std::string ribi::ctm::Helper::CreateSimulatedPhylogeny(
const Parameters& parameters
) const
{
ribi::fileio::FileIo f;
auto& r = ribi::Rinside().Get();
r.parseEvalQ("library(ape)");
r.parseEvalQ("library(geiger)");
const double birth_rate{parameters.GetBirthRate().value()};
const double death_rate{parameters.GetDeathRate().value()};
const int n_taxa{parameters.GetNumberOfTaxa()};
const int rng_seed{parameters.GetRngSeed()};
const double t_end{parameters.GetTime().value()};
assert(t_end == 0 && "Not yet implemented running to a certain time");
r["birth_rate"] = birth_rate;
r["death_rate"] = death_rate;
r["n_taxa"] = n_taxa;
r["rng_seed"] = rng_seed;
r["t_end"] = t_end;
// /home/richel/R/i686-pc-linux-gnu-library/3.1/Rcpp/include/Rcpp/vector/Vector.h
assert(Rcpp::DoubleVector(r["birth_rate"])[0] == birth_rate);
assert(Rcpp::DoubleVector(r["death_rate"])[0] == death_rate);
assert(Rcpp::IntegerVector(r["n_taxa"])[0] == n_taxa);
assert(Rcpp::IntegerVector(r["rng_seed"])[0] == rng_seed);
assert(Rcpp::DoubleVector(r["t_end"])[0] == t_end);
//Vital! If forgotten, the branch lengths will become N/A or 0
std::setlocale(LC_ALL,"en_US.UTF-8");
r.parseEvalQ("tree_full <- sim.bdtree(b=birth_rate,d=death_rate,stop=\"taxa\",n=n_taxa,extinct=FALSE,seed=rng_seed)");
const Rcpp::String s = r.parseEval("write.tree(tree_full)");
return std::string(s);
}
