`envr`

is a new (initially empty) environment that is created when `HACSim`

is loaded.

When a simulation is run via `HAC.simrep`

, `envr`

will contain 26 elements as follows:

`ci.type` |
Type of confidence interval to compute and plot. Defaul is |

`conf.level` |
The desired confidence level. Default is |

`d` |
A dataframe with |

`df_out` |
A dataframe with |

`filename` |
The name of the file where results are to be saved. Default is NULL. |

`Hstar` |
Number of unique species' haplotypes |

`input.seqs` |
Should DNA sequences be inputted? Default is FALSE. |

`iters` |
The number of iterations required to reach convergence |

`N` |
The starting sample size used to initialize the algorithm |

`Nstar` |
The final (extrapolated) sample size |

`Nstar.high` |
The upper endpoint of the desired level confidence interval for the 'true' required sample size |

`Nstar.low` |
The lower endpoint of the desired level confidence interval for the 'true' required sample size |

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

`p` |
The user-specified level of haplotype recovery. Default is |

`perms` |
The user-specified number of permutations (replications). Default is |

`probs` |
Haplotype frequency distribution vector |

`progress` |
Should iteration results be outputted to the console? Default is TRUE. |

`prop.haps` |
If |

`prop.seqs` |
If |

`ptm` |
A timer to track progress of the algorithm in seconds |

`R` |
The proportion of haplotypes recovered by the algorithm |

`R.low` |
The lower endpoint of the desired level confidence interval for the 'true' fraction of haplotypes captured |

`R.up` |
The upper endpoint of the desired level confidence interval for the 'true' fraction of haplotypes captured |

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

`subset.seqs` |
Should a subsample of DNA sequences be taken? Default is FALSE. |

`X` |
Mean number of specimens not sampled |

1 2 3 4 5 6 |

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