# Summarize Demographics and Allele Retention from aRetain

### Description

Summarize pertinent information about the population simulated by `aRetain`

.

### Usage

1 | ```
aRetain.summary(adata, GeneCount, alpha=0.05, dropextinct = FALSE)
``` |

### Arguments

`adata` |
list of output from |

`GeneCount` |
"adult" or "all" as specified for |

`alpha` |
confidence level e.g. 0.05 for 95% intervals |

`dropextinct` |
logical: should simulated populations that decline to zero be omitted from the summary? |

### Value

A matrix in which the rows correspond to simulation years (0,...,nyears) and the columns are summary variables:

`MeanN` |
mean number of adults |

`SEN` |
SE for # adults |

`MeanNNonbr` |
mean # of nonbreeders |

`MeanBrF` |
mean # of breeding females |

`SEBrF` |
SE for # of breeding females |

`MeanBrM` |
mean # of breeding males |

`SEBrM` |
SE for # of breeding males |

`MeanNFound` |
mean # of founders (starters and supplemental individuals) remaining |

`MeanNMigr` |
mean # of immigrants present |

`MeanAge` |
mean age of breeding adults (those that are actually paired that year) |

`P.extant` |
probability that the population is extant (proportion of simulations in which the population does not become extinct) |

`P.xLCL` |
lower bound of the confidence interval for P.extant |

`P.xUCL` |
upper bound of the confidence interval for P.extant |

`P.retain` |
probability that the rare allele is present in the population |

`P.LCL` |
lower bound of the confidence interval for P.retain |

`P.UCL` |
upper bound of the confidence interval for P.retain |

`A.Freq` |
frequency of the rare allele in the simulated population (in adults or in all individuals, as per GeneCount argument in aRetain) |

`A.SE` |
standard error for A.Freq |

### Author(s)

Emily Weiser emily.l.weiser@gmail.com

### References

Weiser, E.L., Grueber, C. E., and I. G. Jamieson. In review. AlleleRetain: A program to assess management options for conserving allelic diversity in small, isolated populations. Molecular Ecology Resources.