LogitBoost | R Documentation |
Train logitboost classification algorithm using decision stumps (one node decision trees) as weak learners.
LogitBoost(xlearn, ylearn, nIter=ncol(xlearn))
xlearn |
A matrix or data frame with training data. Rows contain samples and columns contain features |
ylearn |
Class labels for the training data samples.
A response vector with one label for each row/component of |
nIter |
An integer, describing the number of iterations for which boosting should be run, or number of decision stumps that will be used. |
The function was adapted from logitboost.R function written by Marcel
Dettling. See references and "See Also" section. The code was modified in
order to make it much faster for very large data sets. The speed-up was
achieved by implementing a internal version of decision stump classifier
instead of using calls to rpart
. That way, some of the most time
consuming operations were precomputed once, instead of performing them at
each iteration. Another difference is that training and testing phases of the
classification process were split into separate functions.
An object of class "LogitBoost" including components:
Stump |
List of decision stumps (one node decision trees) used:
If there are more than two classes, than several "Stumps" will be
|
lablist |
names of each class |
Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com
Dettling and Buhlmann (2002), Boosting for Tumor Classification of Gene Expression Data.
predict.LogitBoost
has prediction half of LogitBoost code
logitboost
function from logitboost library (not in CRAN
or BioConductor is very similar but much
slower on very large datasets. It also perform optional cross-validation.
data(iris)
Data = iris[,-5]
Label = iris[, 5]
# basic interface
model = LogitBoost(Data, Label, nIter=20)
Lab = predict(model, Data)
Prob = predict(model, Data, type="raw")
t = cbind(Lab, Prob)
t[1:10, ]
# two alternative call syntax
p=predict(model,Data)
q=predict.LogitBoost(model,Data)
pp=p[!is.na(p)]; qq=q[!is.na(q)]
stopifnot(pp == qq)
# accuracy increases with nIter (at least for train set)
table(predict(model, Data, nIter= 2), Label)
table(predict(model, Data, nIter=10), Label)
table(predict(model, Data), Label)
# example of spliting the data into train and test set
mask = sample.split(Label)
model = LogitBoost(Data[mask,], Label[mask], nIter=10)
table(predict(model, Data[!mask,], nIter=2), Label[!mask])
table(predict(model, Data[!mask,]), Label[!mask])
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