[R] Help with permutation function from Turner et al. 2010 (Ecology)

[Ashley Stasko]

Hello,


I'm using R code that includes a residual permutation that was written as a supplement to the paper:


Turner et al. 2010. A general hypothesis-testing framework for stable isotopes ratios in ecological studies. Ecology 91:2227-2233.
The supplemental code is available at: http://www.esapubs.org/archive/ecol/E091/157/suppl-1.htm


When I execute the function, no warnings are given (seems fine). But the resulting output matrix is simply a matrix of repeating rows (i.e., it appears as if the function is selecting the same "random" sample every time). The function is as follows (please keep in mind that many of the internal functions were written by Turner et al. as well and may not be familiar):


line.1<-c(0,traj.result(traj.size,traj.dir,traj.shape))


permute<-function(y,x2,g,o,p) { 
  p.table<-line.1
  yhat<-predict(x2)
  res<-resid(x2)
  line<-nrow(y)
  
  for(i in 1:p){
    line.rand<-sample(line,replace=FALSE)
    res.temp<-cbind(line.rand,res)
    z<-(order(line.rand))
    res.temp2<-as.matrix(res.temp[z,])
    res.p<-res.temp2[,-1]  # Rows of residuals are now randomized
    y.rand<-yhat+res.p
    
    lm.new<-lm(y.rand~o*g,x=T,model=T) 
    ls<-data.frame(expand.grid(o=levels(o),g=levels(g))) 
    ls[]<-lapply(ls, factor)
    means.r<-predict(lm.new,ls)
    
    traj.r<-arrayspecs(means.r,g,o)
    traj.size.r<-trajsize(traj.r)
    traj.dir.r<-trajorient(traj.r,ang.cor=T)
    traj.shape.r<-trajshape(traj.r)
    result<-traj.result(traj.size.r,traj.dir.r,traj.shape.r)
    p.table<-rbind(p.table,c(i,result))
  }
  p.table
}



But when I try to execute the function the rows in the output matrix repeat the same numbers:


> test3<-permute(Y,lm.2f.red,group,obs,99)
> test3
        [,1]     [,2]      [,3]      [,4]
p.table    0 3.612322 0.9910104 0.3998703
             1 3.612322 0.9910104 0.3998703
             2 3.612322 0.9910104 0.3998703
             3 3.612322 0.9910104 0.3998703
             4 3.612322 0.9910104 0.3998703
             5 3.612322 0.9910104 0.3998703 
     ......


Can anyone see where there may be a problem with the permutation code? I'm relatively new to functions, and especially to writing permutation functions, so I'm having difficulty finding the problem.


Thanks,


Ashley





************************************************
Ashley Stasko
M.Sc. Candidate
Cooperative Freshwater Ecology Unit
Living With Lakes Centre
Laurentian University
Sudbury, ON
Tel: 705-675-1151 ext. 2209
Email: ax_stasko at laurentian.ca