options(repos = c(CRAN = "https://cloud.r-project.org"))

Reminder: All homework solutions must be written up independently, even though you are allowed to discuss with other students. You need to save your homework assignment in a pdf/html format and upload it with the R code (.R or .rmd) into the Canvas before 11:59pm CT on the due day. No late homework assignment will be graded in any circumstance.

Problem 1 (20 points): This exercise involves the Boston housing data set.

  1. To begin, load in the Boston data set. Since the Boston data set is part of the MASS library, you need to install the MASS package into R/Rstudio and then access the package as follows:
#install packages

install.packages("MASS") 
## Installing package into 'C:/Users/jenei/AppData/Local/R/win-library/4.5'
## (as 'lib' is unspecified)
## package 'MASS' successfully unpacked and MD5 sums checked
## Warning: cannot remove prior installation of package 'MASS'
## Warning in file.copy(savedcopy, lib, recursive = TRUE): problem copying
## C:\Users\jenei\AppData\Local\R\win-library\4.5\00LOCK\MASS\libs\x64\MASS.dll to
## C:\Users\jenei\AppData\Local\R\win-library\4.5\MASS\libs\x64\MASS.dll:
## Permission denied
## Warning: restored 'MASS'
## 
## The downloaded binary packages are in
##  C:\Users\jenei\AppData\Local\Temp\RtmpCoFuKb\downloaded_packages
install.packages("mlbench")
## Installing package into 'C:/Users/jenei/AppData/Local/R/win-library/4.5'
## (as 'lib' is unspecified)
## package 'mlbench' successfully unpacked and MD5 sums checked
## 
## The downloaded binary packages are in
##  C:\Users\jenei\AppData\Local\Temp\RtmpCoFuKb\downloaded_packages
install.packages("caret")
## Installing package into 'C:/Users/jenei/AppData/Local/R/win-library/4.5'
## (as 'lib' is unspecified)
## package 'caret' successfully unpacked and MD5 sums checked
## Warning: cannot remove prior installation of package 'caret'
## Warning in file.copy(savedcopy, lib, recursive = TRUE): problem copying
## C:\Users\jenei\AppData\Local\R\win-library\4.5\00LOCK\caret\libs\x64\caret.dll
## to C:\Users\jenei\AppData\Local\R\win-library\4.5\caret\libs\x64\caret.dll:
## Permission denied
## Warning: restored 'caret'
## 
## The downloaded binary packages are in
##  C:\Users\jenei\AppData\Local\Temp\RtmpCoFuKb\downloaded_packages
library(MASS)
## Warning: package 'MASS' was built under R version 4.5.2
library(mlbench)
## Warning: package 'mlbench' was built under R version 4.5.2
library(caret)
## Warning: package 'caret' was built under R version 4.5.2
## Loading required package: ggplot2
## Loading required package: lattice

Load data and basic structure

# Load dataset
data(Boston)

# View dataset
Boston
##         crim    zn indus chas    nox    rm   age     dis rad tax ptratio  black
## 1    0.00632  18.0  2.31    0 0.5380 6.575  65.2  4.0900   1 296    15.3 396.90
## 2    0.02731   0.0  7.07    0 0.4690 6.421  78.9  4.9671   2 242    17.8 396.90
## 3    0.02729   0.0  7.07    0 0.4690 7.185  61.1  4.9671   2 242    17.8 392.83
## 4    0.03237   0.0  2.18    0 0.4580 6.998  45.8  6.0622   3 222    18.7 394.63
## 5    0.06905   0.0  2.18    0 0.4580 7.147  54.2  6.0622   3 222    18.7 396.90
## 6    0.02985   0.0  2.18    0 0.4580 6.430  58.7  6.0622   3 222    18.7 394.12
## 7    0.08829  12.5  7.87    0 0.5240 6.012  66.6  5.5605   5 311    15.2 395.60
## 8    0.14455  12.5  7.87    0 0.5240 6.172  96.1  5.9505   5 311    15.2 396.90
## 9    0.21124  12.5  7.87    0 0.5240 5.631 100.0  6.0821   5 311    15.2 386.63
## 10   0.17004  12.5  7.87    0 0.5240 6.004  85.9  6.5921   5 311    15.2 386.71
## 11   0.22489  12.5  7.87    0 0.5240 6.377  94.3  6.3467   5 311    15.2 392.52
## 12   0.11747  12.5  7.87    0 0.5240 6.009  82.9  6.2267   5 311    15.2 396.90
## 13   0.09378  12.5  7.87    0 0.5240 5.889  39.0  5.4509   5 311    15.2 390.50
## 14   0.62976   0.0  8.14    0 0.5380 5.949  61.8  4.7075   4 307    21.0 396.90
## 15   0.63796   0.0  8.14    0 0.5380 6.096  84.5  4.4619   4 307    21.0 380.02
## 16   0.62739   0.0  8.14    0 0.5380 5.834  56.5  4.4986   4 307    21.0 395.62
## 17   1.05393   0.0  8.14    0 0.5380 5.935  29.3  4.4986   4 307    21.0 386.85
## 18   0.78420   0.0  8.14    0 0.5380 5.990  81.7  4.2579   4 307    21.0 386.75
## 19   0.80271   0.0  8.14    0 0.5380 5.456  36.6  3.7965   4 307    21.0 288.99
## 20   0.72580   0.0  8.14    0 0.5380 5.727  69.5  3.7965   4 307    21.0 390.95
## 21   1.25179   0.0  8.14    0 0.5380 5.570  98.1  3.7979   4 307    21.0 376.57
## 22   0.85204   0.0  8.14    0 0.5380 5.965  89.2  4.0123   4 307    21.0 392.53
## 23   1.23247   0.0  8.14    0 0.5380 6.142  91.7  3.9769   4 307    21.0 396.90
## 24   0.98843   0.0  8.14    0 0.5380 5.813 100.0  4.0952   4 307    21.0 394.54
## 25   0.75026   0.0  8.14    0 0.5380 5.924  94.1  4.3996   4 307    21.0 394.33
## 26   0.84054   0.0  8.14    0 0.5380 5.599  85.7  4.4546   4 307    21.0 303.42
## 27   0.67191   0.0  8.14    0 0.5380 5.813  90.3  4.6820   4 307    21.0 376.88
## 28   0.95577   0.0  8.14    0 0.5380 6.047  88.8  4.4534   4 307    21.0 306.38
## 29   0.77299   0.0  8.14    0 0.5380 6.495  94.4  4.4547   4 307    21.0 387.94
## 30   1.00245   0.0  8.14    0 0.5380 6.674  87.3  4.2390   4 307    21.0 380.23
## 31   1.13081   0.0  8.14    