Breakfast Cereal Data from General Mills (1), Kellogg (2), and Quaker (3)
Brand Manufacturer Calories Protein Fat Sodium Fiber Carbohydrates Sugar Potassium Group
ACCheerios G 110 2 2 180 1.5 4 10 70 1
Cheerios G 110 6 2 290 2.0 13 1 105 1
CocoaPuffs G 110 1 1 180 0.0 7 13 55 1
CountChocula G 110 1 1 180 0.0 7 13 65 1
GoldenGrahams G 110 1 1 280 0.0 11 9 45 1
HoneyNutCheerios G 110 3 1 250 1.5 6 10 90 1

Assuming multivariate normal data with a common covariance matrix, equal costs, and equal priors:

  1. Classify the cereal brands according to manufacturer. Compute the estimated E(AER) using the holdout procedure.
  2. Interpret the coefficients of the discriminant functions. Does it appear as if some manufacturers are associated with more “nutritional” cereals (high protein, low fat, high fiber, low sugar, and so forth) than others?
  3. Plot the cereals in the two-dimensional discriminant space, using different plotting symbols to identify the three manufacturers.
  4. Calculate the Euclidean distances between pairs of cereal brands.
  5. Treating the distances calculated in (d) as measures of (dis)similarity, cluster the cereals using the single linkage and complete linkage hierarchical procedures. Construct dendrograms and compare the results.
  6. Use K-means clustering method. Cluster the cereals into K =2, 3, and 4 groups. Compare the results with those in part (e).

a. Classification according to manufacturer

set.seed(2634)
lda.class <- lda(Manufacturer ~ ., data = df, prior = c(1, 1, 1)/3, CV = T)
lda.class
$class
 [1] Q G G G G G G G G G Q G K K G K G K K K K Q K K K K K G K G K K K G G
[36] K K G G G Q Q Q
Levels: G K Q

$posterior
             G               K               Q
1  0.278140838 0.0288956035984 0.6929635579091
2  0.730719531 0.1254803009451 0.1438001677134
3  0.892517863 0.0147145785487 0.0927675588832
4  0.908670975 0.0058937254859 0.0854352999719
5  0.946025582 0.0235734557260 0.0304009621423
6  0.834693817 0.1242999797820 0.0410062035470
7  0.863002362 0.0832841238998 0.0537135145895
8  0.898741508 0.0181532056189 0.0831052868405
9  0.611557678 0.2686117274092 0.1198305950522
10 0.885693026 0.0296701260959 0.0846368481141
11 0.112184389 0.0002796064574 0.8875360047734
12 0.680369344 0.1867973002972 0.1328333558536
13 0.089987322 0.9099946320610 0.0000180460998
14 0.120934789 0.8165935252200 0.0624716857767
15 0.598145848 0.2015665085673 0.2002876437771
16 0.104519662 0.8519051487649 0.0435751892293
17 0.584428213 0.3637771292141 0.0517946577939
18 0.475810090 0.5231557032391 0.0010342064404
19 0.026391108 0.9707286073204 0.0028802847828
20 0.169418260 0.8262758439537 0.0043058955743
21 0.006311571 0.9914992170217 0.0021892120816
22 0.004888582 0.0000004913226 0.9951109271696
23 0.019651176 0.9795082197202 0.0008406046272
24 0.201829875 0.6770747585056 0.1210953667640
25 0.021316051 0.9778924032989 0.0007915460586
26 0.002358525 0.9912760296143 0.0063654458280
27 0.001825402 0.9981739808290 0.0000006170877
28 0.581189584 0.3172358724258 0.1015745430967
29 0.161801169 0.8377511253629 0.0004477055684
30 0.829202368 0.1232867606857 0.0475108714987
31 0.128971096 0.8686542862038 0.0023746174202
32 0.013130587 0.9833586139792 0.0035107993891
33 0.375295542 0.6218471964108 0.0028572616767
34 0.803257106 0.1946351789989 0.0021077147698
35 0.776510431 0.2191417976383 0.0043477710096
36 0.075498413 0.9237815938592 0.0007199928163
37 0.338119094 0.6603473130406 0.0015335934002
38 0.967229996 0.0178711802686 0.0148988233307
39 0.719405356 0.2741577481113 0.0064368955709
40 0.633077966 0.0348538927703 0.3320681413697
41 0.040617057 0.0003060884612 0.9590768549983
42 0.014304551 0.0001343497100 0.9855610994267
43 0.040795598 0.0173098622694 0.9418945392514

