parse.cc File Reference

#include "genealogy.h"
#include "generics.h"
#include "internal.h"

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

Function Documentation

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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