inst/doc/opt53.md

In genepop: Population Genetic Data Analysis Using Genepop

Sub-option 3: Allele size-based gene diversities and $\rho_{\mathrm{IS}}$

Option 5.3 is analogous to option 5.2. It computes measures of diversity based on allele size, namely mean squared allele size differences within individuals (MSDintra), and among individuals within samples (MSDinter), per locus per sample, and averaged over samples or over loci. Corresponding $\rho_\mathrm{IS}$ (the $F_\mathrm{IS}$ analogue, see Section \@ref(rho-stats)) estimates are also computed. Allele size is the allele name unless it has been given through the AlleleSizes setting.

For haploid data, only the mean squared difference MSDinter among individuals is computed. Multilocus estimates ignore haploid loci, or on the contrary ignore diploid loci if the setting EstimationPloidy=Haploid is used. Single-locus estimates are computed for both haploid and diploid loci irrespective of this setting.

The output is saved in the file yourdata.MSD.

genepop documentation built on Jan. 22, 2023, 1:07 a.m.