[R] Problem with rpart

[Prof Brian Ripley]

You only have 43 cases.  After one split, the groups are too small 
to split again with the default settings.  See  ?rpart.control.



On Fri, 25 May 2007, Silvia Lomascolo wrote:

>
> I work on Windows, R version 2.4.1.  I'm very new with R!
>
> I am trying to build a classification tree using rpart but, although the
> matrix has 108 variables, the program builds a tree with only one split
> using one variable!  I know it is probable that only one variable is
> informative, but I think it's unlikely.  I was wondering if someone can help
> me identify if I'm doing something wrong because I can't see it, nor could I
> find it in the help or in this forum.
>
> I want to see whether I can predict disperser type (5 categories) of a
> species given the volatile compounds that the fruits emit (108 volatiles)
> I am writing:
>
>> dispvol.x<- read.table ('C:\\Documents and
> Settings\\silvia\\...\\volatile_disperser_matrix.txt', header=T)
>> dispvol.df<- as.data.frame (dispvol.x)
>> attach (dispvol.df) #I think I need to do this so the variables are
> identified when I write the regression equation
>> dispvol.ctree <- rpart (disperser~	P3.70	+P4.29	+P5.05	+...	+P30.99	+P32.25
> +TotArea, >data= dispvol.df, method='class')
>
> and I get the following output:
>
> n= 28
>
> node), split, n, loss, yval, (yprob)
>      * denotes terminal node
>
> 1) root 28 15 non (0.036 0.32 0.071 0.11 0.46)
>  2) P10.01>=1.185 10  4 bat (0.1 0.6 0.2 0 0.1) *
>  3) P10.01< 1.185 18  6 non (0 0.17 0 0.17 0.67) *
>
> There is nothing special about P10.01 that I can see in my data and I don't
> know why it chooses that variables and stops there!
>
> My matrix looks something like this (except, with a lot more variables)
>
> disperser	P3.70	P4.29	P6.45	P6.55	P10.01	P10.15	P10.18	TotArea
> ban	0.00	0.00	1.34	0.00	1.49	0.00	0.00	2.83
> non	0.00	0.00	0.00	152.80	0.00	14.31	0.00	167.11
> bat	0.00	0.00	0.00	131.56	0.65	0.00	0.00	132.21
> bat	0.00	0.00	5.05	0.00	13.01	6.85	0.00	24.90
> non	0.00	0.00	72.65	103.26	4.10	0.00	0.00	180.02
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> bat	1.23	0.00	0.48	0.89	0.25	0.00	0.00	2.85
> bat	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> non	0.00	0.00	0.00	0.00	1.06	0.00	0.00	1.06
> bat	0.00	0.00	0.00	0.00	28.69	0.00	21.33	50.02
> mix	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> non	0.00	0.00	0.00	0.00	1.15	0.00	0.00	1.15
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> non	0.00	0.82	0.00	1.65	0.00	0.00	0.00	2.47
> bat	0.00	0.00	133.24	0.00	3.13	0.00	0.00	136.37
> bir	0.00	0.00	11.08	3.16	1.79	2.09	0.48	18.61
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> mix	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
> bat	0.00	0.00	0.00	0.00	1.31	0.00	0.00	1.31
> non	0.00	0.00	0.00	0.00	0.00	0.00	1.23	1.23
> bat	0.00	0.00	1.81	0.00	2.84	0.00	0.00	4.65
> non	0.00	0.00	1.18	0.00	0.73	0.00	0.00	1.91
> bir	0.00	0.00	0.00	0.00	1.40	0.00	0.00	1.40
> bat	0.00	0.00	8.16	1.50	1.22	0.00	0.00	10.88
> mix	0.00	0.55	0.00	0.00	0.00	0.00	0.00	0.55
> non	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
>
> Thanks! Silvia.
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595