sim.coaltrees<-function(model,nsim.blocks,use.alpha=F,path=getwd(),append.sims=F,sim.block.size=1000){
setwd(path)
thou<-0
for(j in 1:nsim.blocks){
sims<-list(NULL)
for(i in 1:nrow(model$I)){
sims[[i]]<-vector()
}
if(append.sims==F){
write.table(t(ms.commander2(model,use.alpha = use.alpha)[[nrow(model$loci)+1]][1,]),file="SampPars.txt",quote=F,row.names=F, col.names = F,sep="\t",append=F)
}
pars<-NULL
for(k in 1:sim.block.size){
com<-ms.commander2(model,use.alpha=F)
pars<-rbind(pars,com[[nrow(model$I)+1]][2,])
for(u in 1:nrow(model$I)){
t<-ms(nreps=1,nsam=sum(as.numeric(model$I[u,4:ncol(model$I)])),opts=paste("-T",com[[u]]))
sims[[u]]<-c(sims[[u]],t[3])
}
print(k+thou)
}
if(append.sims==F){
for(u in 1:nrow(model$I)){
write(sims[[u]],file=paste("locus",u,sep=""), append=F)
}
} else {
for(u in 1:nrow(model$I)){
write(sims[[u]],file=paste("locus",u,sep=""), append=T)
}
}
write.table(pars,file="SampPars.txt",quote=F,row.names=F, col.names = F,sep="\t",append=T)
}
thou<-thou+sim.block.size
}
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