isqg (version 1.2)

set_specie: Constructor of Instances of the Specie Class

Description

Constructor of instances of the Specie class given the map of the genome and optionally a pointer to a C++ function which will drive the meiosis process.

Usage

set_specie(data, meiosis = NULL)

Arguments

data

A data frame with the map of the Genome to be simulates.

meiosis

A pointer to a C++ function of the meiosis process.

Value

Objects of R6 class with methods to mimic in silico Genomes.

Examples

# NOT RUN {
data(ToyMap)
spc_standard <- set_specie(ToyMap)

## generate standard _de novo_ variability
spc_standard$gamete(n = 100)

# }
# NOT RUN {
## write your function is C++ and then wrap it as a pointer
Meiosis <- "
// [[Rcpp::depends(isqg)]]

# include <isqg.h> // loading headers of the package
# include <vector>
# include <algorithm>

// NOTE:
// loci are independent to each other
Map meiosis(Chromosome * group) {

  Map map(group->get_map()) ;

  for (auto it = 0; it < map.size(); it++)
    if (static_cast<bool>(R::rbinom(1., .5))) map.at(it) = 2. + 1. ;

  map.erase(std::remove(map.begin(), map.end(), 2. + 1.), map.end());

  return map ;

}

// wrap the function as external pointer
// [[Rcpp::export]]
MPtr myMeiosis() { return MPtr(new FPtrM(& meiosis), true) ; }
"

## compile the code
Rcpp::sourceCpp(code = Meiosis, rebuild = TRUE)

## define a specie w/ custom meiosis
spp_custom <- set_specie(ToyMap, meiosis = myMeiosis())

## check meiosis process
spp_custom$gamete(n = 100)
# }
# NOT RUN {
# }