$terms
Manufacturer ~ Calories + Protein + Fat + Sodium + Fiber + Carbohydrates + 
    Sugar + Potassium
attr(,"variables")
list(Manufacturer, Calories, Protein, Fat, Sodium, Fiber, Carbohydrates, 
    Sugar, Potassium)
attr(,"factors")
              Calories Protein Fat Sodium Fiber Carbohydrates Sugar
Manufacturer         0       0   0      0     0             0     0
Calories             1       0   0      0     0             0     0
Protein              0       1   0      0     0             0     0
Fat                  0       0   1      0     0             0     0
Sodium               0       0   0      1     0             0     0
Fiber                0       0   0      0     1             0     0
Carbohydrates        0       0   0      0     0             1     0
Sugar                0       0   0      0     0             0     1
Potassium            0       0   0      0     0             0     0
              Potassium
Manufacturer          0
Calories              0
Protein               0
Fat                   0
Sodium                0
Fiber                 0
Carbohydrates         0
Sugar                 0
Potassium             1
attr(,"term.labels")
[1] "Calories"      "Protein"       "Fat"           "Sodium"       
[5] "Fiber"         "Carbohydrates" "Sugar"         "Potassium"    
attr(,"order")
[1] 1 1 1 1 1 1 1 1
attr(,"intercept")
[1] 1
attr(,"response")
[1] 1
attr(,".Environment")
<environment: R_GlobalEnv>
attr(,"predvars")
list(Manufacturer, Calories, Protein, Fat, Sodium, Fiber, Carbohydrates, 
    Sugar, Potassium)
attr(,"dataClasses")
 Manufacturer      Calories       Protein           Fat        Sodium 
     "factor"     "numeric"     "numeric"     "numeric"     "numeric" 
        Fiber Carbohydrates         Sugar     Potassium 
    "numeric"     "numeric"     "numeric"     "numeric" 

$call
lda(formula = Manufacturer ~ ., data = df, prior = c(1, 1, 1)/3, 
    CV = T)

$xlevels
named list()
holdout <- lda.class$class
table(df$Manufacturer, holdout)
   holdout
     G  K  Q
  G 12  3  2
  K  4 15  1
  Q  3  0  3

b. Interpretation of discriminant functions’ coefficients

banana <- lda(Manufacturer ~ ., data = df, prior = c(1, 1, 1)/3)
banana
Call:
lda(Manufacturer ~ ., data = df, prior = c(1, 1, 1)/3)

Prior probabilities of groups:
        G         K         Q 
0.3333333 0.3333333 0.3333333 

Group means:
  Calories  Protein      Fat    Sodium    Fiber Carbohydrates    Sugar
G 110.5882 2.352941 1.235294 203.52941 1.294118      9.705882 8.117647
K 111.0000 2.600000 0.650000 185.50000 2.250000     12.050000 7.950000
Q  90.0000 2.333333 1.333333  98.33333 1.116667      5.500000 5.000000
  Potassium
G  85.00000
K  91.75000
Q  58.33333

Coefficients of linear discriminants:
                       LD1          LD2
Calories      -0.042394995 -0.022385273
Protein       -0.192736441  0.043708862
Fat            1.030238269  0.230557790
Sodium        -0.002097074  0.008271173
Fiber         -0.938811912 -1.424824908
Carbohydrates -0.112847256  0.016979986
Sugar         -0.103510958  0.070253284
Potassium      0.019779960  0.035706831