0 0.5380 5.713  94.1  4.2330   4 307    21.0 360.17
## 32   1.35472   0.0  8.14    0 0.5380 6.072 100.0  4.1750   4 307    21.0 376.73
## 33   1.38799   0.0  8.14    0 0.5380 5.950  82.0  3.9900   4 307    21.0 232.60
## 34   1.15172   0.0  8.14    0 0.5380 5.701  95.0  3.7872   4 307    21.0 358.77
## 35   1.61282   0.0  8.14    0 0.5380 6.096  96.9  3.7598   4 307    21.0 248.31
## 36   0.06417   0.0  5.96    0 0.4990 5.933  68.2  3.3603   5 279    19.2 396.90
## 37   0.09744   0.0  5.96    0 0.4990 5.841  61.4  3.3779   5 279    19.2 377.56
## 38   0.08014   0.0  5.96    0 0.4990 5.850  41.5  3.9342   5 279    19.2 396.90
## 39   0.17505   0.0  5.96    0 0.4990 5.966  30.2  3.8473   5 279    19.2 393.43
## 40   0.02763  75.0  2.95    0 0.4280 6.595  21.8  5.4011   3 252    18.3 395.63
## 41   0.03359  75.0  2.95    0 0.4280 7.024  15.8  5.4011   3 252    18.3 395.62
## 42   0.12744   0.0  6.91    0 0.4480 6.770   2.9  5.7209   3 233    17.9 385.41
## 43   0.14150   0.0  6.91    0 0.4480 6.169   6.6  5.7209   3 233    17.9 383.37
## 44   0.15936   0.0  6.91    0 0.4480 6.211   6.5  5.7209   3 233    17.9 394.46
## 45   0.12269   0.0  6.91    0 0.4480 6.069  40.0  5.7209   3 233    17.9 389.39
## 46   0.17142   0.0  6.91    0 0.4480 5.682  33.8  5.1004   3 233    17.9 396.90
## 47   0.18836   0.0  6.91    0 0.4480 5.786  33.3  5.1004   3 233    17.9 396.90
## 48   0.22927   0.0  6.91    0 0.4480 6.030  85.5  5.6894   3 233    17.9 392.74
## 49   0.25387   0.0  6.91    0 0.4480 5.399  95.3  5.8700   3 233    17.9 396.90
## 50   0.21977   0.0  6.91    0 0.4480 5.602  62.0  6.0877   3 233    17.9 396.90
## 51   0.08873  21.0  5.64    0 0.4390 5.963  45.7  6.8147   4 243    16.8 395.56
## 52   0.04337  21.0  5.64    0 0.4390 6.115  63.0  6.8147   4 243    16.8 393.97
## 53   0.05360  21.0  5.64    0 0.4390 6.511  21.1  6.8147   4 243    16.8 396.90
## 54   0.04981  21.0  5.64    0 0.4390 5.998  21.4  6.8147   4 243    16.8 396.90
## 55   0.01360  75.0  4.00    0 0.4100 5.888  47.6  7.3197   3 469    21.1 396.90
## 56   0.01311  90.0  1.22    0 0.4030 7.249  21.9  8.6966   5 226    17.9 395.93
## 57   0.02055  85.0  0.74    0 0.4100 6.383  35.7  9.1876   2 313    17.3 396.90
## 58   0.01432 100.0  1.32    0 0.4110 6.816  40.5  8.3248   5 256    15.1 392.90
## 59   0.15445  25.0  5.13    0 0.4530 6.145  29.2  7.8148   8 284    19.7 390.68
## 60   0.10328  25.0  5.13    0 0.4530 5.927  47.2  6.9320   8 284    19.7 396.90
## 61   0.14932  25.0  5.13    0 0.4530 5.741  66.2  7.2254   8 284    19.7 395.11
## 62   0.17171  25.0  5.13    0 0.4530 5.966  93.4  6.8185   8 284    19.7 378.08
## 63   0.11027  25.0  5.13    0 0.4530 6.456  67.8  7.2255   8 284    19.7 396.90
## 64   0.12650  25.0  5.13    0 0.4530 6.762  43.4  7.9809   8 284    19.7 395.58
## 65   0.01951  17.5  1.38    0 0.4161 7.104  59.5  9.2229   3 216    18.6 393.24
## 66   0.03584  80.0  3.37    0 0.3980 6.290  17.8  6.6115   4 337    16.1 396.90
## 67   0.04379  80.0  3.37    0 0.3980 5.787  31.1  6.6115   4 337    16.1 396.90
## 68   0.05789  12.5  6.07    0 0.4090 5.878  21.4  6.4980   4 345    18.9 396.21
## 69   0.13554  12.5  6.07    0 0.4090 5.594  36.8  6.4980   4 345    18.9 396.90
## 70   0.12816  12.5  6.07    0 0.4090 5.885  33.0  6.4980   4 345    18.9 396.90
## 71   0.08826   0.0 10.81    0 0.4130 6.417   6.6  5.2873   4 305    19.2 383.73
## 72   0.15876   0.0 10.81    0 0.4130 5.961  17.5  5.2873   4 305    19.2 376.94
## 73   0.09164   0.0 10.81    0 0.4130 6.065   7.8  5.2873   4 305    19.2 390.91
## 74   0.19539   0.0 10.81    0 0.4130 6.245   6.2  5.2873   4 305    19.2 377.17
## 75   0.07896   0.0 12.83    0 0.4370 6.273   6.0  4.2515   5 398    18.7 394.92
## 76   0.09512   0.0 12.83    0 0.4370 6.286  45.0  4.5026   5 398    18.7 383.23
## 77   0.10153   0.0 12.83    0 0.4370 6.279  74.5  4.0522   5 398    18.7 373.66
## 78   0.08707   0.0 12.83    0 0.4370 6.140  45.8  4.0905   5 398    18.7 386.96
## 79   0.05646   0.0 12.83    0 0.4370 6.232  53.7  5.0141   5 398    18.7 386.40
## 80   0.08387   0.0 12.83    0 0.4370 5.874  36.6  4.5026   5 398    18.7 396.06
## 81   0.04113  25.0  4.86    0 0.4260 6.727  33.5  5.4007   4 281    19.0 396.90
## 82   0.04462  25.0  4.86    0 0.4260 6.619  70.4  5.4007   4 281    19.0 395.63
## 83   0.03659  25.0  4.86    0 0.4260 6.302  32.2  5.4007   4 281    19.0 396.90
## 84   0.03551  25.0  4.86    0 0.4260 6.167  46.7  5.4007   4 281    19.0 390.64
## 85   0.05059   0.0  4.49    0 0.4490 6.389  48.0  4.7794   3 247    18.5 396.90
## 86   0.05735   0.0  4.49    0 0.4490 6.630  56.1  4.4377   3 247    18.5 392.30
## 87   0.05188   0.0  4.49    0 0.4490 6.015  45.1  4.4272   3 247    18.5 395.99
## 88   0.07151   0.0  4.49    0 0.4490 6.121  56.8  3.7476   3 247    18.5 395.15
## 89   0.05660   0.0  3.41    0 0.4890 7.007  86.3  3.4217   2 270    17.8 396.90
## 90   0.05302   0.0  3.41    0 0.4890 7.079  63.1  3.4145   2 270    17.8 396.06
## 91   0.04684   0.0  3.41    0 0.4890 6.417  66.1  3.0923   2 270    17.8 392.18
## 92   0.03932   0.0  3.41    0 0.4890 6.405  73.9  3.0921   2 270    17.8 393.55
## 93   0.04203  28.0 15.04    0 0.4640 6.442  53.6  3.6659   4 270    18.2 395.01
## 94   0.02875  28.0 15.04    0 0.4640 6.211  28.9  3.6659   4 270    18.2 396.33
## 95   