Classification problem - rpart
You have slope and tci10 (at least) coded as factors. Run summary() on your data frame. My bet is that you have MISSING in there, and did not declare that when using read.table (or whatever) Do *look* at your data at least cursorily.
On Thu, 10 Apr 2003, Andy Bunn wrote:
I am performing a binary classification using a classification tree. Ironically, the data themselves are 2483 tree (real biological ones) locations as described by a suite of environmental variables (slope, soil moisture, radiation load, etc). I want to separate them from an equal number of random points. Doing eda on the data shows that there is substantial difference between the tree and random classes, e.g., box and whisker plots for slope show separation. The data frame is thus: curvegrid,dir2tl,dist2tl,slope,tasp,tci10,class -0.000244141,266,1852.701,2.382412,0.2124468,131,random 0.3005371,246,1146.342,10.45694,0.8045813,63,random . . . . -0.3000488,90,10,20.25561,-0.1293357,62,tree -0.5,90,10,18.68057,-0.05228489,61,tree -0.6994629,0,0,18.30121,0.0320744,66,tree I've run rpart on similar data without an issue but when I try it on this data as follows: tree <- rpart(class ~ curvegrid + slope + tci10, method="class") I get the following output:
tree
n= 4966
node), split, n, loss, yval, (yprob)
* denotes terminal node
1) root 4966 2483 dw (0.500000000 0.500000000)
2) slope=0.3206026,0.5159777,0.679302,0.7163697,1.1324.......... 2574 94
dw (0.963480963 0.036519037) *
3) slope=0,0.1011371,0.1013844,0.2027681,0.2267014,0.32......... MISSING
2392 3 random (0.001254181 0.998745819) *
This is not like other trees I have run!
And:
summary(tree)
summary(tree)
Call:
rpart(formula = class ~ curvegrid + slope + tci10)
n= 4966
CP nsplit rel error xerror xstd
1 0.9609344 0 1.00000000 1.0322191 0.01418310
2 0.0100000 1 0.03906565 0.7635924 0.01378822
Node number 1: 4966 observations, complexity param=0.9609344
predicted class=dw expected loss=0.5
class counts: 2483 2483
probabilities: 0.500 0.500
left son=2 (2574 obs) right son=3 (2392 obs)
Primary splits:
slope splits as RRRRRRLRRRLRRRRLLRRRRRRR.......
tci10 splits as RRRRRRRRRRLLRLLRLLRLLRLL.......
etc.
Node number 2: 2574 observations
predicted class=dw expected loss=0.03651904
class counts: 2480 94
probabilities: 0.963 0.037
Node number 3: 2392 observations
predicted class=random expected loss=0.001254181
class counts: 3 2389
probabilities: 0.001 0.999
I'm assuming that I have to adjust something in rpart.control. I am also
hesitant at posting prematurely but am in fetters.
It's not rpart, it is your data manipulation: `pilot error'.
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