Proportion of trace:
   LD1    LD2 
0.8095 0.1905 

c. Plotting in 2D discriminant space

plot(banana)

d. Euclidean Distance between pairs

d <- dist(df, method = "euclidean")
d
            1          2          3          4          5          6
2  123.252409                                                       
3   16.678017 129.078465                                            
4    7.290833 125.094964  10.606602                                 
5  109.609107  65.366276 106.763758 108.332821                      
6   77.260922  47.020275  83.119831  78.955090  57.679340           
7   91.832899  76.183167  87.509285  90.043739  23.406730  55.644238
8   16.474412 128.938939   1.500000  10.712143 106.732141  83.065674
9   49.366297  77.005682  58.046318  51.907369  80.351571  34.242244
10  58.345951 130.470902  73.064398  63.153830 142.843993  93.132969
11  86.233694 164.331315 100.546165  91.156630 180.057022 128.694405
12  45.264846 121.091907  33.237780  40.831973  85.920021  79.918122
13 173.226459 173.352243 188.731953 178.310824 220.632613 164.820072
14  49.944031  96.286681  64.194042  54.734587 110.099387  58.933490
15  64.073444 180.860443  53.054218  60.018747 150.067485 135.578967
16  50.135130  96.280839  64.290357  54.847516 110.114713  59.057440
17  25.306249 107.084663  23.165168  23.165168  86.357542  62.220626
18 282.187936 234.355499 297.174191 287.162846 295.808215 248.353642
19  72.298211 192.981864  64.150214  69.211632 165.388180 147.138646
20 123.862449  75.232141 120.023435 122.344289  20.594295  74.179891
21 109.331634 230.924501 102.445717 106.747951 203.317793 185.276567
22 104.561136 169.954038 119.535037 109.720668 192.436028 138.408025
23  61.821568 108.990252  52.058861  58.181827  66.144728  72.337101
24  72.220366 192.900233  64.132675  69.195376 165.354165 147.108060
25  52.684497 128.331115  38.462644  47.611711  87.509285  87.124372
26 193.994281 307.927751 197.248574 194.953841 302.881165 265.648793
27 142.922728 105.943971 157.196135 147.599543 160.033200 107.295882
28  18.317512 136.112086  15.443445  15.443445 117.824021  91.033133
29 114.203355 168.638296 127.610246 118.466767 191.680398 140.156720
30  36.019526 127.341077  22.699119  31.068473  96.199012  83.713238
31  83.894465  85.381497  96.374270  87.823687 115.060853  62.859218
32  34.715360 130.081225  46.342475  38.374796 128.146888  88.304339
33 151.864351  72.109292 149.887458 151.009106  44.471901  89.726146
34 183.571597 167.281948 199.178312 188.737914 220.106792 165.109907
35 123.462165  74.578817 119.539742 121.869808  17.557050  73.478951
36 122.096913 243.894188 118.466767 120.351049 223.059129 198.701173
37  56.705654  82.908082  54.621424  55.641711  54.744863  43.991832
38  57.523093 106.521125  48.628695  54.104066  65.606783  67.393666
39  51.266766  99.283684  45.074938  48.674942  64.708964  58.406175
40  43.139671 149.492893  54.734587  46.993351 148.261172 106.828279
41 209.861338 328.392106 206.136787 208.578223 305.556664 284.281166
42 202.653414 319.691844 201.840593 202.397196 304.047077 276.202202
43 196.151714 308.085704 200.488033 197.662468 305.413574 266.461057
            7          8          9         10         11         12
2                                                                   
3                                                                   
4                                                                   
5                                                                   
6                                                                   
7                                                                   
8   87.380633                                                       
9   69.048896  57.910491                                            
10 129.913553  73.002782  69.731852                                 
11 166.794503 100.479009 100.551759  50.356231                      
12  63.860199  32.897568  63.311729  98.517289 129.705556           
13 217.533618 188.731953 157.924428 119.187484 117.729696 209.967855
14  98.510152  64.000977  30.224163  46.972399  72.142437  80.435533
15 128.908398  53.054218 110.099387 107.839725 122.726449  65.778036
16  98.470173  64.097582  30.279944  47.056150  72.305990  80.386566
17  67.433300  22.921060  39.771221  74.361658 107.143741  27.392974
