phylopomp
Phylodynamics for POMPs
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Encodes the master process. More...
#include <master.h>
Public Types | |
typedef POPN | popul_t |
Public Member Functions | |
size_t | bytesize (void) const |
size of serialized binary form More... | |
master_t (double t0=0) | |
master_t (raw_t *o) | |
constructor from serialized binary form More... | |
master_t (SEXP o) | |
constructor from RAW SEXP (containing binary serialization) More... | |
master_t (const master_t &A) | |
copy constructor More... | |
master_t & | operator= (const master_t &A) |
copy assignment operator More... | |
master_t (master_t &&)=default | |
move constructor More... | |
master_t & | operator= (master_t &&)=default |
move assignment operator More... | |
~master_t (void) | |
destructor More... | |
slate_t | timezero (void) const |
get zero-time More... | |
int | play (double tfin) |
runs the process to time tfin More... | |
slate_t | time (void) const |
current time More... | |
std::string | describe (void) const |
human-readable info More... | |
std::string | yaml (std::string tab="") const |
machine/human readable info More... | |
std::string | newick (void) const |
tree in Newick format More... | |
SEXP | lineage_count (void) const |
lineage count table More... | |
SEXP | structure (void) const |
structure in R list format More... | |
void | birth (name_t i=0, name_t j=0, int n=1) |
n births into deme j with parent in deme i More... | |
void | death (name_t i=0) |
death in deme i More... | |
void | graft (name_t i=0, int m=1) |
new root in deme i More... | |
void | sample (name_t i=0, int n=1) |
sample in deme i More... | |
void | sample_death (name_t i=0, int n=1) |
sample_death in deme i More... | |
void | migrate (name_t i=0, name_t j=0) |
migration from deme i to deme j More... | |
void | rinit (void) |
initialize the state More... | |
void | jump (int e) |
makes a jump More... | |
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 More... | |
raw_t * | operator>> (raw_t *o, master_t &A) |
binary deserialization More... | |
Encodes the master process.
This consists of a population process and a genealogy process.
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inline |
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default |
move constructor
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inline |
n births into deme j with parent in deme i
Definition at line 142 of file master.h.
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inline |
size of serialized binary form
Definition at line 36 of file master.h.
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inlineprivate |
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inline |
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inline |
new root in deme i
Definition at line 159 of file master.h.
void twospecies_genealogy_t::jump | ( | int | e | ) |
makes a jump
Definition at line 72 of file lbdp.cc.
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inline |
lineage count table
Definition at line 132 of file master.h.
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inline |
migration from deme i to deme j
Definition at line 185 of file master.h.
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inline |
tree in Newick format
Definition at line 128 of file master.h.
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default |
move assignment operator
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inline |
void twospecies_genealogy_t::rinit | ( | void | ) |
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inline |
sample in deme i
Definition at line 166 of file master.h.
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inline |
sample_death in deme i
Definition at line 175 of file master.h.
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inline |
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inline |
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inline |
machine/human readable info
Definition at line 121 of file master.h.
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friend |
genealogy_t master_t< POPN, NDEME >::geneal |
inventory_t<ndeme> master_t< POPN, NDEME >::inventory |
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static |