/working/checkVMAT.R

http://github.com/eastman/auteur · R · 27 lines · 25 code · 2 blank · 0 comment · 2 complexity · 6c334580d83df61569a5ab62d451c6c8 MD5 · raw file 

    

  1. require(auteur)
    2. 

  2. bytens=function(x, num) sapply(0:num, function(y)x*(10^y))
    3. 

  3. vcv2 <- function(tree){
    4. 

  4.     res = cophenetic(tree) / 2
    5. 

  5.     max(res) - res
    6. 

  6. }
    7. 

  7. 

  8. n=bytens(20,2)
    9. 

  9. reps=5
    10. 

  10. out=array(dim=c(length(n)*reps,5))
    11. 

  11. for(i in n){
    12. 

  12. 	for(j in 1:reps){
    13. 

  13. 		cat(paste("working on rep", j, "of size", i, "\n",sep=" "))
    14. 

  14. 		phy=rcoal(i)
    15. 

  15. 		ii=which(n==i)
    16. 

  16. 		sA=system.time(vcv(phy)->vA)[3] 
    17. 

  17. 		sR=system.time(vmat(phy)->vR)[3] 
    18. 

  18. 		s2=system.time(vcv2(phy)->v2)[3]
    19. 

  19. 		match=all(vA==vR&vA==v2) 
    20. 

  20. 		out[(ii-1)*reps+j,]=c(match, sA,sR,s2,Ntip(phy))
    21. 

  21. 		}
    22. 

  22. 		
    23. 

  23. 		}
    24. 

  24. out=data.frame(out)
    25. 

  25. out=cbind(out, out[,2]/out[,3],out[,2]/out[,4])
    26. 

  26. names(out)=c("match","ape","rjmcmc","klaus","treesize","speedupRJMCMC","speedupKLAUS")
    27. 

  27. save(out,file="checkVMAT.rda")
    28.