18 300.174324 297.136332 249.881722 241.551819 232.401390 311.981971
19 144.534166  64.167749 120.126496 109.007024 118.477450  81.429417
20  34.007352 119.920286  94.678403 159.604687 194.896848  96.064432
21 182.013736 102.445717 157.135292 137.531474 138.546134 118.457271
22 180.642603 119.469138 113.614480  57.630558  23.841272 147.850854
23  43.757856  51.842309  64.830548 111.763841 145.539621  21.917459
24 144.448520  64.132675 120.051551 108.955409 118.410963  81.277303
25  66.475559  38.433384  73.131730 107.829292 138.326719  15.112081
26 283.343211 197.208646 233.598213 184.372669 154.686477 223.464762
27 161.359846 157.181821 110.471716 105.647557 120.888508 170.594915
28  97.897268  14.924812  62.794307  67.368622  92.034810  41.677332
29 180.997238 127.601430 123.036580  57.386028  69.116071 152.768207
30  75.456113  22.500000  65.495229  88.164087 120.888508  17.937391
31 109.340637  96.292523  60.271262  55.725050  96.614731 107.916634
32 111.323852  46.050244  54.373707  54.033844  64.379976  69.882938
33  64.769785 149.804873 116.445803 180.979367 216.398721 128.177611
34 219.284917 199.167015 161.021350 134.658944 131.569967 218.320865
35  32.293575 119.445594  95.311988 157.839812 195.248640  95.471200
36 201.954822 118.485759 168.528188 137.996943 131.377438 138.614123
37  36.109209  54.332311  40.430496  96.608909 132.328781  38.739515
38  46.099078  48.628695  62.596925 105.210058 141.812486  27.331301
39  45.903431  45.049972  52.703178  96.247240 133.597928  29.008619
40 131.299276  54.549290  74.593901  46.792427  49.240799  84.180609
41 284.407278 206.071286 252.285552 228.562423 206.322942 222.675493
42 283.575387 201.768122 243.263746 213.034988 184.543440 222.498596
43 286.272731 200.403845 234.632535 183.866106 152.063457 227.415262
           13         14         15         16         17         18
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14 135.095799                                                       
15 226.142101 111.419814                                            
16 135.108290   1.060660 111.465241                                 
17 183.549380  54.394393  73.934938  54.404733                      
18 142.523682 234.012019 340.840138 233.985576 286.403780           
19 225.429590 117.637685  17.298844 117.709388  86.240217 342.453646
20 236.707890 124.364384 160.391318 124.332719  99.938731 305.770134
21 248.807908 151.514851  53.318618 151.548260 124.301046 368.528662
22  97.309429  84.200653 143.479528  84.327487 124.128965 217.005472
23 217.259350  88.245396  85.992005  88.200765  38.855502 313.526913
24 225.429590 117.532442  17.168285 117.604209  86.161912 342.424079
25 220.068455  91.253767  63.701452  91.284582  37.349699 322.411034
26 247.958666 212.452642 168.934899 212.465880 216.621502 362.810901
27  71.206566  97.730497 205.009451  97.759271 144.802452 149.741026
28 184.560966  62.883821  49.613506  62.874876  31.908071 295.073296
29  88.149731  98.943166 153.209416  98.937480 130.042301 227.305686
30 202.755395  78.280745  56.564123  78.302299  26.045633 310.956187
31 111.121555  52.317540 143.984374  52.242224  83.671232 219.035956
32 159.646093  39.771221  79.902284  39.728768  50.266788 262.956032
33 243.887269 144.806336 192.783557 144.786912 128.864755 300.382256
34  31.925695 140.268047 240.135899 140.288096 191.615827 113.891396
35 235.026594 124.874437 160.029685 124.833890  99.368632 307.071653
36 240.643668 157.671335  76.903348 157.624950 139.902645 361.666455
37 193.453483  67.408271 101.313869  67.416615  32.982950 286.248581
38 210.444173  85.808653  86.181495  85.880731  36.264652 310.297035
39 200.023749  75.916895  88.130585  75.998355  29.259614 299.917489
40 155.563090  55.742713  76.124076  55.853603  65.897648 267.902268
41 319.346794 240.851614 162.405742 240.872632 226.763092 425.906240
42 294.074608 227.970393 164.306497 228.017269 222.096263 398.586722
43 242.739884 212.476708 174.668833 212.537588 219.387218 356.461816
           19         20         21         22         23         24
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20 176.257979                                                       
21  38.812047 213.427388                                            
22 139.092146 207.948912 157.935113                                 
