... | |
virtual void | rinit (void)=0 |
initialize the state More... | |
virtual void | jump (int e)=0 |
makes a jump More... | |
std::string | yaml (std::string tab) const |
machine/human readable info More... | |
void | update_clocks (void) |
updates clock and next event More... | |
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 More... | |
raw_t * | operator>> (raw_t *o, popul_proc_t &X) |
binary deserialization More... | |
Population process class.
The class for the simulation of the Markov process.
Definition at line 20 of file popul_proc.h.
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protected |
Definition at line 25 of file popul_proc.h.
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protected |
Definition at line 24 of file popul_proc.h.
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inline |
basic constructor for popul_proc class t0 = initial time
Definition at line 74 of file popul_proc.h.
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inline |
constructor from serialized binary form
Definition at line 80 of file popul_proc.h.
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inline |
copy constructor
Definition at line 84 of file popul_proc.h.
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delete |
move constructor
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inline |
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inline |
size of serialized binary form
Definition at line 45 of file popul_proc.h.
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inlineprivate |
double twospecies_proc_t::event_rates | ( | double * | rate, |
int | n | ||
) | const |
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pure virtual |
makes a jump
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inline |
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delete |
move assignment operator
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inline |
run process to a specified time. return number of events that have occurred.
Definition at line 160 of file popul_proc.h.
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pure virtual |
initialize the state
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inline |
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inline |
updates clock and next event
Definition at line 138 of file popul_proc.h.
void twospecies_proc_t::update_IVPs | ( | double * | p, |
int | n | ||
) |
void twospecies_proc_t::update_params | ( | double * | p, |
int | n | ||
) |
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inlinevirtual |
Definition at line 118 of file popul_proc.h.
std::string twospecies_proc_t::yaml | ( | std::string | tab | ) | const |
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friend |
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friend |
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protected |
Definition at line 33 of file popul_proc.h.
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protected |
Definition at line 32 of file popul_proc.h.
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staticprotected |
Definition at line 27 of file popul_proc.h.
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staticprotected |
Definition at line 26 of file popul_proc.h.
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protected |
Definition at line 31 of file popul_proc.h.
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protected |
Definition at line 35 of file popul_proc.h.
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protected |
Definition at line 34 of file popul_proc.h.