init.c File Reference

#include "init.h"
#include "decls.h"
#include "pomplink.h"

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Functions
SEXP	parse_newick (SEXP, SEXP, SEXP)
SEXP	getInfo (SEXP)
SEXP	curtail (SEXP, SEXP, SEXP)
	curtail the given genealogy
SEXP	yaml (SEXP)
	extract a YAML description
SEXP	gendat (SEXP)
	data-frame format
	DECLARATIONS (LBDP)
	DECLARATIONS (Moran)
	DECLARATIONS (S2I2R2)
	DECLARATIONS (SEIR)
	DECLARATIONS (SI2R)
	DECLARATIONS (SIIR)
	DECLARATIONS (SIR)
	DECLARATIONS (TwoSpecies)
void	R_init_phylopomp (DllInfo *info)

Variables
get_userdata_t *	get_userdata
get_userdata_double_t *	get_userdata_double
get_userdata_int_t *	get_userdata_int
static const R_CallMethodDef	callMethods []
static const R_CallMethodDef	extMethods []

Function Documentation

curtail()

SEXP curtail	(	SEXP	State,
		SEXP	Time,
		SEXP	Troot )

curtail the given genealogy

Definition at line 10 of file bare.cc.

                                                   {
    genealogy_t A = State;
    double t, t0;
    t = *REAL(AS_NUMERIC(Time));
    t0 = *REAL(AS_NUMERIC(Troot));
    if (ISNA(t)) t = A.time();
    if (ISNA(t0)) t0 = A.timezero();
    A.curtail(t,t0);
    SEXP out;
    PROTECT(out = serial(A));
    SET_ATTR(out,install("class"),mkString("gpgen"));
    UNPROTECT(1);
    return out;
  }

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DECLARATIONS() [1/8]

DECLARATIONS

(

LBDP

)

DECLARATIONS() [2/8]

DECLARATIONS

(

Moran

)

DECLARATIONS() [3/8]

DECLARATIONS

(

S2I2R2

)

DECLARATIONS() [4/8]

DECLARATIONS

(

SEIR

)

DECLARATIONS() [5/8]

DECLARATIONS

(

SI2R

)

DECLARATIONS() [6/8]

DECLARATIONS

(

SIIR

)

DECLARATIONS() [7/8]

DECLARATIONS

(

SIR

)

DECLARATIONS() [8/8]

DECLARATIONS

(

TwoSpecies

)

gendat()

SEXP gendat

(

SEXP

State

)

data-frame format

Definition at line 32 of file bare.cc.

                           {
    genealogy_t A = State;
    A.prune();
    A.obscure();
    A.trace_lineages();
    return A.gendat();
  }

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getInfo()

SEXP getInfo

(

SEXP

args

)

extract requested information prune and/or obscure if requested

Definition at line 19 of file getinfo.cc.

                           {
    const char *argname[] = {
      "object","prune","obscure",
      "t0","time","nsample","ndeme",
      "description","structure","yaml","newick",
      "lineages","gendat","genealogy"};
    const int narg = sizeof(argname)/sizeof(const char *);
    bool flag[narg];
    SEXP object = R_NilValue;
    size_t nout = 0;
    int k;
 
    for (k = 0; k < narg; k++) flag[k] = false;
    args = CDR(args);
 
    while (args != R_NilValue) {
      const char *name = isNull(TAG(args)) ? "" : CHAR(PRINTNAME(TAG(args)));
      SEXP arg = CAR(args);
      size_t j = matchargs(name,argname,narg);
      if (j == 0) {
        object = arg;
        flag[0] = true;
      } else if (j < 3) {
        flag[j] = *LOGICAL(AS_LOGICAL(arg));
      } else if (j < narg) {
        flag[j] = *LOGICAL(AS_LOGICAL(arg));
        if (flag[j]) nout++;
      } else {
        err("unrecognized argument '%s' in '%s'.",name,__func__);
      }
      args = CDR(args);
    }
 
    if (!flag[0]) err("no genealogy furnished to '%s'",__func__);
    genealogy_t A = object;
 
    // prune and/or obscure if requested
    const bool *f = flag+1;
    if (*(f++)) A.prune();
    if (*(f++)) A.obscure();
    A.trace_lineages();
 