0.04294  28.0 15.04    0 0.4640 6.249  77.3  3.6150   4 270    18.2 396.90
## 96   0.12204   0.0  2.89    0 0.4450 6.625  57.8  3.4952   2 276    18.0 357.98
## 97   0.11504   0.0  2.89    0 0.4450 6.163  69.6  3.4952   2 276    18.0 391.83
## 98   0.12083   0.0  2.89    0 0.4450 8.069  76.0  3.4952   2 276    18.0 396.90
## 99   0.08187   0.0  2.89    0 0.4450 7.820  36.9  3.4952   2 276    18.0 393.53
## 100  0.06860   0.0  2.89    0 0.4450 7.416  62.5  3.4952   2 276    18.0 396.90
## 101  0.14866   0.0  8.56    0 0.5200 6.727  79.9  2.7778   5 384    20.9 394.76
## 102  0.11432   0.0  8.56    0 0.5200 6.781  71.3  2.8561   5 384    20.9 395.58
## 103  0.22876   0.0  8.56    0 0.5200 6.405  85.4  2.7147   5 384    20.9  70.80
## 104  0.21161   0.0  8.56    0 0.5200 6.137  87.4  2.7147   5 384    20.9 394.47
## 105  0.13960   0.0  8.56    0 0.5200 6.167  90.0  2.4210   5 384    20.9 392.69
## 106  0.13262   0.0  8.56    0 0.5200 5.851  96.7  2.1069   5 384    20.9 394.05
## 107  0.17120   0.0  8.56    0 0.5200 5.836  91.9  2.2110   5 384    20.9 395.67
## 108  0.13117   0.0  8.56    0 0.5200 6.127  85.2  2.1224   5 384    20.9 387.69
## 109  0.12802   0.0  8.56    0 0.5200 6.474  97.1  2.4329   5 384    20.9 395.24
## 110  0.26363   0.0  8.56    0 0.5200 6.229  91.2  2.5451   5 384    20.9 391.23
## 111  0.10793   0.0  8.56    0 0.5200 6.195  54.4  2.7778   5 384    20.9 393.49
## 112  0.10084   0.0 10.01    0 0.5470 6.715  81.6  2.6775   6 432    17.8 395.59
## 113  0.12329   0.0 10.01    0 0.5470 5.913  92.9  2.3534   6 432    17.8 394.95
## 114  0.22212   0.0 10.01    0 0.5470 6.092  95.4  2.5480   6 432    17.8 396.90
## 115  0.14231   0.0 10.01    0 0.5470 6.254  84.2  2.2565   6 432    17.8 388.74
## 116  0.17134   0.0 10.01    0 0.5470 5.928  88.2  2.4631   6 432    17.8 344.91
## 117  0.13158   0.0 10.01    0 0.5470 6.176  72.5  2.7301   6 432    17.8 393.30
## 118  0.15098   0.0 10.01    0 0.5470 6.021  82.6  2.7474   6 432    17.8 394.51
## 119  0.13058   0.0 10.01    0 0.5470 5.872  73.1  2.4775   6 432    17.8 338.63
## 120  0.14476   0.0 10.01    0 0.5470 5.731  65.2  2.7592   6 432    17.8 391.50
## 121  0.06899   0.0 25.65    0 0.5810 5.870  69.7  2.2577   2 188    19.1 389.15
## 122  0.07165   0.0 25.65    0 0.5810 6.004  84.1  2.1974   2 188    19.1 377.67
## 123  0.09299   0.0 25.65    0 0.5810 5.961  92.9  2.0869   2 188    19.1 378.09
## 124  0.15038   0.0 25.65    0 0.5810 5.856  97.0  1.9444   2 188    19.1 370.31
## 125  0.09849   0.0 25.65    0 0.5810 5.879  95.8  2.0063   2 188    19.1 379.38
## 126  0.16902   0.0 25.65    0 0.5810 5.986  88.4  1.9929   2 188    19.1 385.02
## 127  0.38735   0.0 25.65    0 0.5810 5.613  95.6  1.7572   2 188    19.1 359.29
## 128  0.25915   0.0 21.89    0 0.6240 5.693  96.0  1.7883   4 437    21.2 392.11
## 129  0.32543   0.0 21.89    0 0.6240 6.431  98.8  1.8125   4 437    21.2 396.90
## 130  0.88125   0.0 21.89    0 0.6240 5.637  94.7  1.9799   4 437    21.2 396.90
## 131  0.34006   0.0 21.89    0 0.6240 6.458  98.9  2.1185   4 437    21.2 395.04
## 132  1.19294   0.0 21.89    0 0.6240 6.326  97.7  2.2710   4 437    21.2 396.90
## 133  0.59005   0.0 21.89    0 0.6240 6.372  97.9  2.3274   4 437    21.2 385.76
## 134  0.32982   0.0 21.89    0 0.6240 5.822  95.4  2.4699   4 437    21.2 388.69
## 135  0.97617   0.0 21.89    0 0.6240 5.757  98.4  2.3460   4 437    21.2 262.76
## 136  0.55778   0.0 21.89    0 0.6240 6.335  98.2  2.1107   4 437    21.2 394.67
## 137  0.32264   0.0 21.89    0 0.6240 5.942  93.5  1.9669   4 437    21.2 378.25
## 138  0.35233   0.0 21.89    0 0.6240 6.454  98.4  1.8498   4 437    21.2 394.08
## 139  0.24980   0.0 21.89    0 0.6240 5.857  98.2  1.6686   4 437    21.2 392.04
## 140  0.54452   0.0 21.89    0 0.6240 6.151  97.9  1.6687   4 437    21.2 396.90
## 141  0.29090   0.0 21.89    0 0.6240 6.174  93.6  1.6119   4 437    21.2 388.08
## 142  1.62864   0.0 21.89    0 0.6240 5.019 100.0  1.4394   4 437    21.2 396.90
## 143  3.32105   0.0 19.58    1 0.8710 5.403 100.0  1.3216   5 403    14.7 396.90
## 144  4.09740   0.0 19.58    0 0.8710 5.468 100.0  1.4118   5 403    14.7 396.90
## 145  2.77974   0.0 19.58    0 0.8710 4.903  97.8  1.3459   5 403    14.7 396.90
## 146  2.37934   0.0 19.58    0 0.8710 6.130 100.0  1.4191   5 403    14.7 172.91
## 147  2.15505   0.0 19.58    0 0.8710 5.628 100.0  1.5166   5 403    14.7 169.27
## 148  2.36862   0.0 19.58    0 0.8710 4.926  95.7  1.4608   5 403    14.7 391.71
## 149  2.33099   0.0 19.58    0 0.8710 5.186  93.8  1.5296   5 403    14.7 356.99
## 150  2.73397   0.0 19.58    0 0.8710 5.597  94.9  1.5257   5 403    14.7 351.85
## 151  1.65660   0.0 19.58    0 0.8710 6.122  97.3  1.6180   5 403    14.7 372.80
## 152  1.49632   0.0 19.58    0 0.8710 5.404 100.0  1.5916   5 403    14.7 341.60
## 153  1.12658   0.0 19.58    1 0.8710 5.012  88.0  1.6102   5 403    14.7 343.28
## 154  2.14918   0.0 19.58    0 0.8710 5.709  98.5  1.6232   5 403    14.7 261.95
## 155  1.41385   0.0 19.58    1 0.8710 6.129  96.0  1.7494   5 403    14.7 321.02
## 156  3.53501   0.0 19.58    1 0.8710 6.152  82.6  1.7455   5 403    14.7  88.01
## 157  2.44668   0.0 19.58    0 0.8710 5.272  94.0  1.7364   5 403    14.7  88.63
## 158  1.22358   0.0 19.58    0 0.6050 6.943  97.4  1.8773   5 403    14.7 