# Random_forest_examples

## Raymaekers, J. and Rousseeuw, P.J.

### 2023-04-23

# Introduction

This vignette visualizes classification results from a random forest, using tools from the package.

    library(randomForest)

    ## Warning: package 'randomForest' was built under R version 4.1.3

    ## randomForest 4.7-1.1

    ## Type rfNews() to see new features/changes/bug fixes.

    ##
    ## Attaching package: 'randomForest'

    ## The following object is masked from 'package:gridExtra':
    ##
    ##     combine

    ## The following object is masked from 'package:ggplot2':
    ##
    ##     margin

    library(classmap)

# Instagram training data

We use the Instagram data to illustrate the visualization of a random forest classification. The data is on the identification of genuine/fake (spam) accounts on Instagram. The original data source is: https://www.kaggle.com/free4ever1/instagram-fake-spammer-genuine-accounts from Bardiya Bakhshandeh.

First we load and inspect the data.

    data("data_instagram")
    traindata <- data_instagram[which(data_instagram$dataType == "train"), -13]
    str(traindata)

    ## 'data.frame':	576 obs. of  12 variables:
    ##  $ profile.pic         : int  1 1 1 1 1 1 1 1 1 1 ...
    ##  $ nums.length.username: num  0.27 0 0.1 0 0 0 0 0 0 0 ...
    ##  $ fullname.words      : int  0 2 2 1 2 4 2 2 0 2 ...
    ##  $ nums.length.fullname: num  0 0 0 0 0 0 0 0 0 0 ...
    ##  $ name..username      : int  0 0 0 0 0 0 0 0 0 0 ...
    ##  $ description.length  : int  53 44 0 82 0 81 50 0 71 40 ...
    ##  $ external.URL        : int  0 0 0 0 0 1 0 0 0 1 ...
    ##  $ private             : int  0 0 1 0 1 0 0 0 0 0 ...
    ##  $ X.posts             : int  32 286 13 679 6 344 16 33 72 213 ...
    ##  $ X.followers         : int  1000 2740 159 414 151 669987 122 1078 1824 12945 ...
    ##  $ X.follows           : int  955 533 98 651 126 150 177 76 2713 813 ...
    ##  $ y                   : Factor w/ 2 levels "genuine","fake": 1 1 1 1 1 1 1 1 1 1 ...

    # The variable names and their interpretation are
    colnames(traindata)

    ##  [1] "profile.pic"          "nums.length.username" "fullname.words"
    ##  [4] "nums.length.fullname" "name..username"       "description.length"
    ##  [7] "external.URL"         "private"              "X.posts"
    ## [10] "X.followers"          "X.follows"            "y"

    # profile.pic: binary, indicates whether profile has picture
    # nums.length.username: ratio of number of numerical chars in username to its length
    # fullname.words: number of words in full name
    # nums.length.fullname: ratio of number of numerical characters in full name to its length
    # name..username: binary, indicates whether name == username of the profile
    # description.length: length of the description/biography of the profile (in number of characters)
    # external.URL: binary, indicates whether profile has external url
    # private: binary, indicates whether profile is private or not
    # X.posts: number of posts made by profile
    # X.followers: number of followers
    # X.follows: numbers of follows
    # y: whether profile is fake or not.

    x_train <- traindata[, -12]
    y_train <- traindata[, 12]

    dim(traindata)

    ## [1] 576  12

    table(traindata$y) # 50/50 split of genuine/fake accounts:

    ##
    ## genuine    fake
    ##     288     288

Now we train a random forest. We set the seed as it is not deterministic.

    set.seed(71)
    rfout <- randomForest(y ~ ., data = traindata, keep.forest = TRUE)

Now we create a list called mytype which describes the types of the variables in the data. The variables that are not listed will be interval-scaled by default. The Instagram data contains mostly numeric variables and 4 symmetric binary variables.

    mytype <- list(symm = c(1, 5, 7, 8))

Now we prepare for the visualization of the random forest classification.

    vcrtrain <- vcr.forest.train(X = x_train, y = y_train,
                                trainfit = rfout, type = mytype)

    names(vcrtrain)

