simpottsidr {Geneclust} | R Documentation |
Simulates some spatially organised populations according to the Potts-Dirichlet model. Plots a map giving each individual population membership.
simpottsdir(path, coordinates, matngh=NULL, npop, psi, nchain = 50000, burnin=40000, stepw = 10, plot=TRUE, ploth=FALSE, print=FALSE, file=path)
path |
path to output files directory |
coordinates |
Spatial coordinates of individuals. A matrix with 2 columns and one line per individual |
matngh |
A neighbourhood matrix with nindiv lines and nindiv columns. If matngh=NULL, neighbourhood relationships are defined by a graph of Delaunay. |
npop |
Number of populations |
psi |
The real value of the hidden markov random field spatial interaction parameter. If psi=0, populations aren't spatially structured |
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 writing steps (if stepw =1, all
states are saved whereas if e.g. stepw =10 only each 10 iterations is saved) |
plot |
if plot=TRUE, the map giving the population membership of each individual is plotted |
ploth |
if ploth=TRUE, other charts concerning the MCMC simulation are plotted |
print |
Logical: if print=TRUE the map is also printed. |
file |
Character: Path to file where the map should be printed |
A list of variables involved in the simulation. The elements of this list are: matngh,popmbrship.
All parameters processed by function simpottsdir
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-Dirichlet system energy for each MCMC update of the population memberships.
Sophie Ancelet
#library(Geneclust) ## Not run: # Below is a sequence of R commands using geneclust functions # Simulation of a dataset according to Potts-Dirichlet model # The dataset is made of 2 populations # on a spatial domain enclosed in a rectangle # (x.coord. in [0,1], y.coord. in [0,1]) # Spatial interaction parameter is 0.4 #To define a place for simulation outputs system("mkdir ./tmpData/") path <- "./tmpData/" #To generate the coordinates of 100 individuals which are supposed # uniformly distributed in a rectangle coordinates<- matrix(runif(200,0,1),nrow=100,ncol=2) data<- simpottsdir(path=path, coordinates=coordinates, matngh=NULL, npop=2, psi=0.4, nchain=50000, burnin=40000, stepw=100, plot=TRUE, ploth=FALSE, print=FALSE, file=path) ## go to file path to see simulation outputs ## End(Not run)