On 09.06.2012 03:57, Ashley Stasko wrote:
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.table0 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.
If the results are suspicious (we cannot reproduce easily since you have
not provided reproducible code as the posting guide asks you), why not
ask the authors of the code? They hopefully know better what they aimed
to get than readers of this list.
Best,
Uwe Ligges
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_sta...@laurentian.ca
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
