Example.untransformed

The data set gives the fragment lengths (in base pairs) for three loci and three populations.
Before the data can be analyzed by the functions included in this
package, the format of the data table has to be transformed. This is
done by using the function <code><a href="/link/inputformat?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::inputformat">inputformat</a></code> or by setting the argument 'format.table' of the following functions of
this package as TRUE: <code><a href="/link/all.pops.D?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::all.pops.D">all.pops.D</a></code>, <code><a href="/link/all.pops.Dest?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::all.pops.Dest">all.pops.Dest</a></code>, <code><a href="/link/all.pops.Dest.Chao?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::all.pops.Dest.Chao">all.pops.Dest.Chao</a></code>,
<code><a href="/link/all.pops.Gst?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::all.pops.Gst">all.pops.Gst</a></code>, <code><a href="/link/all.pops.Gst.est?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::all.pops.Gst.est">all.pops.Gst.est</a></code>, <code><a href="/link/pair.pops.D?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::pair.pops.D">pair.pops.D</a></code>, <code><a href="/link/pair.pops.Dest?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::pair.pops.Dest">pair.pops.Dest</a></code>,
<code><a href="/link/pair.pops.Dest.Chao?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::pair.pops.Dest.Chao">pair.pops.Dest.Chao</a></code>, <code><a href="/link/pair.pops.Gst?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::pair.pops.Gst">pair.pops.Gst</a></code>, <code><a href="/link/pair.pops.Gst.est?package=DEMEtics&version=0.8.1" rd-options="" data-mini-rdoc="DEMEtics::pair.pops.Gst.est">pair.pops.Gst.est</a></code>.

datasets

Out of a table comprising allelic data of at least one
        locus for several individuals and from at least two
        populations, measurements of genetic differentiation (i.e. D,
        Dest, Dest.Chao, Gst and Gst.est (Jost, 2008)) can be
        calculated. P-values and 95% confidence intervals are
        calculated according to Manly (1997) using a bootstrap method.
        Thereby, for each locus, alleles are reallocated over
        populations if they are all in Hardy Weinberg Equilibrium
        (HWE). If not, the genotypes are reallocated, since alleles can
        not be assumed to be inherited independently from each other
        (Goudet, 1996). The p-values state how much the empirical found
        allocation of alleles over populations differs from an
        allocation that could arise by chance alone. In the case that
        more than two populations are compared pairwise, the p-values
        are adjusted besides using bonferroni correction in several
        other ways due to the multiple comparison from one data set.

Example.untransformed: Allelic Data of Three Populations for Three Loci

Description

Usage

Arguments

Examples