DEMEtics-package: Evaluating the genetic differentiation between populations based on Gst and D values.
Description
This package allows to calculate the fixation index Gst
(Nei, 1973) and the differentiation index D (Jost, 2008) pairwise
between or averaged over several populations. P-values, stating the
significance of differentiation, and 95 percent confidence intervals
can be estimated using bootstrap resamplings. In the case that more
than two populations are compared pairwise, the p-values are
adjusted by bonferroni correction and in several other ways due to
the multiple comparison from one data set.Citation
To cite the package 'DEMEtics' in publications use:
Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana
Deppermann (2010).
DEMEtics: Evaluating the genetic differentiation
between populations based on Gst and D values.
R package version 0.8-2.
http://cran.r-project.org/web/packages/DEMEtics/index.htmlDetails
ll{
Package: DEMEtics
Type: Package
Version: 0.8-2
Date: 2011-01-08
Depends: R (>= 2.8.0)
License: GPL (>= 2)
Literature:
Gerlach G., Jueterbock A., Kraemer P., Deppermann J. and Harmand P. 2010
Calculations of population differentiation based on Gst and D:
forget Gst but not all of statistics!
Molecular Ecology 19, p. 3845--3852.
Goudet J., Raymond M., deMeeues T. and Rousset F. 1996
Testing differentiation in diploid populations.
Genetics 144, 4, p. 1933--1940.
Jost, L. 2008
Gst and its relatives do not measure differentiation.
Molecular Ecology 17, 18, p. 4015--4026.
Manly, B.F.J. 1997
Randomization, bootstrap and Monte Carlo methods in
biology
Chapman & Hall.
Nei, M. 1973
Analysis of gene diversity in subdivided populations.
Proceedings of the National Academy of Sciences of the United
States of America
70, 12, p. 3321--3323.
Nei M., Chesser R. 1983
Estimation of fixation indices and gene diversities.
Annals of Human Genetics 47, 253--259.
Wright, S.P. 1992
Adjusted p-values for simultaneous inference.
Biometrics 48, 1005--1013.
LazyLoad: yes
Packaged: 2010-12-18 13:48:33 UTC; alexj
Built: R 2.10.1; ; 2010-12-18 13:48:39 UTC; unix
}Index:
D.Jost-and-Gst.Nei Comparing Populations - Differentiation and
Fixation Indices
Example.transformed Allelic Data of Three Populations For Three
Loci
Example.untransformed Allelic Data of Three Populations for Three
Loci