Classify recent hybrids from microsatellites

The multi-allelic version of classify_hybrids(): a parent with species-2 ancestry a passes on allele x with probability a * freq2(x) + (1 - a) * freq1(x). Each animal is tested against the pure, F1, F2, first- and second-backcross classes and against the best fit under any pair of parental ancestries; if no class fits (likelihood-ratio test at alpha), it is called "later".

Usage

classify_hybrids_microsat(alleles, ms, alpha = 0.01, error = 0.01)

Arguments

alleles

Allele matrix as in microsat_markers().

ms

Output of microsat_markers().

alpha

Significance level of the fit test. Many later-generation animals (for example backcrosses of backcrosses) have genotypes close to an early class and cannot be told apart one at a time. A larger alpha calls more of them "later" at the cost of rejecting some true early hybrids: in a bighorn sheep pedigree with 187 microsatellites, alpha = 0.01 kept 91% of early calls right and called 20% of later-generation sheep "later"; alpha = 0.1 gave 85% and 44%. Population ages from estimate_history() do not depend on this choice.

error

Probability that a called allele is replaced by a random allele of that locus (genotyping error, null alleles).

Value

A data.frame with class, probability and fit_p, one row per animal.

Examples

set.seed(1)
a <- cbind(L1.a1 = c(rep(100, 10), rep(104, 10)), L1.a2 = c(rep(100, 10), rep(104, 10)))
g <- rep(c("sp1", "sp2"), each = 10)
ms <- microsat_markers(a, g, "sp1", "sp2")
classify_hybrids_microsat(rbind(a, c(100, 104)), ms)
#>    class probability fit_p
#> 1  pure1   0.3860411     1
#> 2  pure1   0.3860411     1
#> 3  pure1   0.3860411     1
#> 4  pure1   0.3860411     1
#> 5  pure1   0.3860411     1
#> 6  pure1   0.3860411     1
#> 7  pure1   0.3860411     1
#> 8  pure1   0.3860411     1
#> 9  pure1   0.3860411     1
#> 10 pure1   0.3860411     1
#> 11 pure2   0.3860411     1
#> 12 pure2   0.3860411     1
#> 13 pure2   0.3860411     1
#> 14 pure2   0.3860411     1
#> 15 pure2   0.3860411     1
#> 16 pure2   0.3860411     1
#> 17 pure2   0.3860411     1
#> 18 pure2   0.3860411     1
#> 19 pure2   0.3860411     1
#> 20 pure2   0.3860411     1
#> 21    F1   0.3035949     1