23 102.104726  75.194747 138.885744 162.609963                      
24   1.500000 176.187755  38.783050 139.019333 101.994485           
25  79.972652  97.315209 116.817165 157.006369  24.325912  79.944512
26 152.617168 315.340887 128.322348 162.107603 245.232798 152.572933
27 209.385709 174.535813 240.758177 111.666915 171.794208 209.380336
28  58.615271 130.556022  95.241141 111.318799  62.019150  58.461526
29 150.370792 209.366903 170.162422  55.500000 165.741516 150.355828
30  71.056316 108.690501 108.793957 138.654697  36.171467  70.977109
31 150.389494 132.302211 183.714793  97.043161 110.863091 150.329638
32  83.886083 140.448389 115.431798  84.560629  85.578911  83.738432
33 208.311065  33.591294 245.924531 227.246287 107.786247 208.257053
34 240.636656 234.736821 266.065077 113.639232 223.583038 240.627305
35 175.941752  10.764525 213.161031 207.745939  74.450487 175.877798
36  61.142252 234.076910  32.380550 148.621163 159.994531  61.160649
37 115.392807  68.188159 153.510179 147.156804  29.182615 115.295273
38 101.535708  78.567646 139.229577 157.988528  18.155578 101.502463
39 102.659632  79.138328 140.836341 149.138778  23.116553 102.615788
40  75.202227 161.923593 102.703457  70.738957 102.418260  75.067470
41 148.708187 312.975638 115.558427 223.313681 242.564424 148.609808
42 149.342308 312.846208 119.859293 199.471803 243.208244 149.244347
43 158.482258 318.139515 136.214908 158.200905 249.074289 158.382847
           25         26         27         28         29         30
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26 226.864772                                                       
27 180.455673 272.754697                                            
28  49.306440 185.588254 157.188979                                 
29 161.728940 182.941589 109.294327 120.724376                      
30  22.070908 212.439403 167.829154  32.066337 140.836341           
31 118.057719 239.389849  70.905747  96.723834  83.819001 103.053384
32  79.584860 181.062489 133.828248  38.579463 107.781028  65.974427
33 129.873496 344.461536 177.314340 160.296600 227.082859 139.830254
34 228.588878 268.600540  61.855679 196.041450 114.310433 213.285021
35  96.718018 315.535260 173.575992 130.128782 206.365877 107.110924
36 139.201293  99.221343 240.954353 108.773273 162.062488 128.164445
37  46.147860 248.877982 144.401783  64.097582 150.161163  47.196398
38  26.303517 244.357320 165.907730  60.930288 157.945798  32.726136
39  32.048791 241.546579 155.374950  57.000000 149.146321  32.657312
40  92.149335 159.243917 140.648498  44.585592  94.345111  75.441202
41 222.045603 104.951775 323.982638 197.262832 250.630206 216.637081
42 223.484899  75.768562 304.300427 191.909158 229.891822 215.413266
43 231.235813  15.913084 269.614913 188.791224 180.287552 216.284422
           31         32         33         34         35         36
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32  86.383592                                                       
33 145.623659 166.462834                                            
34 119.370222 168.110455 238.702744                                 
35 129.278769 141.688479  35.273928 234.024037                      
36 188.484416 121.398105 265.773165 259.389427 233.766711           
37  86.650159  76.800879  96.735464 197.965906  67.433300 171.141389
38 103.619496  86.109668 109.479450 217.794628  76.382262 160.089428
39  93.253686  79.138328 108.871484 207.184700  76.998377 160.110509
40  93.728998  25.894015 188.185746 167.976561 162.322595 104.764021
41 280.333507 201.743030 345.102702 335.079655 314.983928 103.238801
42 266.491792 190.417305 343.822447 309.798120 314.876762 101.080414
43 238.743013 182.415326 346.684837 263.275191 318.384125 108.337442
           37         38         39         40         41         42
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38  28.774989                                                       
39  21.685248  10.712143                                            
40  95.712460 100.337555  93.884903                                 
41 255.773093 246.130301 247.220296 188.111004                      
42 252.408152 245.768946 245.255734 174.561594  37.529988           
43 251.351599 247.852681 244.596354 160.112230 114.247872  82.981933

