simpatch {Geneclust} | R Documentation |
Simulates multilocus genotypes and group memberships according to the prior distributions used in the Bayesian algorithm.
simpatch(path, nindiv, coordinates = NULL, coord.lim = c(0,1,0,1), npop, nall, psi, fis, nchain = 50000, burnin=40000, stepw = 100, seed = NULL, plot = TRUE, write=FALSE, print=FALSE, file=path)
path |
path to the MCMC program output files |
nindiv |
Number of individuals |
coordinates |
Spatial coordinates of individuals. A matrix with 2 columns and one line per individual |
coord.lim |
Vector: Ranges of the spatial domain to be considered (xmin,xmax,ymin,ymax) |
npop |
Number of populations |
nall |
Vector of integers giving the number of alleles at each locus |
psi |
A nonnegative spatial interaction parameter. If psi=0, populations are not spatially structured. Typical values are between 0 and 1. |
fis |
Vector of population inbreeding coefficients. If fis[i]=0, there is no inbreeding in population i |
nchain |
Number of MCMC iterations (Gibbs steps) to generate a Potts-Dirichlet configuration |
burnin |
Number of Gibbs steps to throw away. Results are stored in ascii files from burnin and only each thinning cycles. |
stepw |
Number of MCMC iterations between two writting steps (if stepw =1, all
states are saved whereas if e.g. stepw =10 only each 10 iterations is saved) |
seed |
Logical: Seed to initialize the random number generator |
plot |
Logical: if TRUE, the map giving the population membership of each individual and the barplots for allele frequencies are plotted |
write |
Logical: if TRUE, coordinates, allele frequencies, genotypes, population memberships, matngh, number of alleles and other variables involved in the simulation are also written in plain ascci files |
print |
Logical: if TRUE the map and the barplots for allele frequencies are also printed |
file |
Character: Path to file where figures should be printed and/or variables involved in the simulation should be written |
A list of variables involved in the simulation. The elements of this list are: coordinates,matngh,popmbrship,genotypes,frequencies.
All parameters processed by function simpatch
are
written in the directory specified by ‘path’ as follows:
File ‘simpotts.txt’ contains MCMC updates of each individual population membership
File ‘energy.txt’ contains the Potts system energy for each MCMC update of the population memberships
Sophie Ancelet
# library(Geneclust) ## Not run: # Simulation of a dataset 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 # that is to say 0.1 # define a place for simulation outputs system("mkdir ./tmpData/") path <- "./tmpData/" data<- simpatch(path=path, nindiv=100, coordinates=NULL, coord.lim=c(0,1,0,1), npop=2, nall=rep(10,10), psi=0.5, fis=c(0.1,0.1), nchain=50000, burnin=40000, stepw=100, seed=123, plot=TRUE, write=FALSE, print=FALSE, file=path) ## go to file path to read simulation outputs ## End(Not run)