    SEXP out, outnames;
    PROTECT(out = NEW_LIST(nout));
    PROTECT(outnames = NEW_CHARACTER(nout));
    k = 0;
    if (*(f++)) {               // t0
      k = set_list_elem(out,outnames,timezero(A),"t0",k);
    }
    if (*(f++)) {               // time
      k = set_list_elem(out,outnames,time(A),"time",k);
    }
    if (*(f++)) {               // nsample
      k = set_list_elem(out,outnames,nsample(A),"nsample",k);
    }
    if (*(f++)) {               // ndeme
      k = set_list_elem(out,outnames,ndeme(A),"ndeme",k);
    }
    if (*(f++)) {               // description
      k = set_list_elem(out,outnames,describe(A),"description",k);
    }
    if (*(f++)) {               // structure
      k = set_list_elem(out,outnames,structure(A),"structure",k);
    }
    if (*(f++)) {               // yaml
      k = set_list_elem(out,outnames,yaml(A),"yaml",k);
    }
    if (*(f++)) {               // newick
      k = set_list_elem(out,outnames,newick(A),"newick",k);
    }
    if (*(f++)) {               // lineages
      k = set_list_elem(out,outnames,lineage_count(A),"lineages",k);
    }
    if (*(f++)) {               // gendat
      k = set_list_elem(out,outnames,gendat(A),"gendat",k);
    }
    if (*(f++)) {               // genealogy
      SEXP S;
      PROTECT(S = serial(A));
      SET_ATTR(S,install("class"),mkString("gpgen"));
      k = set_list_elem(out,outnames,S,"genealogy",k);
      UNPROTECT(1);
    }
    SET_NAMES(out,outnames);
    UNPROTECT(2);
    return out;
  }

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parse_newick()

SEXP parse_newick	(	SEXP	X,
		SEXP	T0,
		SEXP	Tf )

A parser for Newick code. Returns a genealogy in the phylopomp format.

Definition at line 10 of file parse.cc.

                                               {
    PROTECT(X = AS_CHARACTER(X));
    PROTECT(T0 = AS_NUMERIC(T0));
    PROTECT(Tf = AS_NUMERIC(Tf));
    double t0 = *REAL(T0);
    double tf = *REAL(Tf);
    // parse the Newick representation into a genealogy:
    std::string x = CHAR(STRING_ELT(X,0));
    genealogy_t G(t0);
    G.parse(x,t0);
    if (!ISNA(tf)) {
      G.curtail(tf,t0);
    }
    G.trace_lineages();
    UNPROTECT(3);
    return serial(G);
  }

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R_init_phylopomp()

void R_init_phylopomp

(

DllInfo *

info

)

Definition at line 48 of file init.c.

                                      {
  // Register routines
  R_registerRoutines(info,NULL,callMethods,NULL,extMethods);
  R_useDynamicSymbols(info,TRUE);
  // R_useDynamicSymbols(info,FALSE);
  // R_forceSymbols(info,TRUE);
  get_userdata = (get_userdata_t*) R_GetCCallable("pomp","get_userdata");
  get_userdata_double = (get_userdata_double_t*) R_GetCCallable("pomp","get_userdata_double");
  get_userdata_int = (get_userdata_int_t*) R_GetCCallable("pomp","get_userdata_int");
}

yaml()

SEXP yaml

(

SEXP

State

)

extract a YAML description

Definition at line 26 of file bare.cc.

                         {
    genealogy_t A = State;
    return mkString(A.yaml().c_str());
  }

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Variable Documentation

callMethods

const R_CallMethodDef callMethods[]

static

Initial value:

= {
  METHODS(LBDP),
  METHODS(Moran),
  METHODS(S2I2R2),
  METHODS(SEIR),
  METHODS(SI2R),
  METHODS(SIIR),
  METHODS(SIR),
  METHODS(TwoSpecies),
  {"parse_newick", (DL_FUNC) &parse_newick, 3},
  {"curtail", (DL_FUNC) &curtail, 3},
  {"yaml", (DL_FUNC) &yaml, 1},
  {"gendat", (DL_FUNC) &gendat, 1},
  {NULL, NULL, 0}
}

Definition at line 27 of file init.c.

                                             {
  METHODS(LBDP),
  METHODS(Moran),
  METHODS(S2I2R2),
  METHODS(SEIR),
  METHODS(SI2R),
  METHODS(SIIR),
  METHODS(SIR),
  METHODS(TwoSpecies),
  {"parse_newick", (DL_FUNC) &parse_newick, 3},
  {"curtail", (DL_FUNC) &curtail, 3},
  {"yaml", (DL_FUNC) &yaml, 1},
  {"gendat", (DL_FUNC) &gendat, 1},
  {NULL, NULL, 0}
};

extMethods

const R_CallMethodDef extMethods[]

static

Initial value:

= {
  {"getInfo", (DL_FUNC) &getInfo, -1},
  {NULL, NULL, 0}
}

Definition at line 43 of file init.c.

                                            {
  {"getInfo", (DL_FUNC) &getInfo, -1},
  {NULL, NULL, 0}
};

get_userdata

get_userdata_t* get_userdata

Definition at line 5 of file init.c.

get_userdata_double

get_userdata_double_t* get_userdata_double

Definition at line 6 of file init.c.

get_userdata_int

get_userdata_int_t* get_userdata_int

Definition at line 7 of file init.c.