DEMEtics: Evaluating the genetic differentiation between populations based on Gst and D values.

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.

Author
Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann
Date of publication
2013-12-03 11:59:32
Maintainer
Alexander Jueterbock <Alexander-Jueterbock@web.de>
License
GPL (>= 2)
Version
0.8-7

View on CRAN

Man pages

DEMEtics-package
Evaluating the genetic differentiation between populations...
D.JostaGst.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

Files in this package

DEMEtics
DEMEtics/inst
DEMEtics/inst/CITATION
DEMEtics/NAMESPACE
DEMEtics/data
DEMEtics/data/Example.untransformed.txt.gz
DEMEtics/data/Example.transformed.txt.gz
DEMEtics/R
DEMEtics/R/p.values.loci.calc.r
DEMEtics/R/Hj.r
DEMEtics/R/Calculate.Hj.values.r
DEMEtics/R/Ht.r
DEMEtics/R/Gst.r
DEMEtics/R/critical.ci.values.r
DEMEtics/R/Gendiff.values.r
DEMEtics/R/D.Jost.r
DEMEtics/R/p.value.correcture.r
DEMEtics/R/p.val.r
DEMEtics/R/harmonic.r
DEMEtics/R/Frequency.genotypes.calculation.r
DEMEtics/R/calculate.anzahlk.r
DEMEtics/R/Hardy.Weinberg.r
DEMEtics/R/Hj.values.1pop.r
DEMEtics/R/H.out.r
DEMEtics/R/chosen.calculations.r
DEMEtics/R/locus.means.calc.r
DEMEtics/R/this.genotype.calc.r
DEMEtics/R/Ht.value.calculations.r
DEMEtics/R/over.all.pops.r
DEMEtics/R/Bootstrapping.per.locus.r
DEMEtics/R/Hs.est.r
DEMEtics/R/p.value.loci.calc2.r
DEMEtics/R/Hs.Ht.est.calculation.r
DEMEtics/R/allelefreq.r
DEMEtics/R/pop.allele.proportions.r
DEMEtics/R/Hardy.calc.r
DEMEtics/R/v.loci.calc.r
DEMEtics/R/Dv.locis.corrected.calc.r
DEMEtics/R/Hj.values.one.population.r
DEMEtics/R/Locuswise.HWE.r
DEMEtics/R/D.r
DEMEtics/R/DEMEtics.env.r
DEMEtics/R/Hs.value.calculation.r
DEMEtics/R/Hs.values.calculation.r
DEMEtics/R/v.loci.calc2.r
DEMEtics/R/Hj.values.calculation.r
DEMEtics/R/sample.size.calc.r
DEMEtics/R/Dest.r
DEMEtics/R/Bootstrapping.CI.r
DEMEtics/R/Hs.r
DEMEtics/R/Gst.est.r
DEMEtics/R/Mean.allelefrequency.r
DEMEtics/R/Bootstrapping.p.r
DEMEtics/R/Ht.est.r
DEMEtics/R/calc.r
DEMEtics/R/Gst.Nei.r
DEMEtics/R/pair.pops.r
DEMEtics/R/inputformat.r
DEMEtics/R/allelefreq.calcs.r
DEMEtics/MD5
DEMEtics/DESCRIPTION
DEMEtics/man
DEMEtics/man/Example.transformed.Rd
DEMEtics/man/Example.untransformed.Rd
DEMEtics/man/D.JostaGst.Nei.Rd
DEMEtics/man/DEMEtics-package.Rd