e. Clustering with single/complete linkage hierarchical procedures

set.seed(2634)
# Single Linkage Hierarchical Clustering
clust.single <- hclust(d, method = "single")
clust.single

Call:
hclust(d = d, method = "single")

Cluster method   : single 
Distance         : euclidean 
Number of objects: 43 
plot(clust.single, cex = 0.5)
groups <- cutree(clust.single, k = 3)
groups
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1
[36] 1 1 1 1 1 3 3 3
rect.hclust(clust.single, k = 3, border = "red")

# Complete Linkage Hierarchical Clustering
cluster.complete <- hclust(d, method = "ave")
cluster.complete

Call:
hclust(d = d, method = "ave")

Cluster method   : average 
Distance         : euclidean 
Number of objects: 43 
plot(cluster.complete, cex = 0.5)
groups <- cutree(cluster.complete, k = 3)
groups
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1
[36] 1 1 1 1 1 3 3 3
rect.hclust(cluster.complete, k = 3, border = "red")

f. K-means Clustering

set.seed(2634)
clusters <- kmeans(df[, 2:9], centers = 3, nstart = 10)
clusters
K-means clustering with 3 clusters of sizes 7, 8, 28

Cluster means:
  Calories  Protein      Fat Sodium    Fiber Carbohydrates     Sugar
1 117.1429 3.142857 1.428571 190.00 4.642857      9.571429 10.142857
2  92.5000 2.250000 0.500000  51.25 1.337500      7.375000  7.750000
3 110.0000 2.357143 1.000000 215.00 1.089286     11.178571  6.928571
  Potassium
1 205.71429
2  49.37500
3  64.10714

Clustering vector:
 [1] 3 3 3 3 3 3 3 3 3 3 1 3 1 3 3 3 3 1 2 3 2 1 3 2 3 2 1 3 1 3 3 3 3 1 3
[36] 2 3 3 3 3 2 2 2

Within cluster sum of squares by cluster:
[1] 43204.79 37849.23 88308.60
 (between_SS / total_SS =  63.5 %)

Available components:

[1] "cluster"      "centers"      "totss"        "withinss"    
[5] "tot.withinss" "betweenss"    "size"         "iter"        
[9] "ifault"      
table(clusters$cluster, df$Manufacturer)
   
     G  K  Q
  1  2  5  0
  2  0  5  3
  3 15 10  3

Phoenix!

# Writing the data into R
df <- data.frame(x = seq(from = 24, to = 33, by = 1), y = c(6.5, 7.1, 7, 7.1, 
    7.2, 7.1, 8.1, 8.7, 9.5, 10.1))
attach(df)
# Fitting/summarising the Regression model
fit <- lm(y ~ x, data = df)
summary(fit)

Call:
lm(formula = y ~ x, data = df)

Residuals:
    Min      1Q  Median      3Q     Max 
-0.9236 -0.2655  0.0100  0.3591  0.6073 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) -2.62727    1.61408  -1.628 0.142235    
x            0.36727    0.05635   6.518 0.000185 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.5118 on 8 degrees of freedom
Multiple R-squared:  0.8415,    Adjusted R-squared:  0.8217 
F-statistic: 42.48 on 1 and 8 DF,  p-value: 0.0001846
# Fitting the model in R gives you answers but does not show how those
# answers were calculated so I'll do that here

# Manually defining values in R based on data/model fit
k <- length(fit$coefficients) - 1
n <- length(fit$residuals)
SSE <- sum(fit$residuals^2)
SSyy <- sum((y - mean(y))^2)
res.std.err <- sqrt(SSE/(n - (1 + k)))
r2 <- (SSyy - SSE)/SSyy
# Equivalent R2 calculation: 1 - SSE/SSyy
Fstat <- ((SSyy - SSE)/k)/(SSE/(n - (k + 1)))
# Printing manually defined values
out <- data.frame(k, n, SSE, SSyy, res.std.err, r2, Fstat)
kable(out)
k n SSE SSyy res.std.err r2 Fstat
1 10 2.095636 13.224 0.511815 0.8415278 42.48204