363.43
## 159  1.34284   0.0 19.58    0 0.6050 6.066 100.0  1.7573   5 403    14.7 353.89
## 160  1.42502   0.0 19.58    0 0.8710 6.510 100.0  1.7659   5 403    14.7 364.31
## 161  1.27346   0.0 19.58    1 0.6050 6.250  92.6  1.7984   5 403    14.7 338.92
## 162  1.46336   0.0 19.58    0 0.6050 7.489  90.8  1.9709   5 403    14.7 374.43
## 163  1.83377   0.0 19.58    1 0.6050 7.802  98.2  2.0407   5 403    14.7 389.61
## 164  1.51902   0.0 19.58    1 0.6050 8.375  93.9  2.1620   5 403    14.7 388.45
## 165  2.24236   0.0 19.58    0 0.6050 5.854  91.8  2.4220   5 403    14.7 395.11
## 166  2.92400   0.0 19.58    0 0.6050 6.101  93.0  2.2834   5 403    14.7 240.16
## 167  2.01019   0.0 19.58    0 0.6050 7.929  96.2  2.0459   5 403    14.7 369.30
## 168  1.80028   0.0 19.58    0 0.6050 5.877  79.2  2.4259   5 403    14.7 227.61
## 169  2.30040   0.0 19.58    0 0.6050 6.319  96.1  2.1000   5 403    14.7 297.09
## 170  2.44953   0.0 19.58    0 0.6050 6.402  95.2  2.2625   5 403    14.7 330.04
## 171  1.20742   0.0 19.58    0 0.6050 5.875  94.6  2.4259   5 403    14.7 292.29
## 172  2.31390   0.0 19.58    0 0.6050 5.880  97.3  2.3887   5 403    14.7 348.13
## 173  0.13914   0.0  4.05    0 0.5100 5.572  88.5  2.5961   5 296    16.6 396.90
## 174  0.09178   0.0  4.05    0 0.5100 6.416  84.1  2.6463   5 296    16.6 395.50
## 175  0.08447   0.0  4.05    0 0.5100 5.859  68.7  2.7019   5 296    16.6 393.23
## 176  0.06664   0.0  4.05    0 0.5100 6.546  33.1  3.1323   5 296    16.6 390.96
## 177  0.07022   0.0  4.05    0 0.5100 6.020  47.2  3.5549   5 296    16.6 393.23
## 178  0.05425   0.0  4.05    0 0.5100 6.315  73.4  3.3175   5 296    16.6 395.60
## 179  0.06642   0.0  4.05    0 0.5100 6.860  74.4  2.9153   5 296    16.6 391.27
## 180  0.05780   0.0  2.46    0 0.4880 6.980  58.4  2.8290   3 193    17.8 396.90
## 181  0.06588   0.0  2.46    0 0.4880 7.765  83.3  2.7410   3 193    17.8 395.56
## 182  0.06888   0.0  2.46    0 0.4880 6.144  62.2  2.5979   3 193    17.8 396.90
## 183  0.09103   0.0  2.46    0 0.4880 7.155  92.2  2.7006   3 193    17.8 394.12
## 184  0.10008   0.0  2.46    0 0.4880 6.563  95.6  2.8470   3 193    17.8 396.90
## 185  0.08308   0.0  2.46    0 0.4880 5.604  89.8  2.9879   3 193    17.8 391.00
## 186  0.06047   0.0  2.46    0 0.4880 6.153  68.8  3.2797   3 193    17.8 387.11
## 187  0.05602   0.0  2.46    0 0.4880 7.831  53.6  3.1992   3 193    17.8 392.63
## 188  0.07875  45.0  3.44    0 0.4370 6.782  41.1  3.7886   5 398    15.2 393.87
## 189  0.12579  45.0  3.44    0 0.4370 6.556  29.1  4.5667   5 398    15.2 382.84
## 190  0.08370  45.0  3.44    0 0.4370 7.185  38.9  4.5667   5 398    15.2 396.90
## 191  0.09068  45.0  3.44    0 0.4370 6.951  21.5  6.4798   5 398    15.2 377.68
## 192  0.06911  45.0  3.44    0 0.4370 6.739  30.8  6.4798   5 398    15.2 389.71
## 193  0.08664  45.0  3.44    0 0.4370 7.178  26.3  6.4798   5 398    15.2 390.49
## 194  0.02187  60.0  2.93    0 0.4010 6.800   9.9  6.2196   1 265    15.6 393.37
## 195  0.01439  60.0  2.93    0 0.4010 6.604  18.8  6.2196   1 265    15.6 376.70
## 196  0.01381  80.0  0.46    0 0.4220 7.875  32.0  5.6484   4 255    14.4 394.23
## 197  0.04011  80.0  1.52    0 0.4040 7.287  34.1  7.3090   2 329    12.6 396.90
## 198  0.04666  80.0  1.52    0 0.4040 7.107  36.6  7.3090   2 329    12.6 354.31
## 199  0.03768  80.0  1.52    0 0.4040 7.274  38.3  7.3090   2 329    12.6 392.20
## 200  0.03150  95.0  1.47    0 0.4030 6.975  15.3  7.6534   3 402    17.0 396.90
## 201  0.01778  95.0  1.47    0 0.4030 7.135  13.9  7.6534   3 402    17.0 384.30
## 202  0.03445  82.5  2.03    0 0.4150 6.162  38.4  6.2700   2 348    14.7 393.77
## 203  0.02177  82.5  2.03    0 0.4150 7.610  15.7  6.2700   2 348    14.7 395.38
## 204  0.03510  95.0  2.68    0 0.4161 7.853  33.2  5.1180   4 224    14.7 392.78
## 205  0.02009  95.0  2.68    0 0.4161 8.034  31.9  5.1180   4 224    14.7 390.55
## 206  0.13642   0.0 10.59    0 0.4890 5.891  22.3  3.9454   4 277    18.6 396.90
## 207  0.22969   0.0 10.59    0 0.4890 6.326  52.5  4.3549   4 277    18.6 394.87
## 208  0.25199   0.0 10.59    0 0.4890 5.783  72.7  4.3549   4 277    18.6 389.43
## 209  0.13587   0.0 10.59    1 0.4890 6.064  59.1  4.2392   4 277    18.6 381.32
## 210  0.43571   0.0 10.59    1 0.4890 5.344 100.0  3.8750   4 277    18.6 396.90
## 211  0.17446   0.0 10.59    1 0.4890 5.960  92.1  3.8771   4 277    18.6 393.25
## 212  0.37578   0.0 10.59    1 0.4890 5.404  88.6  3.6650   4 277    18.6 395.24
## 213  0.21719   0.0 10.59    1 0.4890 5.807  53.8  3.6526   4 277    18.6 390.94
## 214  0.14052   0.0 10.59    0 0.4890 6.375  32.3  3.9454   4 277    18.6 385.81
## 215  0.28955   0.0 10.59    0 0.4890 5.412   9.8  3.5875   4 277    18.6 348.93
## 216  0.19802   0.0 10.59    0 0.4890 6.182  42.4  3.9454   4 277    18.6 393.63
## 217  0.04560   0.0 13.89    1 0.5500 5.888  56.0  3.1121   5 276    16.4 392.80
## 218  0.07013   0.0 13.89    0 0.5500 6.642  85.1  3.4211   5 276    16.4 392.78
## 219  0.11069   0.0 13.89    1 0.5500 5.951  93.8  2.8893   5 276    16.4 396.90
## 220  0.11425   0.0 13.89    1 0.5500 6.373  92.4  3.3633   5 276    16.4 393.74
## 221  0.35809   0.0  6.20    1 0.5070 6.951  88.5  2.8617   8 307    17.4 391.70
## 222  0.40771   0.0  6.20    1 0.5070 6.164  91.3  3.0480   