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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 |