GstH {FinePop}R Documentation

Hedrick's G'st

Description

This function estimates pairwise G'st (Hedrick 2005) among subpopulations from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

Usage

GstH(popdata)

Arguments

popdata

Population data object created by read.genepop function from a GENEPOP file.

Value

Matrix of estimated pairwise Hedrick's G'st.

Author(s)

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

References

Hedrick P (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

See Also

read.genepop

Examples

# Example of GENEPOP file
data(jsmackerel)
jsm.ms.genepop.file <- tempfile()
jsm.popname.file <- tempfile()
cat(jsmackerel$MS.genepop, file=jsm.ms.genepop.file, sep="\n")
cat(jsmackerel$popname, file=jsm.popname.file, sep=" ")

# Data load
# Prepare your GENEPOP file and population name file in the working directory
# Replace "jsm.ms.genepop.file" and "jsm.popname.file" by your file names.
popdata <- read.genepop(genepop=jsm.ms.genepop.file, popname=jsm.popname.file)

# Hedrick's G'st estimation
result.GstH <- GstH(popdata)
print(as.dist(result.GstH))

[Package FinePop version 1.5.2 Index]