Hi Listers I need to calculate and then plot a frequency histogram of the best tree calculated using the 1-se rule. I have included some code that has worked well for me in the past but it was only for selecting the minimum cross-validation error. I include the code for my model, some relevant output and the code for selecting and plotting the frequency histogram of minimum xerror.
Here is the output that is being referenced in the code below Regression tree: rpart(formula = chbiomsq ~ HC + BC + POC + RUG + Depth + Exp + DFP + FI + LAT, data = ch, method = "anova", control = rpart.control(minsplit = 10, cp = 0.01, xval = 10)) Variables actually used in tree construction: [1] BC Depth DFP Exp Root node error: 47456/99 = 479.35 n= 99 CP nsplit rel error xerror xstd 1 0.344626 0 1.00000 1.02074 0.139585 2 0.179054 1 0.65537 0.76522 0.107470 3 0.072037 2 0.47632 0.68115 0.092627 4 0.063469 3 0.40428 0.67320 0.094830 5 0.036190 4 0.34081 0.58516 0.096726 6 0.034677 5 0.30462 0.56747 0.074953 7 0.018219 6 0.26995 0.52036 0.069447 8 0.017033 7 0.25173 0.54695 0.074249 9 0.010672 8 0.23469 0.55741 0.075119 10 0.010000 9 0.22402 0.55756 0.074017 #Here is the code to run the model 50 times and take the minimum xerror each time, followed by the histogram. However to calculate the appropriate tree size which satisfies the 1-se rule I need to select "minimum xerror" < xerror < "(minimum xerror + xstd error)" and which also has the smallest "nsplit". > cp50 <- replicate(50,{ fit1 <- rpart(chbiomsq~HC+BC+POC+RUG+Depth+Exp+DFP+FI+LAT, data=ch,method="anova", control=rpart.control(minsplit=10,cp=0.01,xval=10));x=printcp(fit1);x[which.min(x[,"xerror"]),"nsplit"]}) > hist(cp50,main="optimal splits for tree",xlab= "no. of optimal tree splits", ylab= "frequency") Any help appreciated. Andy -- Andrew Halford Ph.D Adjunct Research Scientist University of Guam & Curtin University Ph: +61 (0) 468 419 473 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.