Hello Robert, I tried over the week-end and managed, thanks to your help, to get my whole 0/1 matrix into the model. However when I call summary(tree1) I get:
> summary(tree1) Classification tree: tree(formula = factor(dat$loc) ~ sp0.m) Variables actually used in tree construction: [1] "sp0.m.Pni" "sp0.m.Bbe" [3] "sp0.m.Arid" "sp0.m.Pca" Number of terminal nodes: 5 Residual mean deviance: 4.714 = 150.8 / 32 Misclassification error rate: 0.8649 = 32 / 37 The plot() output looks reasonable considering that only 5 locations are plotted. However I have 400 variabels (in the 0/1 matrix sp0.m) and 50 locations (data$loc) and not just 5 terminal nodes. Is there a way to force tree() to plot all locations and their respective variables in the tree construction? regards, Martin On Friday 23 September 2005 19:19, Dave Roberts wrote: > Martin, > > Sorry, I don't think I read your message carefully enough. > > When you say the error message is "+", that woudl seem to indicate > that you still had an unclosed parenthesis and that the function was > looking for more input. > > Using a smaller data set (160 samples, 169 rows, only 5 classes) it > did work fine for me. pa = presence/absence dataframe, opt.5$clustering > = cluster IDs. > > ********************************************************************* > > > test <- tree(factor(opt.5$clustering)~pa) > > test > > node), split, n, deviance, yval, (yprob) > * denotes terminal node > > 1) root 160 371.000 3 ( 0.23750 0.08750 0.57500 0.07500 0.02500 ) > 2) pa.symore < 0.5 79 216.500 1 ( 0.48101 0.17722 0.15190 0.13924 > 0.05063 ) > 4) pa.artarb < 0.5 42 123.600 2 ( 0.07143 0.33333 0.26190 0.23810 > 0.09524 ) > 8) pa.macgri < 0.5 31 75.280 2 ( 0.09677 0.45161 0.00000 > 0.32258 0.12903 ) > . . . > . . . > . . . > 3) pa.symore > 0.5 81 10.780 3 ( 0.00000 0.00000 0.98765 0.01235 > 0.00000 ) > 6) pa.carrss < 0.5 11 6.702 3 ( 0.00000 0.00000 0.90909 0.09091 > 0.00000 ) * > 7) pa.carrss > 0.5 70 0.000 3 ( 0.00000 0.00000 1.00000 0.00000 > 0.00000 ) * > > ************************************************************************ > > I'll try agin with a larger dataset and see if it's a memory limitation. > > Dave Roberts > > Martin Wegmann wrote: > > On Friday 23 September 2005 17:08, Dave Roberts wrote: > >>Martin, > >> > >> If the data are actually coded 0/1, the tree function would > >>probably intepret them as integers and try a regression instead of a > >>classification. If the dependent variable is called "var", try > > > > thanks, but I think I provided too less informations. > > My dependent variable are the locations which are names (I could > > transform them to numbers from 1 - n). The independent variables consist > > of 0/1 data (species). > > If I do > > tree(locations~factor(species1)+factor(species2)+.....+factor(speciesn), > > sp_data) > > I receive the same results as without the factor() part. > > BTW just a subset of the locations are displayed what is pretty weird > > considering that I included all locations in the analysis. > > > > Martin > > > >>x <- tree(factor(var)~species) > >> > >>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >>David W. Roberts office 406-994-4548 > >>Professor and Head FAX 406-994-3190 > >>Department of Ecology email [EMAIL PROTECTED] > >>Montana State University > >>Bozeman, MT 59717-3460 > >> > >>Martin Wegmann wrote: > >>>Dear R-user, > >>> > >>>I tried to generate classification / regression tree with a > >>>absence/presence matrix of species (400) in different locations (50) to > >>>visualise species which are important for splitting up two locations. > >>>Rpart and tree did not work for more than 10 species which is logical > >>> due to the limited amount of locations (n=50). However the error prompt > >>> is a "+" and no specific message, but I am pretty sure that I did not > >>> enter a false sign by mistake. > >>>Is it allowed at all to use 0/1 data for this statistical technique and > >>>if yes is there a way or different method to use all 400 species > >>> entries? Otherwise I would apply a PCA beforehand but I would prefer to > >>> have the raw species informations. > >>> > >>>using R 2.1.1-1 (debian repos.) > >>> > >>>regards, Martin > >> > >>______________________________________________ > >>R-help@stat.math.ethz.ch mailing list > >>https://stat.ethz.ch/mailman/listinfo/r-help > >>PLEASE do read the posting guide! > >>http://www.R-project.org/posting-guide.html > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html -- Martin Wegmann DLR - German Aerospace Center German Remote Sensing Data Center @ Dept.of Geography Remote Sensing and Biodiversity Unit && Dept. of Animal Ecology and Tropical Biology University of Wuerzburg Am Hubland 97074 Würzburg phone: +49-(0)931 - 888 4797 mobile: +49-(0)175 2091725 fax: +49-(0)931 - 888 4961 http://www.biota-africa.org http://www.biogis.de ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html