Summarize Demographics and Allele Retention from aRetain

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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 aRetain

GeneCount

"adult" or "all" as specified for aRetain

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.