aniso: A simulated haploid genotypic data set exhibiting zonal...

In ggene: Semivariogram and Exploratory Spatial Analysis of Genetic Data

Description

aniso provides a simulated dataset illustrating how variogram can be used to explore spatial anisotropies in genetic data. Functions svariog and svarmap can be used to compute the variogram in different directions and determine if it behaves differently in some of them. If the variogram changes according to directions, it is said to be anisotropic. If not, the variogram is said to be isotropic. The dataset aniso is an object of class ggene with 400 individuals described by means of 3 locus for a total of 13 alleles.

Usage

data(aniso)

Format

An object of class ggene.

Examples

data(aniso)

# checking anisotropy using a variogram map
map <- svarmap(X=aniso,cutoff=20, width=1) ; plot(map)

# compute omnidirectional and directional variograms
va <- svariog(X=aniso, plot=TRUE)

d0_225 <- svariog(X=aniso,direction=0, tolerance=22.5, unit.angle="degrees")
d45_225 <- svariog(X=aniso,direction=45, tolerance=22.5, unit.angle="degrees")
d90_225 <- svariog(X=aniso,direction=90, tolerance=22.5, unit.angle="degrees")
d135_225 <- svariog(X=aniso,direction=135, tolerance=22.5, unit.angle="degrees")
                    
plot(va$svario$u, va$svario$v, type="b", ylim=range(c(va$svario$v, d0_225$svario$v,
  d45_225$svario$v, d90_225$svario$v, d135_225$svario$v)) ,xlab="distance", 
  ylab="semi-variance")

points(d0_225$svario$u, d0_225$svario$v, type="b", lty=2)
points(d45_225$svario$u, d45_225$svario$v, type="b", col="red", lty=2)
points(d90_225$svario$u, d90_225$svario$v, type="b", col="blue", lty=2)
points(d135_225$svario$u, d135_225$svario$v, type="b", col="green", lty=2)

legend("topleft", legend=c("omnidirectional", expression(0 * degree), 
    expression(45 * degree), expression(90 * degree), 
    expression(135 * degree)), lty=c(1,2,2,2,2,2), 
    col=c("black","black","red","blue","green"), bty="n")
 

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