runall: Batch run subsampling corrections for allelic richness w/...

In romunov/resamplediversity: Data and code: Reference population yardstick to calibrate and compare genetic diversity

Batch run subsampling corrections for allelic richness w/ function subsample.gen

Description

Batch wrapper for subsample.gen function. Batch runs corrections for unequal sampling for a subset of loci and a vector of sample sizes. Streamlines usage of subsample.gen function to process a number of populations of different sample size that were analyzed using the same panel of markers.

Usage

runall(N, genotypes, loci, nboots = 1000)

Arguments

N	Vector of sample sizes. Sample sizes are the numbers of samples to use in each subsample - equal to the sample sizes in the set of compared populations.
genotypes	Genind object of genotypes (adegenet package) for the reference popoulation.
loci	Subset of loci. Vector of generic locus names in the genotypes object c("L01","L03",...) common in both the reference and the compared populations.
nboots	Number of bootstrap resamples. Default=1000.

Value

Dataframe with summarized data (parameter means over all subsamples) for each sample size. N: sample size A: allelic diversity SEA: standard error of A He: expected deterozygosity SEHe: standard error of expected heterozygosity Ho: observed deterozygosity SEHo: standard error of observed heterozygosity

Note

SLOW! Be patient. Produces a lot of text as I don't know how to stop the summary function of adegenet package to print out every iteration.

Author(s)

Tomaž Skrbinšek [e-mail]

References

Skrbinšek T, Jelenčič M, Waits LP, Potočnik H, Kos I, Trontelj P(2012) Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear. Heredity, In press.

Leberg PL (2002) Estimating allelic richness: Effects of sample size and bottlenecks. Molecular Ecology, 11, 2445-2449.

See Also

subsample.gen, genind

Examples

# For examples, see vignette
vignette("resamplediversity")

romunov/resamplediversity documentation built on July 31, 2023, 2:23 a.m.