You can tune trees by setting namevalue pairs in fitctree
and fitrtree
. The remainder of this section
describes how to determine the quality of a tree, how to decide which namevalue pairs
to set, and how to control the size of a tree.
Resubstitution error is the difference between the response training data and the predictions the tree makes of the response based on the input training data. If the resubstitution error is high, you cannot expect the predictions of the tree to be good. However, having low resubstitution error does not guarantee good predictions for new data. Resubstitution error is often an overly optimistic estimate of the predictive error on new data.
This example shows how to examine the resubstitution error of a classification tree.
Load Fisher's iris data.
load fisheriris
Train a default classification tree using the entire data set.
Mdl = fitctree(meas,species);
Examine the resubstitution error.
resuberror = resubLoss(Mdl)
resuberror = 0.0200
The tree classifies nearly all the Fisher iris data correctly.
To get a better sense of the predictive accuracy of your tree for new data, cross validate the tree. By default, cross validation splits the training data into 10 parts at random. It trains 10 new trees, each one on nine parts of the data. It then examines the predictive accuracy of each new tree on the data not included in training that tree. This method gives a good estimate of the predictive accuracy of the resulting tree, since it tests the new trees on new data.
This example shows how to examine the resubstitution and crossvalidation accuracy of a regression tree for predicting mileage based on the carsmall
data.
Load the carsmall
data set. Consider acceleration, displacement, horsepower, and weight as predictors of MPG.
load carsmall
X = [Acceleration Displacement Horsepower Weight];
Grow a regression tree using all of the observations.
rtree = fitrtree(X,MPG);
Compute the insample error.
resuberror = resubLoss(rtree)
resuberror = 4.7188
The resubstitution loss for a regression tree is the meansquared error. The resulting value indicates that a typical predictive error for the tree is about the square root of 4.7, or a bit over 2.
Estimate the crossvalidation MSE.
rng 'default';
cvrtree = crossval(rtree);
cvloss = kfoldLoss(cvrtree)
cvloss = 25.6450
The crossvalidated loss is almost 25, meaning a typical predictive error for the tree on new data is about 5. This demonstrates that crossvalidated loss is usually higher than simple resubstitution loss.
The standard CART algorithm tends to select continuous predictors that have many levels. Sometimes, such a selection can be spurious and can also mask more important predictors that have fewer levels, such as categorical predictors. That is, the predictorselection process at each node is biased. Also, standard CART tends to miss the important interactions between pairs of predictors and the response.
To mitigate selection bias and increase detection of important interactions, you
can specify usage of the curvature or interaction tests using the
'PredictorSelection'
namevalue pair argument. Using the
curvature or interaction test has the added advantage of producing better predictor
importance estimates than standard CART.
This table summarizes the supported predictorselection techniques.
Technique  'PredictorSelection'
Value  Description  Training speed  When to specify 

Standard CART [1]  Default 
Selects the split predictor that maximizes the splitcriterion gain over all possible splits of all predictors.  Baseline for comparison 
Specify if any of these conditions are true:

Curvature test [2][3]  'curvature'  Selects the split predictor that minimizes the pvalue of chisquare tests of independence between each predictor and the response.  Comparable to standard CART 
Specify if any of these conditions are true:

Interaction test [3]  'interactioncurvature'  Chooses the split predictor that minimizes the pvalue of chisquare tests of independence between each predictor and the response (that is, conducts curvature tests), and that minimizes the pvalue of a chisquare test of independence between each pair of predictors and response.  Slower than standard CART, particularly when data set contains many predictor variables. 
Specify if any of these conditions are true:

