subsample {Geneclust} | R Documentation |
Make a subsample from an initial dataset
Description
This function enables to make a subsample from an initial dataset by
reducing the number of loci to consider.
Usage
subsample(data, nloci, lst = NULL)
Arguments
data |
An object of class geneclustdata |
nloci |
Number of loci to consider to make the new dataset |
lst |
The indices of loci chosen to make the new dataset. If
lst=NULL, these indices are chosen randomly |
Value
new.dat |
The new dataset which is again an object of class
geneclustdata . Genetics information are reduced to "nloci"
number of loci. |
Author(s)
Olivier Francois
Examples
#library(Geneclust)
## Not run:
# Simulation of a dataset according to the prior distributions. This one
# is made of 2 populations
# 10 loci and 10 alleles per loci
# on a spatial domain enclosed in a rectangle
# (x.coord. in [0,1], y.coord. in [0,1])
# Spatial interaction parameter is 0.5
# We suppose the inbreeding coefficients are the same in each population
# and equal to 0.1
#define a place for simulation outputs
system("mkdir ./tmpData/")
path <- "./tmpData/"
data<-simpatch(path=path,nindiv=100,npop=2,nall=rep(10,10),psi=0.5,fis=c(0.1,0.1),nchain=20000,burnin=10000,stepw=10,plot=FALSE)
datagc<- as.geneclustdata(data$coordinates[,1],data$coordinates[,2],data$genotypes)
#Subsample with 5 randomly chosen loci
geneclustobjsub<- subsample(data=datagc,nloci=5,lst=NULL)
## End(Not run)
[Package
Geneclust version 1.0.0
Index]