1 data(sleep)
   2 
   3 ## use of tapply
   4 tapply(sleep$extra,sleep$group,FUN = mean)
   5 
   6 ## use of replicate
   7 ## roll 6 dice
   8 sample(1:6,size = 1)
   9 ## roll 6 dice 10000 times 
  10 dice <- replicate(10000,sum(sample(1:6,size = 6,replace = T)))
  11 table(dice)
  12 
  13 ### Permutation tests
  14 ## calculate the difference between the group means
  15 diff(tapply(sleep$extra,sleep$group,FUN = mean))
  16 
  17 ## calculate the absolute difference (two-sided test)
  18 orig.diff <- abs(diff(tapply(sleep$extra,sleep$group,FUN = mean)))
  19 
  20 ## do it a 10000 times
  21 res <- replicate(10000, abs(diff(tapply(sleep$extra,sample(sleep$group),mean))))
  22 sum(orig.diff <= res)/10000 ## p-value
  23 
  24 ## compare with t-test
  25 t.test(sleep$extra ~ sleep$group)
  26 
  27 ## wilcox signed rank
  28 pre.test <- c(17,12,20,12,20,21,23,10,15,17,18,18)
  29 post.test <- c(19,25,18,18,26,19,27,14,20,22,16,18)
  30 
  31 wilcox.test(pre.test,post.test,paired = T)
  32 
  33 require(coin)
  34 wilcoxsign_test(pre.test ~ post.test)
  35