8 307    17.4 395.24
## 223  0.62356   0.0  6.20    1 0.5070 6.879  77.7  3.2721   8 307    17.4 390.39
## 224  0.61470   0.0  6.20    0 0.5070 6.618  80.8  3.2721   8 307    17.4 396.90
## 225  0.31533   0.0  6.20    0 0.5040 8.266  78.3  2.8944   8 307    17.4 385.05
## 226  0.52693   0.0  6.20    0 0.5040 8.725  83.0  2.8944   8 307    17.4 382.00
## 227  0.38214   0.0  6.20    0 0.5040 8.040  86.5  3.2157   8 307    17.4 387.38
## 228  0.41238   0.0  6.20    0 0.5040 7.163  79.9  3.2157   8 307    17.4 372.08
## 229  0.29819   0.0  6.20    0 0.5040 7.686  17.0  3.3751   8 307    17.4 377.51
## 230  0.44178   0.0  6.20    0 0.5040 6.552  21.4  3.3751   8 307    17.4 380.34
## 231  0.53700   0.0  6.20    0 0.5040 5.981  68.1  3.6715   8 307    17.4 378.35
## 232  0.46296   0.0  6.20    0 0.5040 7.412  76.9  3.6715   8 307    17.4 376.14
## 233  0.57529   0.0  6.20    0 0.5070 8.337  73.3  3.8384   8 307    17.4 385.91
## 234  0.33147   0.0  6.20    0 0.5070 8.247  70.4  3.6519   8 307    17.4 378.95
## 235  0.44791   0.0  6.20    1 0.5070 6.726  66.5  3.6519   8 307    17.4 360.20
## 236  0.33045   0.0  6.20    0 0.5070 6.086  61.5  3.6519   8 307    17.4 376.75
## 237  0.52058   0.0  6.20    1 0.5070 6.631  76.5  4.1480   8 307    17.4 388.45
## 238  0.51183   0.0  6.20    0 0.5070 7.358  71.6  4.1480   8 307    17.4 390.07
## 239  0.08244  30.0  4.93    0 0.4280 6.481  18.5  6.1899   6 300    16.6 379.41
## 240  0.09252  30.0  4.93    0 0.4280 6.606  42.2  6.1899   6 300    16.6 383.78
## 241  0.11329  30.0  4.93    0 0.4280 6.897  54.3  6.3361   6 300    16.6 391.25
## 242  0.10612  30.0  4.93    0 0.4280 6.095  65.1  6.3361   6 300    16.6 394.62
## 243  0.10290  30.0  4.93    0 0.4280 6.358  52.9  7.0355   6 300    16.6 372.75
## 244  0.12757  30.0  4.93    0 0.4280 6.393   7.8  7.0355   6 300    16.6 374.71
## 245  0.20608  22.0  5.86    0 0.4310 5.593  76.5  7.9549   7 330    19.1 372.49
## 246  0.19133  22.0  5.86    0 0.4310 5.605  70.2  7.9549   7 330    19.1 389.13
## 247  0.33983  22.0  5.86    0 0.4310 6.108  34.9  8.0555   7 330    19.1 390.18
## 248  0.19657  22.0  5.86    0 0.4310 6.226  79.2  8.0555   7 330    19.1 376.14
## 249  0.16439  22.0  5.86    0 0.4310 6.433  49.1  7.8265   7 330    19.1 374.71
## 250  0.19073  22.0  5.86    0 0.4310 6.718  17.5  7.8265   7 330    19.1 393.74
## 251  0.14030  22.0  5.86    0 0.4310 6.487  13.0  7.3967   7 330    19.1 396.28
## 252  0.21409  22.0  5.86    0 0.4310 6.438   8.9  7.3967   7 330    19.1 377.07
## 253  0.08221  22.0  5.86    0 0.4310 6.957   6.8  8.9067   7 330    19.1 386.09
## 254  0.36894  22.0  5.86    0 0.4310 8.259   8.4  8.9067   7 330    19.1 396.90
## 255  0.04819  80.0  3.64    0 0.3920 6.108  32.0  9.2203   1 315    16.4 392.89
## 256  0.03548  80.0  3.64    0 0.3920 5.876  19.1  9.2203   1 315    16.4 395.18
## 257  0.01538  90.0  3.75    0 0.3940 7.454  34.2  6.3361   3 244    15.9 386.34
## 258  0.61154  20.0  3.97    0 0.6470 8.704  86.9  1.8010   5 264    13.0 389.70
## 259  0.66351  20.0  3.97    0 0.6470 7.333 100.0  1.8946   5 264    13.0 383.29
## 260  0.65665  20.0  3.97    0 0.6470 6.842 100.0  2.0107   5 264    13.0 391.93
## 261  0.54011  20.0  3.97    0 0.6470 7.203  81.8  2.1121   5 264    13.0 392.80
## 262  0.53412  20.0  3.97    0 0.6470 7.520  89.4  2.1398   5 264    13.0 388.37
## 263  0.52014  20.0  3.97    0 0.6470 8.398  91.5  2.2885   5 264    13.0 386.86
## 264  0.82526  20.0  3.97    0 0.6470 7.327  94.5  2.0788   5 264    13.0 393.42
## 265  0.55007  20.0  3.97    0 0.6470 7.206  91.6  1.9301   5 264    13.0 387.89
## 266  0.76162  20.0  3.97    0 0.6470 5.560  62.8  1.9865   5 264    13.0 392.40
## 267  0.78570  20.0  3.97    0 0.6470 7.014  84.6  2.1329   5 264    13.0 384.07
## 268  0.57834  20.0  3.97    0 0.5750 8.297  67.0  2.4216   5 264    13.0 384.54
## 269  0.54050  20.0  3.97    0 0.5750 7.470  52.6  2.8720   5 264    13.0 390.30
## 270  0.09065  20.0  6.96    1 0.4640 5.920  61.5  3.9175   3 223    18.6 391.34
## 271  0.29916  20.0  6.96    0 0.4640 5.856  42.1  4.4290   3 223    18.6 388.65
## 272  0.16211  20.0  6.96    0 0.4640 6.240  16.3  4.4290   3 223    18.6 396.90
## 273  0.11460  20.0  6.96    0 0.4640 6.538  58.7  3.9175   3 223    18.6 394.96
## 274  0.22188  20.0  6.96    1 0.4640 7.691  51.8  4.3665   3 223    18.6 390.77
## 275  0.05644  40.0  6.41    1 0.4470 6.758  32.9  4.0776   4 254    17.6 396.90
## 276  0.09604  40.0  6.41    0 0.4470 6.854  42.8  4.2673   4 254    17.6 396.90
## 277  0.10469  40.0  6.41    1 0.4470 7.267  49.0  4.7872   4 254    17.6 389.25
## 278  0.06127  40.0  6.41    1 0.4470 6.826  27.6  4.8628   4 254    17.6 393.45
## 279  0.07978  40.0  6.41    0 0.4470 6.482  32.1  4.1403   4 254    17.6 396.90
## 280  0.21038  20.0  3.33    0 0.4429 6.812  32.2  4.1007   5 216    14.9 396.90
## 281  0.03578  20.0  3.33    0 0.4429 7.820  64.5  4.6947   5 216    14.9 387.31
## 282  0.03705  20.0  3.33    0 0.4429 6.968  37.2  5.2447   5 216    14.9 392.23
## 283  0.06129  20.0  3.33    1 0.4429 7.645  49.7  5.2119   5 216    14.9 377.07
## 284  0.01501  90.0  1.21    1 0.4010 7.923  24.8  5.8850   1 198    13.6 395.52
## 285  0.00906  90.0  2.97    0 0.4000 7.088  20.8  7.3073   1 285    15.3 394.72
## 286  0.01096  55.0  2.25    0 0.3890 6.453  