Description Arguments Author(s) See Also Examples

The object that contains the set parameter values can be passed to the function MS. This class simpliifes the process of passing on all necessary values to the MS function.

`theta` |
mutation parameter theta (4Nmu), where N is the diplod effective population size and mu the mutation rate per locus. It needs to be provided as a vector of length n.regions |

`seeds` |
specify 3 random number seeds. a vector of length 3 with positive integer values is expected |

`fixedSegsites` |
usually the number of segregating sites varies in each iteration. Please provide a single numeric value if the number of segregating sites needs to be fixed. |

`recombination` |
provide a vector of format: c(p, nsites), p = cross-over parameter rate, nsites is the number of sites between which recombination occurs |

`geneConv` |
in addition to recombination, intra-locus non-cross-over exchange gene conversion can be included in the simulation; the expected format is c(f, gamma), where f denotes the ratio g/r (r is the probability per generation of crossing-over between adjacent sites (see Wiuf and Hein 2000), and gamma is the mean conversion tract length. |

`growth` |
population size is assumed to be $N(t) = N0 exp^alpha*t$. Provide alpha as an integer value. Negative values indicate that population was larger in the past than present, positive values indicate that it was smaller. |

`migration` |
specify the migration rate between populations. Please provide a single numeric value. |

`demography` |
vector of length 3 or 4 with first value denoted as 'type' |

Bastian Pfeifer

MS

1 2 3 | ```
# params <- new("test.params")
# [email protected] <- rep(5,n.regions)
# [email protected] <- 3
``` |

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