larix1350: A dataset corresponding to the microsatellite data for a set...

In ggene: Semivariogram and Exploratory Spatial Analysis of Genetic Data

Description

A set of 13 locus for 189 individuals of European larch (Larix decidua) sampled in an experimental plot at the altitude of 1350 m asl near the village of Villar-Saint-Pancrace (Hautes-Alpes, France). 10 individuals were removed from the published dataset because they showed some null alleles.

Usage

data(larix1350)

Format

An object of class ggene.

Source

Nardin, M., Guerin, V., Musch, B., Rousselle, Y., Sanchez, L., Rossi, J.-P., Gerber, S., Paques, L., Rozenberg, P. 2015. Genetic differentiation of European larch along an altitudinal gradient in the French Alps. Annals of Forest Science 72, 517-527.

Examples

data(larix1350)

# check sampling scheme
plot(larix1350$coord[,1],larix1350$coord[,2], asp=1)

# compute variogram
va <- svariog(X=larix1350, uvec=distlag(dist=larix1350$coord, dmin=0, distance.lag=3),
 plot=FALSE)
plot(va$svario$u, va$svario$v)

## Not run: 
# compute statistical envelope
env <- randsvariog(var=va, X=larix1350, nsim=30, bounds=c(0.025, 0.975), save.sim=FALSE)

# plot results
plot(env$svario$u, env$svario$v, ylim=range(env$env), xlab="distance", ylab="semi-variance")
points(env$svario$u, env$env[,1], type="l")
points(env$svario$u, env$env[,2], type="l")
## End(Not run)

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