phylopomp
Phylodynamics for POMPs
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#include "internal.h"
Go to the source code of this file.
Macros | |
#define | MAKEFN(X, TYPE) |
#define | REVIVEFN(X, TYPE) |
#define | RUNFN(X, TYPE) |
#define | GENEALFN(X, TYPE) |
#define | YAMLFN(X, TYPE) |
#define | GENERICS(X, TYPE) |
Functions | |
template<class TYPE > | |
SEXP | ndeme (TYPE &X) |
template<class TYPE > | |
SEXP | nsample (TYPE &X) |
template<class TYPE > | |
SEXP | timezero (TYPE &X) |
template<class TYPE > | |
SEXP | time (TYPE &X) |
template<class TYPE > | |
SEXP | serial (const TYPE &X) |
binary serialization More... | |
template<class TYPE > | |
SEXP | yaml (const TYPE &X) |
human/machine readable output More... | |
template<class TYPE > | |
SEXP | describe (const TYPE &X) |
human readable output More... | |
template<class TYPE > | |
SEXP | structure (const TYPE &X) |
structure in R list format More... | |
template<class TYPE > | |
SEXP | newick (const TYPE &X) |
tree in newick format More... | |
template<class TYPE > | |
SEXP | lineage_count (const TYPE &G) |
number of lineages through time More... | |
template<class TYPE > | |
SEXP | gendat (const TYPE &G) |
data-frame format More... | |
template<class TYPE > | |
SEXP | make (SEXP Params, SEXP IVPs, SEXP T0) |
initialization More... | |
template<class TYPE > | |
SEXP | revive (SEXP State, SEXP Params) |
refresh parameters More... | |
template<class TYPE > | |
SEXP | run (SEXP State, SEXP Tout) |
run simulations More... | |
template<class TYPE > | |
SEXP | genealogy (SEXP State) |
extract the bare genealogy More... | |
#define GENEALFN | ( | X, | |
TYPE | |||
) |
Definition at line 141 of file generics.h.
#define GENERICS | ( | X, | |
TYPE | |||
) |
Definition at line 149 of file generics.h.
#define MAKEFN | ( | X, | |
TYPE | |||
) |
Definition at line 129 of file generics.h.
#define REVIVEFN | ( | X, | |
TYPE | |||
) |
Definition at line 133 of file generics.h.
#define RUNFN | ( | X, | |
TYPE | |||
) |
Definition at line 137 of file generics.h.
#define YAMLFN | ( | X, | |
TYPE | |||
) |
Definition at line 145 of file generics.h.
SEXP describe | ( | const TYPE & | X | ) |
human readable output
Definition at line 44 of file generics.h.
SEXP gendat | ( | const TYPE & | G | ) |
SEXP genealogy | ( | SEXP | State | ) |
extract the bare genealogy
Definition at line 120 of file generics.h.
SEXP lineage_count | ( | const TYPE & | G | ) |
number of lineages through time
Definition at line 62 of file generics.h.
SEXP make | ( | SEXP | Params, |
SEXP | IVPs, | ||
SEXP | T0 | ||
) |
SEXP ndeme | ( | TYPE & | X | ) |
SEXP newick | ( | const TYPE & | X | ) |
tree in newick format
Definition at line 56 of file generics.h.
SEXP nsample | ( | TYPE & | X | ) |
SEXP revive | ( | SEXP | State, |
SEXP | Params | ||
) |
refresh parameters
Definition at line 93 of file generics.h.
SEXP run | ( | SEXP | State, |
SEXP | Tout | ||
) |
run simulations
Definition at line 105 of file generics.h.
SEXP serial | ( | const TYPE & | X | ) |
binary serialization
Definition at line 28 of file generics.h.
SEXP structure | ( | const TYPE & | X | ) |
structure in R list format
Definition at line 50 of file generics.h.
SEXP time | ( | TYPE & | X | ) |
SEXP timezero | ( | TYPE & | X | ) |
SEXP yaml | ( | const TYPE & | X | ) |
human/machine readable output
Definition at line 38 of file generics.h.