iterating ready to go!

vignettes/Iterating_Over_Loci.Rmd

@@ -20,30 +20,29 @@ Here show how to use \pkg{kalis} to efficiently iterate over loci sequentially.
 
 ```{r, results='hide'}
 require(kalis)
-# 
-# total.nthreads <- 4
-# n.checkpoints <- 7
-# 
-# nthreads <- as.integer(0:(total.nthreads-1))
-# CacheHaplotypes(SmallHaps)
-# 
-# m <- rbeta(L()-1,1,10)*1e-6
-# pars <- Parameters(CalcRho(cM = m, s = 1, gamma = 1), mu = 1e-8, use.speidel = TRUE)
-# 
-# fwd <- MakeForwardTable(pars)
-# bck <- MakeBackwardTable(pars)
-# M <- matrix(0,N(),N())
-# 
-# Iter <- ForwardIterator(pars,n.checkpoints)
-# 
-# start.time <- proc.time()
-# 
-# for(t in L():1){
-#   Iter(fwd,pars,t,nthreads = nthreads)
-#   Backward(bck,pars,t, nthreads = nthreads)
-#   # Optional: DistMat(fwd,bck,M,type="minus.min", nthreads = total.nthreads)
-#   print(paste("At locus",t))
-# }
-# 
-# print(proc.time() - start.time)
+
+n.checkpoints <- 7
+
+nthreads <- 4
+CacheHaplotypes(SmallHaps)
+
+m <- rbeta(L()-1,1,10)*1e-6
+pars <- Parameters(CalcRho(cM = m, s = 1, gamma = 1), mu = 1e-8, use.speidel = TRUE)
+
+fwd <- MakeForwardTable(pars)
+bck <- MakeBackwardTable(pars)
+M <- matrix(0,N(),N())
+
+Iter <- ForwardIterator(pars,n.checkpoints)
+
+start.time <- proc.time()
+
+for(t in L():1){
+  Iter(fwd,pars,t,nthreads = nthreads)
+  Backward(bck,pars,t, nthreads = nthreads)
+  if(t==200){plot(DistMat(fwd,bck,M,type="minus.min", nthreads = nthreads))}
+  print(paste("At locus",t))
+}
+
+print(proc.time() - start.time)
 ```