e1071 Package – SVM Training and Testing Models in R

1. Objective

Today, in this blog, we are going to discuss the e1071 package in R. Moreover, we will discuss the SVM training and testing models in R. Along with this, we will look at the main functions of e1071 package i.e. svm(), predict(), plot(), tune() to execute SVM in R.

So, let’s start the e1071 Package in R Tutorial.

e1071

e1071 Package – SVM Training and Testing Models in R

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2. R – SVM Training and Testing Models

There are several packages to execute SVM in R. The first and most intuitive package is the e1071 package.
The e1071 Package – 
This package was the first implementation of SVM in R.
The svm() function in e1071 provides a rigid interface to libsvm. By using visualization and parameter tuning methods. Refer some of the features of libsvm library given below:

  • Offers quick and easy implementation of SVMs.
  • Provides most common kernels, including linear, polynomial, RBF, and sigmoid.
  • Offers computation power for decision and probability values for predictions. Also provides class weighting in the classification mode, and cross-validation.

First, you need to set the path to include the directory where the e1071 package is. Then you have to install and include it.
You can use > ?svm to see the help information of the interface.
Install e1071 package and load using the following commands:

install.packages (‘e1071’, dependencies = TRUE)
library(e1071)

The R implementation depends on the S3 class mechanisms. It provides a training function with standard and formula interfaces, and a predict() method. Also provides a plot() method for visualizing data, support vectors, and decision boundaries. We can do Hyperparameter tuning by using the tune() framework. It performs a grid search over specified parameter ranges.

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3. e1071 Package – Main Functions

The main functions in the e1071 package are:

  • svm() – Used to train SVM.
  • predict() – Using this method obtains predictions from the model, as well as decision values from the binary classifiers.
  • plot() – Visualizing data, support vectors, and decision boundaries if provided.
  • tune() – Hyperparameter tuning uses tune() to perform a grid search over specified parameter ranges.

i. The svm() Function

The svm() function trains an SVM. It can do general regression and classification, as well as density-estimation. Provides a formula interface.
The below data describes some import parameters of the svm() function:
a. Data – Specifies an optional data frame that contains the variables present in a model. When you use this parameter, then you do not need to use the x and y parameters. Take the variables by default from the environment which ‘svm’ is called from.

  • X – a data matrix, a vector, or a sparse matrix (object of class Matrix provided by the Matrix package). It represents the instances of the dataset and their respective properties. In a data matrix- rows represent the instances, columns represent the properties

b. Type – We can use svm as a classification machine, regression machine, or for novelty detection. depending on whether y is a factor or not. The default setting for type is C-classification or eps-regression. It may be overwritten by setting an explicit value. Valid options are:

  • C-classification
  • nu-classification
  • one-classification (for novelty detection)
  • eps-regression
  • nu-regression
  • degree

c. parameter – It requires for the kernel of type polynomial (default: 3)

  • gamma – parameter needed for all kernels except linear (default: 1/(data dimension))
  • coef0 – parameter needed for kernels of type polynomial and sigmoid (default: 0)
  • cost – the cost of constraints violation (default: 1)—it is the ‘C’-constant of the regularization term in the Lagrange formulation.

ii. The plot() Function

Use the plot() function to view the built model with a scatter plot of the input. It optionally draws a filled contour plot of the class regions. plot() function used to represent data, support vectors and models in a visual form. How to use this function:
plot.svm(x, data, formula, fill = TRUE, grid = 50, slice = list(),symbolPalette = palette(), svSymbol = "x", dataSymbol = "o", ...)
Here,

  • x – An object of class svm.
  • Formula – Formula selecting the visualized two dimensions. Only needed when we use more than two input variables.
  • Fill – Switch indicating whether a contour plot for the class regions should add.
  • Grid – Granularity for the contour plot.
  • Slice – A list of named numeric values for the dimensions held constant. If dimensions not specified, we can fix it at 0.
  • Model – Represents an object of class svm data, which results from the svm() function.
  • Data – Represents the data to visualize. It should use the same data used for building the model in the svm() function.
  • symbolPalette – Color palette used for the class the data points and support vectors belong to.
  • svSymbol – Symbol used for support vectors.
  • dataSymbo – Symbol used for data points (other than support vectors).
  • svm allows a simple graphical visualization of classification models.

