sim03: A haploid genotypic data set simulated with the software...

In ggene: Semivariogram and Exploratory Spatial Analysis of Genetic Data

Description

The genetic data of sim03 correspond to the first 100 individuals of the data contained in sim01 (See sim01 for details).

Usage

data(sim03)

Format

An object of class ggene.

Source

Leblois, R., A. Estoup and F. Rousset 2009. IBDSim: a computer program to simulate genotypic data under isolation by distance. Molecular Ecology Resources 9: 107-109.

Examples

data(sim03)

# plot the spatial distribution of individuals
plot(sim03$coord[,1], sim03$coord[,2], asp=1)

# compute variogram
va <- svariog(X=sim03, uvec=distlag(dist=sim03$coord, dmin=1, distance.lag=1), plot=FALSE)
plot(va$svario$u, va$svario$v, xlab="distance", ylab="semivariance")
abline(h=va$Hhat, col="red", lty="dashed")

## Not run: 
  # compute statistical envelope
  env <- randsvariog(var=va, X=sim03, nsim=30, bounds=c(0.025, 0.975), save.sim=FALSE)
  # plot results
  plot(env$svario$u, env$svario$v, ylim=range(env$env), xlab="distance", ylab="semi-variance")
  abline(h=va$Hhat, col="red", lty="dashed")
  points(env$svario$u, env$env[,1], type="l")
  points(env$svario$u, env$env[,2], type="l")

## End(Not run)

# fit exponential model to the empirical variogram
fit <- fitsvariog(vario=va, ini.cov.pars=c(0.5,20), nugget=0.8, max.dist=30, plot = FALSE)
fit$param

# plot results
plot(va$svario$u, va$svario$v)
lines(fit$fit)

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