inbreedR (version 0.3.0)

HHC: Calculates heterzygosity-heterozygosity correlations with standardized multilocus heterozygosities (sMLH)

Description

Loci are randomly devided into two equal groups and the correlation coefficient between the resulting sMLH values is calculated.

Usage

HHC(genotypes, reps = 100, CI = 0.95)

Arguments

genotypes

data.frame with individuals in rows and loci in columns, containing genotypes coded as 0 (homozygote), 1 (heterozygote) and NA (missing)

reps

number of repetitions, i.e. splittings of the dataset

CI

size of the confidence interval around the mean het-het correlation (default is 0.95)

Value

• call
  function call.
• HHC_vals
  vector of HHC's obtained by randomly splitting the dataset
• summary_exp_r2
  r2 mean and sd for each number of subsetted loci
• nobs
  number of observations
• nloc
  number of markers

References

Balloux, F., Amos, W., & Coulson, T. (2004). Does heterozygosity estimate inbreeding in real populations?. Molecular Ecology, 13(10), 3021-3031.

Examples

data(mouse_msats)
genotypes <- convert_raw(mouse_msats)
(out <- HHC(genotypes, reps = 100, CI = 0.95))

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