All,
I am trying to replicate figure 2 in Glenn De'Ath's 2002 report, Ecology 
83:1105-1117
The figure caption says that data were spes standardized andsite 
standardized to the same mean, and that euclidean distance was usedin 
the analysis.
here is my script, using the "spider" data in the mvpart package:

I tried two different standardizing functions, which do not produce the 
same scaling result:

1. using sweep (which produces a dataset that I was able to duplicate in 
excel)

data(spider)

spider.mean<-sweep(spider[,1:12],2,apply(spider[,1:12],2,mean))

spider.means<-sweep(spider.mean,1,apply(spider.mean,1,mean))

spider.mrt<-mvpart(data.matrix(spider.means[1:12]) 
~herbs+reft+moss+sand+twigs+water,spider, method="mrt", dissim="euc", 
xv="min")

The resulting tree has first split with "herbs" instead of with twigs 
(as in De'Ath).


2.using scaler (which produces a different dataset:

spider.std<- scaler(spider, col="mean1", row="mean1")

spider.std.dat<-as.data.frame(spider.std)

spider.mrt<-mvpart(data.matrix(spider.std.dat[1:12])
~herbs+reft+moss+sand+twigs+water,spider.std.dat,method="mrt",dissim="euc",xv="1se")

  Here, the first split is with "water".

so I have not been able to reproduce De'Ath's result, and
there are at least 3 different configurations of the regression tree for 
spider data, depending on how it is calculated.

So, can I obtain consistent results using mvpart with my own data, in 
order to compare them to the clusters that I obtained with hclust?

with thanks,
Mike Marsh
acting Conservation Chair,
Washington Native Plant Society



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