For more details on predictor selection techniques:
For classification trees, see PredictorSelection
and Node Splitting Rules.
For regression trees, see PredictorSelection
and Node Splitting Rules.
When you grow a decision tree, consider its simplicity and predictive power. A deep tree with many leaves is usually highly accurate on the training data. However, the tree is not guaranteed to show a comparable accuracy on an independent test set. A leafy tree tends to overtrain (or overfit), and its test accuracy is often far less than its training (resubstitution) accuracy. In contrast, a shallow tree does not attain high training accuracy. But a shallow tree can be more robust — its training accuracy could be close to that of a representative test set. Also, a shallow tree is easy to interpret. If you do not have enough data for training and test, estimate tree accuracy by cross validation.
fitctree
and fitrtree
have three namevalue pair arguments that control the depth
of resulting decision trees:
MaxNumSplits
— The maximal number of branch
node splits is MaxNumSplits
per tree. Set a large
value for MaxNumSplits
to get a deep tree. The
default is size(X,1) – 1
.
MinLeafSize
— Each leaf has at least
MinLeafSize
observations. Set small values of
MinLeafSize
to get deep trees. The default is
1
.
MinParentSize
— Each branch node in the tree
has at least MinParentSize
observations. Set small
values of MinParentSize
to get deep trees. The
default is 10
.
If you specify MinParentSize
and
MinLeafSize
, the learner uses the setting that yields trees with
larger leaves (i.e., shallower trees):
MinParent =
max(MinParentSize,2*MinLeafSize)
If you supply MaxNumSplits
, the software splits a tree until
one of the three splitting criteria is satisfied.
For an alternative method of controlling the tree depth, see Pruning.
This example shows how to control the depth of a decision tree, and how to choose an appropriate depth.
Load the ionosphere
data.
load ionosphere
Generate an exponentially spaced set of values from 10
through 100
that represent the minimum number of observations per leaf node.
leafs = logspace(1,2,10);
Create crossvalidated classification trees for the ionosphere
data. Specify to grow each tree using a minimum leaf size in leafs
.
rng('default') N = numel(leafs); err = zeros(N,1); for n=1:N t = fitctree(X,Y,'CrossVal','On',... 'MinLeafSize',leafs(n)); err(n) = kfoldLoss(t); end plot(leafs,err); xlabel('Min Leaf Size'); ylabel('crossvalidated error');
The best leaf size is between about 20
and 50
observations per leaf.
Compare the nearoptimal tree with at least 40
observations per leaf with the default tree, which uses 10
observations per parent node and 1
observation per leaf.
DefaultTree = fitctree(X,Y); view(DefaultTree,'Mode','Graph')
OptimalTree = fitctree(X,Y,'MinLeafSize',40); view(OptimalTree,'mode','graph')
resubOpt = resubLoss(OptimalTree); lossOpt = kfoldLoss(crossval(OptimalTree)); resubDefault = resubLoss(DefaultTree); lossDefault = kfoldLoss(crossval(DefaultTree)); resubOpt,resubDefault,lossOpt,lossDefault
resubOpt = 0.0883
resubDefault = 0.0114
lossOpt = 0.1054
lossDefault = 0.1111
The nearoptimal tree is much smaller and gives a much higher resubstitution error. Yet, it gives similar accuracy for crossvalidated data.
Pruning optimizes tree depth (leafiness) by merging leaves on the same tree branch. Control Depth or “Leafiness” describes one method for selecting the optimal depth for a tree. Unlike in that section, you do not need to grow a new tree for every node size. Instead, grow a deep tree, and prune it to the level you choose.
Prune a tree at the command line using the prune
method (classification) or prune
method (regression). Alternatively, prune a tree interactively
with the tree viewer:
view(tree,'mode','graph')
To prune a tree, the tree must contain a pruning sequence. By default, both
fitctree
and fitrtree
calculate a pruning sequence for a tree during
construction. If you construct a tree with the 'Prune'
namevalue
pair set to 'off'
, or if you prune a tree to a smaller level, the
tree does not contain the full pruning sequence. Generate the full pruning sequence
with the prune
method (classification) or
prune
method (regression).
This example creates a classification tree for the ionosphere
data, and prunes it to a good level.
Load the ionosphere
data:
load ionosphere
Construct a default classification tree for the data:
tree = fitctree(X,Y);
View the tree in the interactive viewer:
view(tree,'Mode','Graph')
Find the optimal pruning level by minimizing crossvalidated loss:
[~,~,~,bestlevel] = cvLoss(tree,... 'SubTrees','All','TreeSize','min')
bestlevel = 6
Prune the tree to level 6
:
view(tree,'Mode','Graph','Prune',6)
Alternatively, use the interactive window to prune the tree.
The pruned tree is the same as the nearoptimal tree in the "Select Appropriate Tree Depth" example.
Set 'TreeSize'
to 'SE'
(default) to find the maximal pruning level for which the tree error does not exceed the error from the best level plus one standard deviation:
[~,~,~,bestlevel] = cvLoss(tree,'SubTrees','All')
bestlevel = 6
In this case the level is the same for either setting of 'TreeSize'
.
Prune the tree to use it for other purposes:
tree = prune(tree,'Level',6); view(tree,'Mode','Graph')
[1] Breiman, L., J. H. Friedman, R. A. Olshen, and C. J. Stone. Classification and Regression Trees. Boca Raton, FL: Chapman & Hall, 1984.
[2] Loh, W.Y. and Y.S. Shih. “Split Selection Methods for Classification Trees.” Statistica Sinica, Vol. 7, 1997, pp. 815–840.
[3] Loh, W.Y. “Regression Trees with Unbiased Variable Selection and Interaction Detection.” Statistica Sinica, Vol. 12, 2002, pp. 361–386.
ClassificationTree
 RegressionTree
 fitctree
 fitrtree
 predict (CompactClassificationTree)
 predict (CompactRegressionTree)
 prune (ClassificationTree)
 prune (RegressionTree)