DJ: Jost's D

In FinePop: Fine-Scale Population Analysis

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)

Arguments

popdata

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

Value

Matrix of estimated pairwise Jost's D.

Author(s)

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)
cat(jsmackerel$MS.genepop, file="JSM_MS_genepop.txt", sep="\n")
cat(jsmackerel$popname, file="JSM_popname.txt", sep=" ")

# Data load
# Prepare your GENEPOP file and population name file in the working directory
# (Here, these files were provided as "JSM_MS_genepop.txt" and "JSM_popname.txt".)
popdata <- read.genepop(genepop="JSM_MS_genepop.txt", popname="JSM_popname.txt")

# Jost's D estimation
result.DJ <- DJ(popdata)
write.csv(result.DJ, "result_DJ.csv", na="")
print(as.dist(result.DJ))

FinePop documentation built on May 2, 2019, 3:30 p.m.