Description Usage Arguments Value Author(s) See Also Examples

`compareSH`

tests the nullhypothesis that replicated allele frequency trajectories were generated with identical selection coefficients (s) and dominance (h).

1 2 3 4 |

`x` |
object of class "compsh" as returned by |

`traj` |
numeric matrix of allele frequency trajectories, where columns correspond to individual time points |

`t` |
numeric vector indicating the number of generations for each column in |

`Ne` |
numeric specifying the effective population size |

`haploid` |
logical indicating wether a population of haploid ( |

`h` |
numeric defining the dominance that should be assumed. If |

`N.ctraj` |
numeric determining the number of simulations that should be performed to correct for bias in the consensus trajectory (by default |

`N.pval` |
integer; the number of simulations performed to estimate the p-value (by default |

`cov` |
numeric matrix of sequence coverages, where columns and rows correspond to measurement time points and replicates, respectively |

`method` |
character string defining the method that should be used to estimate s (and p0 or h). |

`...` |
currently not used. |

A list with class "compsh" containing the following components:

`traj` |
matrix with observed allele frequency trajectories. |

`t` |
generations of each measurement time point. |

`Ne` |
effective population size. |

`haploid` |
logical for diploid or haploid individuals. |

`ctraj` |
consensus trajectory used to estimate s and h. |

`N.ctraj` |
number of simulations to correct 'ctraj' from bias. |

`s` |
estimated common s. |

`s.sep` |
individual estimates of s, one for each replicate. |

`h` |
if |

`h.sep` |
individual estimates of h, one for each replicate. |

`h.given` |
dominance defined in |

`cov` |
matrix with observed sequence coverages. |

`s.p.value` |
p-value for s. |

`h.p.value` |
p-value for h. |

`N.pval` |
number of simulations to estimate p-value(s). |

Thomas Taus

1 2 3 4 5 6 7 | ```
# simulate allele frequency trajectories under constant selection coefficient (and dominance)
tp <- seq(0, 100, by=10)
Ne <- 1000
traj <- wf.traj(p0=rep(0.05, times=3), Ne=Ne, t=tp, s=0.1, h=0.5, haploid=FALSE)
# test the null hypothesis that selection coefficients are identical between replicates
compareSH(traj=traj, t=tp, Ne=Ne, haploid=FALSE, N.pval = 100, h=0.5) ##### takes about 15 sec #####
``` |

ThomasTaus/poolSeq documentation built on Oct. 22, 2018, 7:21 p.m.

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