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Calculate gene diversity from founder genome equivalents

Source: R/calcGeneDiversity.R
calcGeneDiversity.Rd

Part of the Genetic Value Analysis

Usage

calcGeneDiversity(fg)

Arguments

fg

Founder genome equivalents scalar, as returned by calcFG() or the $FG element of calcFEFG(). NA yields NA.

Value

The gene diversity GD = 1 - 1 / (2 * fg): a single number in [0, 1), or NA when fg is NA.

Details

Gene diversity is the expected heterozygosity retained relative to the founding gene pool, GD = 1 - 1 / (2 * FG), where FG is the founder genome equivalents (see calcFG). It summarizes how much of the founders' allelic diversity still survives: 0 means none is retained, and it approaches (never reaches) 1 as FG grows.

GD is a diversity proportion, not a count of effective individuals, and it is computed over the same analysis set as FG. NA propagates: when FG is NA (the zero-retention degeneracy calcFG() reports), GD is NA.

References

Gene diversity is derived here from the founder genome equivalents (calcFG) of Lacy RC. 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol 8:111-123.

See also

Other genetic value analysis: calcA(), calcFE(), calcFEFG(), calcFG(), calcFGSE(), calcGU(), calcGUSE(), calcNeSexRatio(), calcNeVariance(), calcRetention()

Examples

calcGeneDiversity(20) # 0.975
#> [1] 0.975
calcGeneDiversity(52.75) # gene diversity at the qcPed FG
#> [1] 0.9905213