Author: Przemyslaw Biecek
Date: 2018-06-11

# How to use breakDown package for SVM models

#### Przemyslaw Biecek

#### 2018-06-11

This example demonstrates how to use the `breakDown` package for models created with the kernlab package.

    library("breakDown")
    library(kernlab)
    #>
    #> Attaching package: 'kernlab'
    #> The following object is masked from 'package:ggplot2':
    #>
    #>     alpha

    wine_svm_model <- ksvm(quality~., data = wine)
    wine_svm_model
    #> Support Vector Machine object of class "ksvm"
    #>
    #> SV type: eps-svr  (regression)
    #>  parameter : epsilon = 0.1  cost C = 1
    #>
    #> Gaussian Radial Basis kernel function.
    #>  Hyperparameter : sigma =  0.0812662700662813
    #>
    #> Number of Support Vectors : 4196
    #>
    #> Objective Function Value : -2269.019
    #> Training error : 0.522769

    # or with the e1071:::svm

    library(e1071)
    wine_svm_model <- svm(quality~., data = wine)
    wine_svm_model
    #>
    #> Call:
    #> svm(formula = quality ~ ., data = wine)
    #>
    #>
    #> Parameters:
    #>    SVM-Type:  eps-regression
    #>  SVM-Kernel:  radial
    #>        cost:  1
    #>       gamma:  0.09090909
    #>     epsilon:  0.1
    #>
    #>
    #> Number of Support Vectors:  4176

Now we are ready to call the `broken()` function. Since `kernlab` is useing S4 methods we need to pass here the hook to `kernlab:::predict` method.

    library("breakDown")
    nobs <- wine[5, , drop = FALSE]
    base_prediction <- predict(wine_svm_model, nobs)
    set.seed(1313)

    explain_5_up <- broken(wine_svm_model, new_observation = nobs,
                        data = wine, predict.function = predict,
                        baseline = "intercept", direction = "up")
    explain_5_up
    #>                              contribution
    #> (Intercept)                         0.000
    #> + density = 0.9956                 -0.290
    #> + chlorides = 0.058                -0.061
    #> + alcohol = 9.9                    -0.079
    #> + pH = 3.19                        -0.031
    #> + total.sulfur.dioxide = 186       -0.023
    #> + sulphates = 0.4                  -0.027
    #> + free.sulfur.dioxide = 47         -0.005
    #> + quality = 6                       0.000
    #> + citric.acid = 0.32                0.019
    #> + residual.sugar = 8.5              0.098
    #> + volatile.acidity = 0.23           0.102
    #> + fixed.acidity = 7.2               0.146
    #> final_prognosis                    -0.152
    #> baseline:  5.842347

    explain_5_down <- broken(wine_svm_model, new_observation = nobs,
                        data = wine, predict.function = predict,
                        baseline = "intercept", direction = "down")
    explain_5_down
    #>                              contribution
    #> (Intercept)                         0.000
    #> - density = 0.9956                 -0.290
    #> - residual.sugar = 8.5              0.195
    #> - alcohol = 9.9                    -0.080
    #> - volatile.acidity = 0.23           0.103
    #> - total.sulfur.dioxide = 186       -0.071
    #> - sulphates = 0.4                  -0.066
    #> - fixed.acidity = 7.2               0.072
    #> - pH = 3.19                        -0.025
    #> - citric.acid = 0.32                0.049
    #> - free.sulfur.dioxide = 47         -0.038
    #> - chlorides = 0.058                -0.001
    #> - quality = 6                       0.000
    #> final_prognosis                    -0.152
    #> baseline:  5.842347

And plot it.

    library(ggplot2)
    plot(explain_5_up) + ggtitle(paste0("Prediction for SVM model ", round(base_prediction, 3)))

    plot(explain_5_down) +  ggtitle(paste0("Prediction for SVM model ", round(base_prediction, 3)))