Download R for Classification

R for Classification
Jennifer Broughton
Shimadzu Research Laboratory
Manchester, UK
[email protected]
2 nd May 2013
Classification?
Automatic Identification
of Type (Class) of Object
from Measured Variables (Features)
Object Type
Label 1
Label 2
……
Label m
Feature1
val[1,1]
val[2,1]
…….
val[m,1]
Feature2
val[1,2]
val[2,2]
…….
val[m.2]
Feature3
val[1,3]
val[2,3]
…….
val[m,3]
…….
…….
…….
…….
…….
Feature n
val[1,n]
val[2,n]
………
val[m,n]
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Example Data
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Data Preparation & Investigation
EDA Technique
Training
Set
Box Plots
PCA
Decision Trees
Clustering
• Best features to distinguish
between classes
• Relationships between
features
• Feature reduction
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Box Plots
PCA & Multivariate Analysis:
ade4
FactoMineR
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Example Classifier
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Classification Algorithms in R
Rattle: R Analytical Tool to Learn Easily (Rattle: A Data Mining GUI for R, Graham J Williams, The R Journal, 1(2):45-55 )
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SVM
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Ensemble Algorithm
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Training and Testing
Trained
Classifier
Training Set
(labelled)
Classification
Results
Classification Algorithm:
Test Set
(unlabelled)
Neural Network
Support Vector Machine
Random Forest
Assess
Predictions:
Confusion Matrix
ROC Curve
(2 categories) ….
+ Labels
Prediction
Results
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Using Classifiers in R
Select Training Data
Build Classifier
classifier  algorithm(formula, data, options)
(boosting and nnet)
Run Classifier
classifier.pred  predict(classifier, newdata, options)
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SVM & Neural Net Tuning
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Classifier Feedback
print(classifier)
plot(classifier)
high Gini Coefficient = high dispersion
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Classifier Prediction Results
predict(type = “class”)
predict(type = “prob”)
confusion matrix
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Binary Classification Results
Class Present?
N
Y
Y
Class
Detected?
N




True
Positive
False
Negative
False
Positive
True
Negative
𝑻𝑷𝑹 =
𝑻𝑷
= 𝑺𝒆𝒏𝒔𝒊𝒕𝒊𝒗𝒊𝒕𝒚
𝑻𝑷 + 𝑭𝑵
𝑭𝑷𝑹 =
𝑭𝑷
= 𝟏 − 𝑺𝒑𝒆𝒄𝒊𝒇𝒊𝒄𝒊𝒕𝒚
𝑻𝑵 + 𝑭𝑷
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ROC Curves in R
ROCR package
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Example Results
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