Hybrid index estimation

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Documentation for package ‘HIest’ version 2.0

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HIest-package Functions for estimating hybrid indices (ancestry and heterozygosity) and fitting genomic clines.
Bluestone Original marker data for hybrid tiger salamander larvae collected from Bluestone Quarry pond.
Cline.fit Fit alternative cline functions to data from one or more genetic loci.
Cline.plot Graph genomic clines fit to data
gcline.fn Fit a genomic cline using maximum likelihood
HIC Closed form maximum-likelihood estimates of ancestry and heterozygosity for diagnostic markers
HIC3 Closed form maximum-likelihood estimates of ancestry and heterozygosity for diagnostic markers in a three-way hybrid zone
HIclass Calculate likelihoods for early generation hybrid genotype classes
HIest Find the joint maximum likelihood estimates of ancestry and interclass heterozygosity in a sample of hybrids.
HILL Hybrid Index Log Likelihood
HIsurf Describe the joint likelihood surface of ancestry and heterozygosity for a hybrid genotype.
HItest Compare the likelihood of hybrid classification to MLE estimates of ancestry and heterozygosity.
HItest3 Compare the likelihood of hybrid classification to MLE estimates of ancestry and heterozygosity for three-way hybrid zones.
longX2 Longs heterogeneity test for admixture proportions in a single population.
spatial.AD Simulate admixture in continuous, 2-dimensional space
spatial.HZ Simulate a hybrid zone in continuous, 2-dimensional space
thirdclass Calculate likelihoods for early generation hybrid genotype classes in a three-way hybrid zone.
threeway Find joint maximum-likelihood estimates of ancestry and heterozygosity for a sample of hybrids in a three-way hybrid zone