This is a small, lightweight package that lets users investigate the distribution of genotypes in genotypebysequencing (GBS) data where they expect (by and large) HardyWeinberg equilibrium, in order to assess rates of genotyping errors and the dependence of those rates on read depth. It implements a Markov chain Monte Carlo (MCMC) sampler using 'Rcpp' to compute a Bayesian estimate of what we call the heterozygote miscall rate for restrictionassociated digest (RAD) sequencing data and other types of reduced representation GBS data. It also provides functions to generate plots of expected and observed genotype frequencies. Some background on these topics can be found in a recent paper "Recent advances in conservation and population genomics data analysis" by Hendricks et al. (2018) <doi:10.1111/eva.12659>, and another paper describing the MCMC approach is in preparation with Gordon Luikart and Thierry Gosselin.
Package details 


Author  Eric C. Anderson [aut, cre] 
Maintainer  Eric C. Anderson <[email protected]> 
License  CC0 
Version  0.0.1 
Package repository  View on CRAN 
Installation 
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