Wagner: The example data set used in Wagner et al (2005)

In ggene: Semivariogram and Exploratory Spatial Analysis of Genetic Data

Description

A toy data set used in Wagner al at (2005) p. 1750

Usage

data(Wagner)

Format

An object of class ggene.

Note

Using this dataset with varioWeight and svariog leads to various warning messages because there are some co-locatted individuals. This has no effect upon results.

Source

Wagner, H. H., R. Holderegger, S. Werth, F. Gugerli, S. E. Hoebee and C. Scheidegger. 2005. Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data. Genetics 169, 1739-1752.

Examples

data(Wagner)

count <- genocount(X=Wagner)
count
mat <- genoweight(X=Wagner,genotypes=count$vec)
mat
# NB: individuals 1 and 2 are similar, the weight of this couple is 0

# compute variogram for genetic diversity
wa <- varioWeight(X=Wagner, weights=mat, uvec=c(1,2,3))
# NB: the third distance class corresponding to a lag of 3 distance units is 
#	omitted here because it involves only one data pair
wa$svario$u # corresponds distance r in Wagner et al 2005 p 1751
wa$svario$gamma # raw semivariances corrsponding to Hhat(r) in Wagner et al 2005 p 1751
wa$svario$n # corresponds distance nr in Wagner et al 2005 p 1751
wa$svario$v # is the weighted semivariance for geneotypic diversity not to be mistaken 
#	for the values reported for the molecular variance in Wagner et al 2005 p 1752
 

ggene documentation built on May 2, 2019, 5:54 p.m.