31.9  7.3073   1 300    15.3 394.72
## 287  0.01965  80.0  1.76    0 0.3850 6.230  31.5  9.0892   1 241    18.2 341.60
## 288  0.03871  52.5  5.32    0 0.4050 6.209  31.3  7.3172   6 293    16.6 396.90
## 289  0.04590  52.5  5.32    0 0.4050 6.315  45.6  7.3172   6 293    16.6 396.90
## 290  0.04297  52.5  5.32    0 0.4050 6.565  22.9  7.3172   6 293    16.6 371.72
## 291  0.03502  80.0  4.95    0 0.4110 6.861  27.9  5.1167   4 245    19.2 396.90
## 292  0.07886  80.0  4.95    0 0.4110 7.148  27.7  5.1167   4 245    19.2 396.90
## 293  0.03615  80.0  4.95    0 0.4110 6.630  23.4  5.1167   4 245    19.2 396.90
## 294  0.08265   0.0 13.92    0 0.4370 6.127  18.4  5.5027   4 289    16.0 396.90
## 295  0.08199   0.0 13.92    0 0.4370 6.009  42.3  5.5027   4 289    16.0 396.90
## 296  0.12932   0.0 13.92    0 0.4370 6.678  31.1  5.9604   4 289    16.0 396.90
## 297  0.05372   0.0 13.92    0 0.4370 6.549  51.0  5.9604   4 289    16.0 392.85
## 298  0.14103   0.0 13.92    0 0.4370 5.790  58.0  6.3200   4 289    16.0 396.90
## 299  0.06466  70.0  2.24    0 0.4000 6.345  20.1  7.8278   5 358    14.8 368.24
## 300  0.05561  70.0  2.24    0 0.4000 7.041  10.0  7.8278   5 358    14.8 371.58
## 301  0.04417  70.0  2.24    0 0.4000 6.871  47.4  7.8278   5 358    14.8 390.86
## 302  0.03537  34.0  6.09    0 0.4330 6.590  40.4  5.4917   7 329    16.1 395.75
## 303  0.09266  34.0  6.09    0 0.4330 6.495  18.4  5.4917   7 329    16.1 383.61
## 304  0.10000  34.0  6.09    0 0.4330 6.982  17.7  5.4917   7 329    16.1 390.43
## 305  0.05515  33.0  2.18    0 0.4720 7.236  41.1  4.0220   7 222    18.4 393.68
## 306  0.05479  33.0  2.18    0 0.4720 6.616  58.1  3.3700   7 222    18.4 393.36
## 307  0.07503  33.0  2.18    0 0.4720 7.420  71.9  3.0992   7 222    18.4 396.90
## 308  0.04932  33.0  2.18    0 0.4720 6.849  70.3  3.1827   7 222    18.4 396.90
## 309  0.49298   0.0  9.90    0 0.5440 6.635  82.5  3.3175   4 304    18.4 396.90
## 310  0.34940   0.0  9.90    0 0.5440 5.972  76.7  3.1025   4 304    18.4 396.24
## 311  2.63548   0.0  9.90    0 0.5440 4.973  37.8  2.5194   4 304    18.4 350.45
## 312  0.79041   0.0  9.90    0 0.5440 6.122  52.8  2.6403   4 304    18.4 396.90
## 313  0.26169   0.0  9.90    0 0.5440 6.023  90.4  2.8340   4 304    18.4 396.30
## 314  0.26938   0.0  9.90    0 0.5440 6.266  82.8  3.2628   4 304    18.4 393.39
## 315  0.36920   0.0  9.90    0 0.5440 6.567  87.3  3.6023   4 304    18.4 395.69
## 316  0.25356   0.0  9.90    0 0.5440 5.705  77.7  3.9450   4 304    18.4 396.42
## 317  0.31827   0.0  9.90    0 0.5440 5.914  83.2  3.9986   4 304    18.4 390.70
## 318  0.24522   0.0  9.90    0 0.5440 5.782  71.7  4.0317   4 304    18.4 396.90
## 319  0.40202   0.0  9.90    0 0.5440 6.382  67.2  3.5325   4 304    18.4 395.21
## 320  0.47547   0.0  9.90    0 0.5440 6.113  58.8  4.0019   4 304    18.4 396.23
## 321  0.16760   0.0  7.38    0 0.4930 6.426  52.3  4.5404   5 287    19.6 396.90
## 322  0.18159   0.0  7.38    0 0.4930 6.376  54.3  4.5404   5 287    19.6 396.90
## 323  0.35114   0.0  7.38    0 0.4930 6.041  49.9  4.7211   5 287    19.6 396.90
## 324  0.28392   0.0  7.38    0 0.4930 5.708  74.3  4.7211   5 287    19.6 391.13
## 325  0.34109   0.0  7.38    0 0.4930 6.415  40.1  4.7211   5 287    19.6 396.90
## 326  0.19186   0.0  7.38    0 0.4930 6.431  14.7  5.4159   5 287    19.6 393.68
## 327  0.30347   0.0  7.38    0 0.4930 6.312  28.9  5.4159   5 287    19.6 396.90
## 328  0.24103   0.0  7.38    0 0.4930 6.083  43.7  5.4159   5 287    19.6 396.90
## 329  0.06617   0.0  3.24    0 0.4600 5.868  25.8  5.2146   4 430    16.9 382.44
## 330  0.06724   0.0  3.24    0 0.4600 6.333  17.2  5.2146   4 430    16.9 375.21
## 331  0.04544   0.0  3.24    0 0.4600 6.144  32.2  5.8736   4 430    16.9 368.57
## 332  0.05023  35.0  6.06    0 0.4379 5.706  28.4  6.6407   1 304    16.9 394.02
## 333  0.03466  35.0  6.06    0 0.4379 6.031  23.3  6.6407   1 304    16.9 362.25
## 334  0.05083   0.0  5.19    0 0.5150 6.316  38.1  6.4584   5 224    20.2 389.71
## 335  0.03738   0.0  5.19    0 0.5150 6.310  38.5  6.4584   5 224    20.2 389.40
## 336  0.03961   0.0  5.19    0 0.5150 6.037  34.5  5.9853   5 224    20.2 396.90
## 337  0.03427   0.0  5.19    0 0.5150 5.869  46.3  5.2311   5 224    20.2 396.90
## 338  0.03041   0.0  5.19    0 0.5150 5.895  59.6  5.6150   5 224    20.2 394.81
## 339  0.03306   0.0  5.19    0 0.5150 6.059  37.3  4.8122   5 224    20.2 396.14
## 340  0.05497   0.0  5.19    0 0.5150 5.985  45.4  4.8122   5 224    20.2 396.90
## 341  0.06151   0.0  5.19    0 0.5150 5.968  58.5  4.8122   5 224    20.2 396.90
## 342  0.01301  35.0  1.52    0 0.4420 7.241  49.3  7.0379   1 284    15.5 394.74
## 343  0.02498   0.0  1.89    0 0.5180 6.540  59.7  6.2669   1 422    15.9 389.96
## 344  0.02543  55.0  3.78    0 0.4840 6.696  56.4  5.7321   5 370    17.6 396.90
## 345  0.03049  55.0  3.78    0 0.4840 6.874  28.1  6.4654   5 370    17.6 387.97
## 346  0.03113   0.0  4.39    0 0.4420 6.014  48.5  8.0136   3 352    18.8 385.64
## 347  0.06162   0.0  4.39    0 0.4420 5.898  52.3  8.0136   3 352    18.8 364.61
## 348  0.01870  85.0  4.15    0 0.4290 6.516  27.7  8.5353   4 351    17.9 392.43
## 349  0.01501  80.0  2.01    0 0.4350 6.635  29.7  8.3440   4 280    17.0 390.94
## 350  0.02899  40.0  1.25    