Description Usage Arguments Value Examples

Helper function which creates an object containing necessary information to run a simulation of haplotype accumulation for a real species of interest

1 2 |

`perms` |
Number of permutations (replications) |

`p` |
Proportion of haplotypes to recover |

`conf.level` |
Desired confidence level for graphical output and interval estimation |

`ci.type` |
Type of confidence interval for graphical output. Choose from "quantile" or "asymptotic" |

`subsample` |
Is a subsample of DNA sequences desired? |

`prop` |
If subsample = TRUE, the proportion of DNA sequences to subsample |

`num.iters` |
Number of iterations to compute |

`progress` |
Should iteration output be printed to the R console? |

`filename` |
Name of file where simulation results are to be saved |

A list object of class "HAC" with 13 elements that can be passed to `HAC.simrep`

as follows:

`input.seqs` |
Should a FASTA file of aligned/trimmed DNA sequences be inputted? Default is TRUE |

`subset.seqs` |
Should a subsample of DNA sequences be taken? Default is FALSE (can be altered by user) |

`prop.seqs` |
Proportion of DNA sequences to subsample. Default is NA (can be altered by user) |

`prop.haps` |
Proportion of haplotype labels to subsample. Default is NULL |

`subset.haps` |
Should a subsample of haplotype labels be taken? Default is NULL |

`N` |
Number of individuals. NA by default (computed automatically by algorithm) |

`Hstar` |
Number of unique species' haplotypes. NA by default (computed automatically by algorithm) |

`probs` |
Haplotype frequency distribution vector. NA by default (computed automatically by algorithm) |

`p` |
Proportion of haplotypes to recover. |

`perms` |
Number of permutations (replications). |

`conf.level` |
Desired confidence level for graphical output and interval estimation. |

`ci.type` |
Type of confidence interval for graphical output. |

`num.iters` |
Number of iterations to compute. |

`progress` |
Should iteration output be printed to the R console? Default is TRUE |

`filename` |
Name of file where simulation results are to be saved. |

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## Simulate real species ##
# outputs file called "output.csv"
HACSObj <- HACReal(filename = "output")
## Simulate real species - subsampling ##
# subsamples 25% of DNA sequences
HACSObj <- HACReal(subsample = TRUE, prop = 0.25, conf.level = 0.95,
filename = "output")
## Simulate real species and all parameters changed - subsampling ##
HACSObj <- HACReal(perms = 10000, p = 0.90, subsample = TRUE,
prop = 0.15, conf.level = 0.99, num.iters = 1, filename = "output")
``` |

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