sim.coexp2<-function(nsims,
var.zeta,
coexp.prior,
buffer,
Ne.prior,
NeA.prior,
time.prior,
gene.prior,
alpha=F,
append.sims=F,
path=getwd())
{
setwd(path)
if(append.sims==F){
simulations<-matrix(nrow=1,ncol=32)
simulations[1,]<-c("zeta","ts","E(t)","DI",
"var.pi","mean.pi","skew.pi","kur.pi",
"var.ss","mean.ss","skew.ss","kur.ss",
"var.H","mean.H","skew.H","kur.H",
"var.TD","mean.TD","skew.TD","kur.TD")
write.table(simulations,file="simulations.txt", quote=F,row.names=F, col.names=F, sep="\t")
populations.par<-matrix(nrow=1,ncol=nrow(NeA.prior)*4)
pop.names<-NULL
for(i in 1:nrow(NeA.prior)){
pop.names<-cbind(pop.names,t(c(paste("Ne",i,sep=""),paste("Exp.time",i,sep=""),paste("NeA",i,sep=""),paste("mi",i,sep=""))))
}
populations.par[1,]<-pop.names
write.table(populations.par,file="pop_parameters.txt", quote=F,row.names=F, col.names=F, sep="\t")
}
TIME<-system.time(for (i in 1:nsims){
x<-coexp.sample.pars2(nruns=1,var.zeta=var.zeta,coexp.prior=coexp.prior,Ne.prior=Ne.prior,
NeA.prior=NeA.prior,time.prior=time.prior,gene.prior=gene.prior)
y<-coexp.MS(MS.par=x$MS.par, gene.prior = gene.prior,alpha=alpha)
z<-coexp.sumstat(ms.output=y,gene.prior=gene.prior)
simulations<-c(x$coexp.par,z)
populations.par<-unlist(x$pop.par)
write.table(t(simulations),file="simulations.txt", quote=F,row.names=F, col.names=F, append=T, sep="\t")
write.table(t(populations.par),file="pop_parameters.txt", quote=F,row.names=F, col.names=F, append=T,sep="\t")
print(paste(i,"sims of",nsims,"| zeta = ",x$coexp.par[,1]))
})
print(TIME)
}
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