0 0.4290 6.939  34.5  8.7921   1 335    19.7 389.85
## 351  0.06211  40.0  1.25    0 0.4290 6.490  44.4  8.7921   1 335    19.7 396.90
## 352  0.07950  60.0  1.69    0 0.4110 6.579  35.9 10.7103   4 411    18.3 370.78
## 353  0.07244  60.0  1.69    0 0.4110 5.884  18.5 10.7103   4 411    18.3 392.33
## 354  0.01709  90.0  2.02    0 0.4100 6.728  36.1 12.1265   5 187    17.0 384.46
## 355  0.04301  80.0  1.91    0 0.4130 5.663  21.9 10.5857   4 334    22.0 382.80
## 356  0.10659  80.0  1.91    0 0.4130 5.936  19.5 10.5857   4 334    22.0 376.04
## 357  8.98296   0.0 18.10    1 0.7700 6.212  97.4  2.1222  24 666    20.2 377.73
## 358  3.84970   0.0 18.10    1 0.7700 6.395  91.0  2.5052  24 666    20.2 391.34
## 359  5.20177   0.0 18.10    1 0.7700 6.127  83.4  2.7227  24 666    20.2 395.43
## 360  4.26131   0.0 18.10    0 0.7700 6.112  81.3  2.5091  24 666    20.2 390.74
## 361  4.54192   0.0 18.10    0 0.7700 6.398  88.0  2.5182  24 666    20.2 374.56
## 362  3.83684   0.0 18.10    0 0.7700 6.251  91.1  2.2955  24 666    20.2 350.65
## 363  3.67822   0.0 18.10    0 0.7700 5.362  96.2  2.1036  24 666    20.2 380.79
## 364  4.22239   0.0 18.10    1 0.7700 5.803  89.0  1.9047  24 666    20.2 353.04
## 365  3.47428   0.0 18.10    1 0.7180 8.780  82.9  1.9047  24 666    20.2 354.55
## 366  4.55587   0.0 18.10    0 0.7180 3.561  87.9  1.6132  24 666    20.2 354.70
## 367  3.69695   0.0 18.10    0 0.7180 4.963  91.4  1.7523  24 666    20.2 316.03
## 368 13.52220   0.0 18.10    0 0.6310 3.863 100.0  1.5106  24 666    20.2 131.42
## 369  4.89822   0.0 18.10    0 0.6310 4.970 100.0  1.3325  24 666    20.2 375.52
## 370  5.66998   0.0 18.10    1 0.6310 6.683  96.8  1.3567  24 666    20.2 375.33
## 371  6.53876   0.0 18.10    1 0.6310 7.016  97.5  1.2024  24 666    20.2 392.05
## 372  9.23230   0.0 18.10    0 0.6310 6.216 100.0  1.1691  24 666    20.2 366.15
## 373  8.26725   0.0 18.10    1 0.6680 5.875  89.6  1.1296  24 666    20.2 347.88
## 374 11.10810   0.0 18.10    0 0.6680 4.906 100.0  1.1742  24 666    20.2 396.90
## 375 18.49820   0.0 18.10    0 0.6680 4.138 100.0  1.1370  24 666    20.2 396.90
## 376 19.60910   0.0 18.10    0 0.6710 7.313  97.9  1.3163  24 666    20.2 396.90
## 377 15.28800   0.0 18.10    0 0.6710 6.649  93.3  1.3449  24 666    20.2 363.02
## 378  9.82349   0.0 18.10    0 0.6710 6.794  98.8  1.3580  24 666    20.2 396.90
## 379 23.64820   0.0 18.10    0 0.6710 6.380  96.2  1.3861  24 666    20.2 396.90
## 380 17.86670   0.0 18.10    0 0.6710 6.223 100.0  1.3861  24 666    20.2 393.74
## 381 88.97620   0.0 18.10    0 0.6710 6.968  91.9  1.4165  24 666    20.2 396.90
## 382 15.87440   0.0 18.10    0 0.6710 6.545  99.1  1.5192  24 666    20.2 396.90
## 383  9.18702   0.0 18.10    0 0.7000 5.536 100.0  1.5804  24 666    20.2 396.90
## 384  7.99248   0.0 18.10    0 0.7000 5.520 100.0  1.5331  24 666    20.2 396.90
## 385 20.08490   0.0 18.10    0 0.7000 4.368  91.2  1.4395  24 666    20.2 285.83
## 386 16.81180   0.0 18.10    0 0.7000 5.277  98.1  1.4261  24 666    20.2 396.90
## 387 24.39380   0.0 18.10    0 0.7000 4.652 100.0  1.4672  24 666    20.2 396.90
## 388 22.59710   0.0 18.10    0 0.7000 5.000  89.5  1.5184  24 666    20.2 396.90
## 389 14.33370   0.0 18.10    0 0.7000 4.880 100.0  1.5895  24 666    20.2 372.92
## 390  8.15174   0.0 18.10    0 0.7000 5.390  98.9  1.7281  24 666    20.2 396.90
## 391  6.96215   0.0 18.10    0 0.7000 5.713  97.0  1.9265  24 666    20.2 394.43
## 392  5.29305   0.0 18.10    0 0.7000 6.051  82.5  2.1678  24 666    20.2 378.38
## 393 11.57790   0.0 18.10    0 0.7000 5.036  97.0  1.7700  24 666    20.2 396.90
## 394  8.64476   0.0 18.10    0 0.6930 6.193  92.6  1.7912  24 666    20.2 396.90
## 395 13.35980   0.0 18.10    0 0.6930 5.887  94.7  1.7821  24 666    20.2 396.90
## 396  8.71675   0.0 18.10    0 0.6930 6.471  98.8  1.7257  24 666    20.2 391.98
## 397  5.87205   0.0 18.10    0 0.6930 6.405  96.0  1.6768  24 666    20.2 396.90
## 398  7.67202   0.0 18.10    0 0.6930 5.747  98.9  1.6334  24 666    20.2 393.10
## 399 38.35180   0.0 18.10    0 0.6930 5.453 100.0  1.4896  24 666    20.2 396.90
## 400  9.91655   0.0 18.10    0 0.6930 5.852  77.8  1.5004  24 666    20.2 338.16
## 401 25.04610   0.0 18.10    0 0.6930 5.987 100.0  1.5888  24 666    20.2 396.90
## 402 14.23620   0.0 18.10    0 0.6930 6.343 100.0  1.5741  24 666    20.2 396.90
## 403  9.59571   0.0 18.10    0 0.6930 6.404 100.0  1.6390  24 666    20.2 376.11
## 404 24.80170   0.0 18.10    0 0.6930 5.349  96.0  1.7028  24 666    20.2 396.90
## 405 41.52920   0.0 18.10    0 0.6930 5.531  85.4  1.6074  24 666    20.2 329.46
## 406 67.92080   0.0 18.10    0 0.6930 5.683 100.0  1.4254  24 666    20.2 384.97
## 407 20.71620   0.0 18.10    0 0.6590 4.138 100.0  1.1781  24 666    20.2 370.22
## 408 11.95110   0.0 18.10    0 0.6590 5.608 100.0  1.2852  24 666    20.2 332.09
## 409  7.40389   0.0 18.10    0 0.5970 5.617  97.9  1.4547  24 666    20.2 314.64
## 410 14.43830   0.0 18.10    0 0.5970 6.852 100.0  1.4655  24 666    20.2 179.36
## 411 51.13580   0.0 18.10    0 0.5970 5.757 100.0  1.4130  24 666    20.2   2.60
## 412 14.05070   0.0 18.10    0 0.5970 6.657 100.0  1.5275  24 666    20.2  35.05
## 413 18.81100   0.0 18.10    0 0.5970 4.628 100.0  1.5539  24 666    20.2  28.79
## 414 28.65580   