FinePop (version 1.5.2)

DJ: Jost's D

Description

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

Usage

DJ(popdata)

Value

Matrix of estimated pairwise Jost's D.

Arguments

popdata

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

Author

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

References

Jost L (2008) Gst and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.

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)

# Jost's D estimation
result.DJ <- DJ(popdata)
print(as.dist(result.DJ))