On Fri, 20 Aug 2010, Kay Cichini wrote:
hello,
my data-collection is not yet finished, but i though have started
investigating possible analysis methods.
below i give a very close simulation of my future data-set, however there
might be more nominal explanatory variables - there will be no continous at
all (maybe some ordered nominal..).
i tried several packages today, but the one i fancied most was ctree of the
party package.
i can't see why the given no. of datapoints (n=100) might pose a problem
here - but please teach me better, as i might be naive..
See
http://biostat.mc.vanderbilt.edu/wiki/Main/ComplexDataJournalClub#Sebastiani_et_al_Nature_Genetics
The recursive partitioning simulation there will give you an idea -
you can modify the R code to simulate a situation more like yours.
When you simulate the true patterns and see how far the tree is from
discovering the true patterns, you'll be surprised.
Frank
>
i'd be very glad about comments on the use of ctree on suchalike dataset and
if i oversee possible pitfalls....
thank you all,
kay
######################################################################################
# an example with 3 nominal explanatory variables:
# Y is presence of a certain invasive plant species
# introduced effect for fac1 and fac3, fac2 without effect.
# presence with prob. 0.75 in factor combination fac1=I (say fac1 is geogr.
region) and
# fac3 = a|b|c (say all richer substrates).
# presence is not influenced by fac2, which might be vegetation type, i.e.
######################################################################################
library(party)
dat<-cbind(
expand.grid(fac1=c("I","II"),
fac2=LETTERS[1:5],
fac3=letters[1:10]))
print(dat<-dat[order(dat$fac1,dat$fac2,dat$fac3),])
dat$fac13<-paste(dat$fac1,dat$fac3,sep="")
for(i in 1:nrow(dat)){
ifelse(dat$fac13[i]=="Ia"|dat$fac13[i]=="Ib"|dat$fac13[i]=="Ic",
dat$Y[i]<-rbinom(1,1,0.75),
dat$Y[i]<-rbinom(1,1,0))
}
dat$Y<-as.factor(dat$Y)
tr<-ctree(Y~fac1+fac2+fac3,data=dat)
plot(tr)
######################################################################################
-----
------------------------
Kay Cichini
Postgraduate student
Institute of Botany
Univ. of Innsbruck
------------------------
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