    ##  [1] "X"         "yint"      "y"         "levels"    "predint"   "pred"
    ##  [7] "altint"    "altlab"    "PAC"       "figparams" "fig"       "farness"
    ## [13] "ofarness"  "trainfit"

    vcrtrain$predint[c(1:10, 301:310)] # prediction as integer

    ##   1   2   3   4   5   6   7   8   9  10 301 302 303 304 305 306 307 308 309 310
    ##   1   1   1   1   1   1   1   1   1   1   2   2   2   2   2   2   2   2   2   2

    vcrtrain$pred[c(1:10, 301:310)]    # prediction as label

    ##  [1] "genuine" "genuine" "genuine" "genuine" "genuine" "genuine" "genuine"
    ##  [8] "genuine" "genuine" "genuine" "fake"    "fake"    "fake"    "fake"
    ## [15] "fake"    "fake"    "fake"    "fake"    "fake"    "fake"

    vcrtrain$altint[c(1:10, 301:310)]  # alternative label as integer

    ##  [1] 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1

    vcrtrain$altlab[c(1:10, 301:310)]  # alternative label

    ##  [1] "fake"    "fake"    "fake"    "fake"    "fake"    "fake"    "fake"
    ##  [8] "fake"    "fake"    "fake"    "genuine" "genuine" "genuine" "genuine"
    ## [15] "genuine" "genuine" "genuine" "genuine" "genuine" "genuine"

    # Probability of Alternative Class (PAC) of each object:
    vcrtrain$PAC[1:3]

    ## [1] 0.124 0.000 0.036

    #
    summary(vcrtrain$PAC)

    ##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
    ## 0.00000 0.00000 0.01200 0.04935 0.05600 0.48400

    # f(i, g) is the distance from case i to class g:
    vcrtrain$fig[1:3, ] # for the first 3 objects:

    ##           [,1]      [,2]
    ## [1,] 0.8896095 0.9053458
    ## [2,] 0.2818389 0.9392232
    ## [3,] 0.6013421 0.5258344

    # The farness of an object i is the f(i, g) to its own class:
    vcrtrain$farness[1:3]

    ## [1] 0.8896095 0.2818389 0.6013421

    #
    summary(vcrtrain$farness)

    ##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
    ## 0.02329 0.24326 0.50000 0.49483 0.74443 0.99996

    # The "overall farness" of an object is defined as the
    # lowest f(i, g) it has to any class g (including its own):
    summary(vcrtrain$ofarness)

    ##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
    ## 0.02329 0.22795 0.46616 0.47415 0.70684 0.99996

    sum(vcrtrain$ofarness > 0.99, na.rm = TRUE)

    ## [1] 6

    # With the default cutoff = 0.99 we find 6 outliers,
    # also shown in the last column of the confusion matrix:

    confmat.vcr(vcrtrain)

    ##
    ## Confusion matrix:
    ##          predicted
    ## given     genuine fake outl
    ##   genuine     283    0    5
    ##   fake          0  287    1
    ##
    ## The accuracy is 100%.

    # If we do not want to show the outliers:
    confmat.vcr(vcrtrain, showOutliers = FALSE)

    ##
    ## Confusion matrix:
    ##          predicted
    ## given     genuine fake
    ##   genuine     288    0
    ##   fake          0  288
    ##
    ## The accuracy is 100%.

    # Note that the accuracy is computed before any objects
    # are flagged, so it does not depend on the cutoff.
    # Here the accuracy is `perfect' due to overfitting.
    # The out-of-box prediction accuracy is about 92%.
    cols <- c("blue", "red3")

Now we can use the visualization tools from this package.

    stackedplot(vcrtrain, classCols = cols, main =
                  "Instagram training data")

    # Silhouette plot:
    silplot(vcrtrain, classCols = cols)

    ##  classNumber classLabel classSize classAveSi
    ##            1    genuine       288        0.9
    ##            2       fake       288        0.9

    # Here all the s(i) are nonnegative (due to overfitting).

    # Class maps:
    classmap(vcrtrain, "genuine", classCols = cols) #, identify = TRUE)

    # farness outliers from furthest to closer: 45, 25, 41
    x_train[c(45, 25, 41), ] # they have huge numbers of followers.

    ##    profile.pic nums.length.username fullname.words nums.length.fullname
    ## 45           1                    0              4                    0
    ## 25           1                    0              0                    0
    ## 41           1                    0              0                    0
    ##    name..username description.length external.URL private X.posts X.followers
    ## 45              0                 35            0       0    4494    12397719
    ## 25              0                  0            0       0     148    15338538
    ## 41              0                  2            0       0    7389      890969
    ##    X.follows
    ## 45         8
    ## 25        61
    ## 41        11

    classmap(vcrtrain, "fake", classCols = cols) #, identify = TRUE)

    # only case 261 is borderline far.

The classification of the training data is not very realistic due to overfitting, so let us look at the test data.

# Instagram test data

Now we consider the test data. First we load the data.

    testdata <- data_instagram[which(data_instagram$dataType == "test"), -13]
    Xnew <- testdata[, -12]
    ynew <- testdata[, 12]

We can now prepare for visualization:

    vcrtest <- vcr.forest.newdata(Xnew, ynew, vcrtrain)

    confmat.vcr(vcrtest)

    ##
    ## Confusion matrix:
    ##          predicted
    ## given     genuine fake outl
    ##   genuine      54    5    1
    ##   fake          5   54    1
    ##
    ## The accuracy is 91.67%.

