stamppNeisD: Genetic Distance Calculation

In StAMPP: Statistical Analysis of Mixed Ploidy Populations

Description

This function calculates Nei's genetic distance (Nei 1972) between populations or individuals

Usage

stamppNeisD(geno, pop = TRUE)

Arguments

geno	a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels
pop	logical. True if genetic distance should be calculated between populations, false if it should be calculated between individual

Value

A object of class matrix which contains the genetic distance between each population or individual

Author(s)

Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>

References

Nei M (1972) Genetic Distance between Populations. The American Naturalist 106, 283-292.

Examples

# import genotype data and convert to allele frequecies
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")
# Calculate genetic distance between individuals
potato.D.ind <- stamppNeisD(potato.freq, FALSE)
# Calculate genetic distance between populations
potato.D.pop <- stamppNeisD(potato.freq, TRUE)

Example output

Loading required package: pegas
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 

   /// adegenet 2.1.3 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4

Attaching package: ‘pegas’

The following object is masked from ‘package:ade4’:

    amova

The following object is masked from ‘package:ape’:

    mst

StAMPP documentation built on Aug. 8, 2021, 9:07 a.m.