Jost's D
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.
DJ(popdata)
popdata |
Population data object created by read.genepop function from a GENEPOP file. |
Matrix of estimated pairwise Jost's D.
Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
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.
# 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))
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