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For hybrids with up to three parental lineages, the function estimates genomic proportions and ancestry indices by numerically searching likelihood space.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: threeway
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thirdclass uses genetic marker data and parental allele frequencies to calculate the likelihoods for each of the 15 diploid genotype classes possible in the first two generations of admixture (each parental, F1, F2, and each backcross) for each pair of parental lineages.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: thirdclass
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Simulate hybrid zone dynamics with or without selection on a few loci.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: spatial.HZ
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Simulate admixture dynamics with or without selection on a few loci. Although space matters for local density-dependent competition, mating and dispersal are random (uniform) with respect to space.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: spatial.AD
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For hybrid individuals genotyped with diagnostic markers (one allele fixed in each parental lineage), the null hypothesis that variation in allele frequencies is explained by sampling and drift (no selection) is evaluated with a chi-squared test statistic.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: longX2
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HItest3 compares the best fit of fifteen early generation diploid hybrid genotypes (parental, F1, F2, backcross between all three pairs of parental lineages) to the maximum likelihood genotype proportions estimated by threeway or HIC3.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: HItest3
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HItest compares the best fit of six early generation diploid hybrid genotypes (parental, F1, F2, backcross) to the maximum likelihood genotype decribed by ancestry (S) and interclass heterozygosity (H).
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: HItest
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HIsurf calculates the log likelihood of points on a bivariate grid to describe the joint likelihood surface of ancestry and interclass heterozygosity for a genotype given parental allele frequencies.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: HIsurf
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HILL calulates the log-likelihood of a hybrid genotype given parental allele frequencies, an ancestry index (S), and interclass heterozygosity (H). This function is used by HIest and HIclass for data analysis.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: HILL
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HIest provides approaches to find maximum likelihood estimates of S and H, using the likelihood functions described by Fitzpatrick (2012).
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: HIest
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providing 
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