cblv.cc File Reference

#include "genealogy.h"
#include "generics.h"
#include "internal.h"
#include <utility>
#include <vector>
#include <R.h>
#include <Rdefines.h>
#include <Rinternals.h>

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Functions
static R_INLINE SEXP	make_matrix (size_t nrow, size_t ncol, const char **names)
SEXP	cblv (genealogy_t &A)
SEXP	cblv (SEXP State)
	construct CBLV representation as a matrix
SEXP	parse_cblv (SEXP XY, SEXP T0, SEXP Time)
	parse CBLV representation

Function Documentation

cblv() [1/2]

SEXP cblv

(

genealogy_t &

A

)

Definition at line 150 of file cblv.cc.

{
  const char *colnames[] = {"tip","node"};
  double *x, *y;
  size_t i, n;
  SEXP S;
  std::pair<std::vector<slate_t>, std::vector<slate_t>> rep;
  rep = A.prune().obscure().insert_zlb().cblv();
  n = rep.first.size();
  PROTECT(S = make_matrix(n,2,colnames));
  x = REAL(S);
  y = REAL(S)+n;
  for (i = 0; i < n; i++) {
    x[i] = rep.first[i];
    y[i] = rep.second[i];
  }
  UNPROTECT(1);
  return S;
}

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cblv() [2/2]

SEXP cblv

(

SEXP

State

)

construct CBLV representation as a matrix

Definition at line 174 of file cblv.cc.

                         {
    genealogy_t A = State;
    return cblv(A);
  }

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make_matrix()

static R_INLINE SEXP make_matrix ( size_t nrow, size_t ncol, const char ** names )

static

Definition at line 12 of file cblv.cc.

{
  SEXP dim, x;
  SEXP dimnm, nm;
  int *dimp;
  size_t k;
  PROTECT(dim = NEW_INTEGER(2));
  PROTECT(dimnm = Rf_allocVector(VECSXP,2));
  PROTECT(nm = NEW_CHARACTER(ncol));
  for (k = 0; k < ncol; k++)
    SET_STRING_ELT(nm,k,mkChar(names[k]));
  dimp = INTEGER(dim);
  dimp[0] = nrow; dimp[1] = ncol;
  PROTECT(x = Rf_allocArray(REALSXP,dim));
  SET_ELEMENT(dimnm,0,R_NilValue);
  SET_ELEMENT(dimnm,1,nm);
  SET_DIMNAMES(x,dimnm);
  UNPROTECT(4);
  return x;
}

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parse_cblv()

SEXP parse_cblv	(	SEXP	XY,
		SEXP	T0,
		SEXP	Time )

parse CBLV representation

Definition at line 180 of file cblv.cc.

                                                {
    int *n = INTEGER(GET_DIM(XY));
    if (n[1] != 2)
      err("in 'parse_cblv': 'xy' must be a two-column matrix.");
    double *xp = REAL(XY);
    double *yp = xp+n[0];
    double *t0 = REAL(T0);
    double *time = REAL(Time);
    genealogy_t A(*t0);
    A.parse_cblv(xp,yp,*n,*time);
    return serial(A);
  }

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