ezPerm within vs. between and repeated measures

[ljk...@hotmail.com]

Hello,

This is my first time writing in Google groups so apologies if I'm somehow not following the rules of posting.

I have a dataset (called jun) with repeated measures within a group not between groups - the data looks something like this:

TrapID lat.group log.pul
1              A      0.1 
1              A      0.2 
2              A      0.3 
3              B      0.5 
3              B      0.6 
3              B      0.7 

4              B      0.1 
4              B      0.2 
5              C      0.3 
5              C      0.5 
6              C      0.6 
7              C      0.7 

So I have repeated measures within each group (so the same TrapID (subject) will only appear in 1 group), but it is unbalanced as not all subjects have the same amount of repeats. I know for sure that the data isn't normal, so I have been trying to run ezPerm to test for differences between groups. I found the below R-script in the package documentation, and since this is my first time using permuation tests, I'm afraid that I may not understand it correctly or if I am running the right test. The below script is testing differences between groups and not within (which is exactly what I want) - but I am unsure as to whether it takes the repeated observations into account. Can someone help me out here or point me in the right direction?

Thanks,

Lene

#Compute some useful statistics per cell.

cell_stats = ddply(

  .data = jun

  , .variables = .( TrapID , lat.group  )

  , .fun = function(x){

    #Compute mean RT (only accurate trials).

    mean_rt = mean(x$log.pul)

    #Compute SD RT (only accurate trials).

    sd_rt = sd(x$log.pul)

    to_return = data.frame(

      mean_rt = mean_rt

      , sd_rt = sd_rt

    )

    return(to_return)

  }

)

#Compute the grand mean RT per Ss.

gmrt = ddply(

  .data = cell_stats

  , .variables = .(TrapID ,lat.group )

  , .fun = function(x){

    to_return = data.frame(

      mrt = mean(x$mean_rt)

    )

    return(to_return)

  }

)

#Run a purely between-Ss permutation test on the mean_rt data.

mean_rt_perm = ezPerm(

  data = gmrt

  , dv = mrt

  , wid =TrapID

  , between =lat.group

  , perms = 1e3 #1e3 or higher is best for publication

)

#Show the Permutation test.

print(mean_rt_perm)