iii. The predict() Function

The predict() function predicts values based on a model derived by an SVM. It returns the class labels in case of classification with a class membership value or the decision values of the classifier. It also returns a vector of predicted labels for a classification problem.
Following are the steps to execute the predict() function:
Step 1: Divide the dataset into a training set and a test set. We can do it by using below commands:

Index <- 1:nrow(cats)
Testindex <- sample(index,trunk(length(index)/3))
Testset <- cats[Testindex, ]
Trainset <- cats[-testindex, ]

Step 2: Run the model again and predict classes by using the training set. Use commands as below:
Model <-svm(Sex~., data=trainset)
Prediction <- predict (model, testset[-1])

Step 3: Generate the confusion matrix by cross-tabulating the true and predicted values
Tab <- table(pred=prediction, true=testset[,1])
The confusion matrix is a tabular layout. It represents the performance of a supervised learning algorithm in the graphical form. In a confusion matrix, each column represents instances by the predicted class. On the other hand, each row of the matrix represents the instance of the actual class.

iv. The Tune() Function

It tunes hyper parameters of statistical methods using a grid search over supplied parameter ranges.
Below is represented how to use this function:

tune(method, train.x, train.y = NULL, data = list(), validation.x = NULL, validation.y = NULL, ranges = NULL, predict.func = predict, tunecontrol = tune.control(), ...)
best.tune(...)

  • Method – It is the function to be tuned or a character string naming such a function.
  • x – It is a formula or a matrix of predictors.
  • y – It is the response variable if train.x is a predictor matrix. It is ignored if train.x is a formula.
  • Data – It is the data when a formula interface is used. It is ignored if predictor matrix and response are supplied directly.
  • x – It is an optional validation set. The response can be included in validation.x or separately specified using validation.y depending on whether a formula interface is used or not.
  • y – It is only used for bootstrap and fixed validation set (see tune.control)
  • ranges – It is a named list of parameter vectors spanning the sampling space. The vectors will usually be created by seq.
  • func – It is optional when the standard predict behavior is inadequate.
  • Tunecontrol – It is the object of class “tune.control”, as created by the function tune.control(). when omitted, then tune.control() gives the defaults.
  • … – Further parameters passed to the training functions.

So, this was all in e1071 Packages in R. Hope you like our explanation.

4. Conclusion – e1071 in R

Hence, in this tutorial of e1071 packages in R, we discussed the training and testing models in R. Moreover, we saw the main functions of e1071 packages in R that are SVM, Plot, Predict, Tune. If you get any query or suggestion related to SVM training and testing models in R, feel free to share with us. Hope we will solve them.
See Also-

Reference for R 

No Responses

  1. JAVED AKHTER says:

    I’m trying to predict using SVM from package “e1071”. But I’m getting repeated values as predicted outcomes. I have run this several times but getting same results. Please help me to find what wrong is going here.
    >library(e1071)
    >tuneResult tunedModel predict.datapredict.data
    2006-03-01 2006-04-01 2006-05-01 2006-06-01 2006-07-01 2006-08-01 2006-09-01 2006-10-01 2006-11-01 2006-12-01 2007-01-01 2007-02-01 2007-03-01 2007-04-01 2007-05-01
    0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676
    2007-06-01 2007-07-01 2007-08-01 2007-09-01 2007-10-01 2007-11-01 2007-12-01 2008-01-01 2008-02-01 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01
    0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676
    2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 2009-03-01 2009-04-01 2009-05-01 2009-06-01 2009-07-01 2009-08-01 2009-09-01 2009-10-01 2009-11-01
    0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676 0.05798676
    …..and so on.
    Please help me to find out a solution.

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