aRetainSummarize pertinent information about the population simulated by aRetain.
aRetain.summary(adata, GeneCount, alpha=0.05, dropextinct = FALSE)list of output from aRetain
"adult" or "all" as specified for aRetain
confidence level e.g. 0.05 for 95% intervals
logical: should simulated populations that decline to zero be omitted from the summary?
A matrix in which the rows correspond to simulation years (0,...,nyears) and the columns are summary variables:
mean number of adults
SE for # adults
mean # of nonbreeders
mean # of breeding females
SE for # of breeding females
mean # of breeding males
SE for # of breeding males
mean # of founders (starters and supplemental individuals) remaining
mean # of immigrants present
mean age of breeding adults (those that are actually paired that year)
probability that the population is extant (proportion of simulations in which the population does not become extinct)
lower bound of the confidence interval for P.extant
upper bound of the confidence interval for P.extant
probability that the rare allele is present in the population
lower bound of the confidence interval for P.retain
upper bound of the confidence interval for P.retain
frequency of the rare allele in the simulated population (in adults or in all individuals, as per GeneCount argument in aRetain)
standard error for A.Freq
Weiser, E.L., Grueber, C. E., and I. G. Jamieson. 2012. AlleleRetain: A program to assess management options for conserving allelic diversity in small, isolated populations. Molecular Ecology Resources 12:1161-1167.