Description Details Citation Author(s)
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.
Package: | DEMEtics |
Type: | Package |
Version: | 0.8-7 |
Date: | 2013-12-02 |
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:
1 2 3 4 5 6 | 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
|
To cite the package 'DEMEtics' in publications use:
Gerlach, G., Jueterbock, A., Kraemer, P., Deppermann, J. and Harmand,
P. 2010
Calculations of population differentiation based on G(ST) and D:
forget G(ST)
but not all of statistics! Molecular Ecology
19, 3845-3852
Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann
Maintainer: Alexander Jueterbock <Alexander-Jueterbock@web.de>
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