First we visualize using the stacked plot and the silhouette plot:

    stackedplot(vcrtest, classCols = cols,
                main = "RF on Instagram test data")

    # Silhouette plot:
    silplot(vcrtest, classCols = cols, main =
              "Silhouettes of RF on Instagram test data") # now some s(i) are negative

    ##  classNumber classLabel classSize classAveSi
    ##            1    genuine        60       0.75
    ##            2       fake        60       0.75

Now we make the class maps

    ## Class of genuine accounts:

    classmap(vcrtest, "genuine", classCols = cols) #, identify = TRUE)

    # one farness outlier:
    Xnew[c(30), ]

    ##     profile.pic nums.length.username fullname.words nums.length.fullname
    ## 606           1                    0              2                    0
    ##     name..username description.length external.URL private X.posts X.followers
    ## 606              0                147            1       0    1879     4021842
    ##     X.follows
    ## 606      5514

    # has very lengthy bio/description
    # has large number of X.posts
    # has very large number of followers and follows

    # genuine misclassified as fake: from highest PAC to lowest
    Xnew[c(21, 29, 51), ] # and 2 more borderline cases

    ##     profile.pic nums.length.username fullname.words nums.length.fullname
    ## 597           1                 0.50              1                    0
    ## 605           1                 0.33              1                    0
    ## 627           1                 0.00              3                    0
    ##     name..username description.length external.URL private X.posts X.followers
    ## 597              0                  0            0       1       0         189
    ## 605              0                  0            0       1       5         348
    ## 627              0                  0            0       0       9          62
    ##     X.follows
    ## 597       276
    ## 605       347
    ## 627        47

    # They have some unusual characteristics for their class:
    # * 21, 29 have a (very) high nums.length.username, i.e. the
    #   percentage of numerical characters in the username.
    # * 21, 29 have a full name of only 1 word.
    # * 21, 29 and 51 have description.length = 0, i.e. no
    #   description/biography of their profile.
    # * they all have low X.posts (even 0 for case 21), i.e.
    #   relatively few previous posts.
    # All of these characteristics are more common for fake profiles
    # than for genuine profiles, as we can see below:

    trcols <- cols[as.numeric(y_train)]

    plot(x_train[, 1], col = trcols, main = "profile.pic")

    # fakes are less likely to have a profile picture
    plot(x_train[, 2], col = trcols, main = "nums.length.username")

    # is higher for fakes
    plot(x_train[, 3], col = trcols, main = "fullname.words")

    # is lower for fakes
    plot(x_train[, 4], col = trcols, main = "nums.length.fullname")

    # is a bit higher for fakes
    plot(x_train[, 5], col = trcols, main = "name..username")

    # mostly 0 for genuine; fakes have a few values 1
    plot(x_train[, 6], col = trcols, main = "description.length")

    # fakes are typically lower, and more often zero
    plot(x_train[, 7], col = trcols, main = "external.URL")

    # fakes never had them, genuines sometimes did
    plot(x_train[, 8], col = trcols, main = "private")

    # no visible difference
    plot((x_train[, 9])^0.1, col = trcols, main = "X.posts")

    # fakes have fewer posts, and often none
    plot((x_train[, 10])^0.1, col = trcols, main = "X.followers")

    # fakes have fewer followers, sometimes none
    plot((x_train[, 11])^0.1, col = trcols, main = "X.follows")

    # fakes follow a bit fewer, but the difference is small.

    ## Class of fake accounts:

    classmap(vcrtest, "fake", classCols = cols) #, identify = TRUE)

    # Fake identified as genuine, from highest PAC to lower:
    # c(27, 51, 34, 23, 58)
    Xnew[which(ynew == "fake")[c(27, 34, 51, 23, 58)], ]

    ##     profile.pic nums.length.username fullname.words nums.length.fullname
    ## 663           1                    0              3                    0
    ## 670           1                    0              0                    0
    ## 687           1                    0              1                    0
    ## 659           1                    0              2                    0
    ## 694           1                    0              2                    0
    ##     name..username description.length external.URL private X.posts X.followers
    ## 663              0                 58            0       0       4        1742
    ## 670              0                  0            0       0      15         772
    ## 687              0                  0            0       0       1         193
    ## 659              0                  0            0       0       3        1789
    ## 694              0                  0            0       0       3         833
    ##     X.follows
    ## 663      6172
    ## 670      3239
    ## 687       669
    ## 659      6153
    ## 694      3572

    # These have a number of characteristics which are more common
    # for genuine profiles:
    #
    # all have profile pictures
    # none have numerical characters in username
    # none have numerical characters in fullname
    # 27 has a lengthy bio description
    # all have a relatively high number of followers
    # all have a relatively high number of follows.