SummaryInfo.jl

PopGen.jl/src/SummaryInfo.jl

📦 not exported	🔵 exported by PopGen.jl

🔵 alleleaverage

alleleaverage(data::PopData, rounding::Bool = true)

Returns a NamedTuple of the average number of alleles ('mean') and standard deviation (stdev) of a PopData. Use rounding = false to not round results. Default (true) roundsto 4 digits.

Example

alleleaverage(@nancycats, rounding = false)

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🔵 richness

richness(data::PopData)

Calculates various allelic richness and returns a table of per-locus allelic richness. Use populations = true to calculate richness by locus by population.

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🔵 summary

summary(data::PopData; by::String = "global")

Provides summary statistics for a PopData object. Use by = "locus" for summary information by locus. Global values are given as unweighted means of the per-locus parameters.

Het_obs

observed heterozygosity given as:

1 - ∑ₖ ∑ᵢ Pₖᵢᵢ/np

where Pkii represents the proportion of homozygote i in sample k and np is the number of samples in that population

HT

overall gene diversity given as:

1 - ∑ᵢ(p̄ᵢ² + (HS / (ñ × np)) - Het_obs / (2 × ñ × np)) where p̄ᵢ = ∑ₖpₖᵢ / np

HS

within population gene diversity given as:

1 - ∑ᵢ(pᵢ² + HS / (ñ × np) - Het_obs / (2 × ñ × np)) where ñ = np / ∑ₖ(1/nₖ) where p̄ᵢ² = ∑ₖ(pᵢₖ² / np)

DST

amount of gene diversity among samples given as:

HT - HS

DST′

amount of gene diversity among samples adjusted for sample size given as:

(np / (np-1)) × Dst

HT′

overall gene diversity adjusted for sample size given as:

HS + DST′

FST

proportion of the total genetic variance in subpopulations relative to the total genetic variance given as:

DST / HT

FST′

proportion of the total genetic variance in subpopulations relative to the total genetic variance, adjusted for heterozygosity given as:

DST′ / HT′

FIS

proportion of the genetic variance in a locus relative to the genetic variance within subpopulations given as:

1 - (Het_obs / HS)

DEST

population differentiation (Jost 2008) given as:

(np/(np-1)) × (Ht'-Hs) / (1-Hs)