0.0 18.10    0 0.5970 5.155 100.0  1.5894  24 666    20.2 210.97
## 415 45.74610   0.0 18.10    0 0.6930 4.519 100.0  1.6582  24 666    20.2  88.27
## 416 18.08460   0.0 18.10    0 0.6790 6.434 100.0  1.8347  24 666    20.2  27.25
## 417 10.83420   0.0 18.10    0 0.6790 6.782  90.8  1.8195  24 666    20.2  21.57
## 418 25.94060   0.0 18.10    0 0.6790 5.304  89.1  1.6475  24 666    20.2 127.36
## 419 73.53410   0.0 18.10    0 0.6790 5.957 100.0  1.8026  24 666    20.2  16.45
## 420 11.81230   0.0 18.10    0 0.7180 6.824  76.5  1.7940  24 666    20.2  48.45
## 421 11.08740   0.0 18.10    0 0.7180 6.411 100.0  1.8589  24 666    20.2 318.75
## 422  7.02259   0.0 18.10    0 0.7180 6.006  95.3  1.8746  24 666    20.2 319.98
## 423 12.04820   0.0 18.10    0 0.6140 5.648  87.6  1.9512  24 666    20.2 291.55
## 424  7.05042   0.0 18.10    0 0.6140 6.103  85.1  2.0218  24 666    20.2   2.52
## 425  8.79212   0.0 18.10    0 0.5840 5.565  70.6  2.0635  24 666    20.2   3.65
## 426 15.86030   0.0 18.10    0 0.6790 5.896  95.4  1.9096  24 666    20.2   7.68
## 427 12.24720   0.0 18.10    0 0.5840 5.837  59.7  1.9976  24 666    20.2  24.65
## 428 37.66190   0.0 18.10    0 0.6790 6.202  78.7  1.8629  24 666    20.2  18.82
## 429  7.36711   0.0 18.10    0 0.6790 6.193  78.1  1.9356  24 666    20.2  96.73
## 430  9.33889   0.0 18.10    0 0.6790 6.380  95.6  1.9682  24 666    20.2  60.72
## 431  8.49213   0.0 18.10    0 0.5840 6.348  86.1  2.0527  24 666    20.2  83.45
## 432 10.06230   0.0 18.10    0 0.5840 6.833  94.3  2.0882  24 666    20.2  81.33
## 433  6.44405   0.0 18.10    0 0.5840 6.425  74.8  2.2004  24 666    20.2  97.95
## 434  5.58107   0.0 18.10    0 0.7130 6.436  87.9  2.3158  24 666    20.2 100.19
## 435 13.91340   0.0 18.10    0 0.7130 6.208  95.0  2.2222  24 666    20.2 100.63
## 436 11.16040   0.0 18.10    0 0.7400 6.629  94.6  2.1247  24 666    20.2 109.85
## 437 14.42080   0.0 18.10    0 0.7400 6.461  93.3  2.0026  24 666    20.2  27.49
## 438 15.17720   0.0 18.10    0 0.7400 6.152 100.0  1.9142  24 666    20.2   9.32
## 439 13.67810   0.0 18.10    0 0.7400 5.935  87.9  1.8206  24 666    20.2  68.95
## 440  9.39063   0.0 18.10    0 0.7400 5.627  93.9  1.8172  24 666    20.2 396.90
## 441 22.05110   0.0 18.10    0 0.7400 5.818  92.4  1.8662  24 666    20.2 391.45
## 442  9.72418   0.0 18.10    0 0.7400 6.406  97.2  2.0651  24 666    20.2 385.96
## 443  5.66637   0.0 18.10    0 0.7400 6.219 100.0  2.0048  24 666    20.2 395.69
## 444  9.96654   0.0 18.10    0 0.7400 6.485 100.0  1.9784  24 666    20.2 386.73
## 445 12.80230   0.0 18.10    0 0.7400 5.854  96.6  1.8956  24 666    20.2 240.52
## 446 10.67180   0.0 18.10    0 0.7400 6.459  94.8  1.9879  24 666    20.2  43.06
## 447  6.28807   0.0 18.10    0 0.7400 6.341  96.4  2.0720  24 666    20.2 318.01
## 448  9.92485   0.0 18.10    0 0.7400 6.251  96.6  2.1980  24 666    20.2 388.52
## 449  9.32909   0.0 18.10    0 0.7130 6.185  98.7  2.2616  24 666    20.2 396.90
## 450  7.52601   0.0 18.10    0 0.7130 6.417  98.3  2.1850  24 666    20.2 304.21
## 451  6.71772   0.0 18.10    0 0.7130 6.749  92.6  2.3236  24 666    20.2   0.32
## 452  5.44114   0.0 18.10    0 0.7130 6.655  98.2  2.3552  24 666    20.2 355.29
## 453  5.09017   0.0 18.10    0 0.7130 6.297  91.8  2.3682  24 666    20.2 385.09
## 454  8.24809   0.0 18.10    0 0.7130 7.393  99.3  2.4527  24 666    20.2 375.87
## 455  9.51363   0.0 18.10    0 0.7130 6.728  94.1  2.4961  24 666    20.2   6.68
## 456  4.75237   0.0 18.10    0 0.7130 6.525  86.5  2.4358  24 666    20.2  50.92
## 457  4.66883   0.0 18.10    0 0.7130 5.976  87.9  2.5806  24 666    20.2  10.48
## 458  8.20058   0.0 18.10    0 0.7130 5.936  80.3  2.7792  24 666    20.2   3.50
## 459  7.75223   0.0 18.10    0 0.7130 6.301  83.7  2.7831  24 666    20.2 272.21
## 460  6.80117   0.0 18.10    0 0.7130 6.081  84.4  2.7175  24 666    20.2 396.90
## 461  4.81213   0.0 18.10    0 0.7130 6.701  90.0  2.5975  24 666    20.2 255.23
## 462  3.69311   0.0 18.10    0 0.7130 6.376  88.4  2.5671  24 666    20.2 391.43
## 463  6.65492   0.0 18.10    0 0.7130 6.317  83.0  2.7344  24 666    20.2 396.90
## 464  5.82115   0.0 18.10    0 0.7130 6.513  89.9  2.8016  24 666    20.2 393.82
## 465  7.83932   0.0 18.10    0 0.6550 6.209  65.4  2.9634  24 666    20.2 396.90
## 466  3.16360   0.0 18.10    0 0.6550 5.759  48.2  3.0665  24 666    20.2 334.40
## 467  3.77498   0.0 18.10    0 0.6550 5.952  84.7  2.8715  24 666    20.2  22.01
## 468  4.42228   0.0 18.10    0 0.5840 6.003  94.5  2.5403  24 666    20.2 331.29
## 469 15.57570   0.0 18.10    0 0.5800 5.926  71.0  2.9084  24 666    20.2 368.74
## 470 13.07510   0.0 18.10    0 0.5800 5.713  56.7  2.8237  24 666    20.2 396.90
## 471  4.34879   0.0 18.10    0 0.5800 6.167  84.0  3.0334  24 666    20.2 396.90
## 472  4.03841   0.0 18.10    0 0.5320 6.229  90.7  3.0993  24 666    20.2 395.33
## 473  3.56868   0.0 18.10    0 0.5800 6.437  75.0  2.8965  24 666    20.2 393.37
## 474  4.64689   0.0 18.10    0 0.6140 6.980  67.6  2.5329  24 666    20.2 374.68
## 475  8.05579   0.0 18.10    0 0.5840 5.427  95.4  2.4298  24 666    20.2 352.58
## 476  6.39312   0.0 18.10    0 0.5840 6.162  97.4  2.2060  24 666    20.2 302.76
## 477  4.87141   0.0 18.10    0 0.6140 6.484  93.6  2.3053  24 666    20.2 396.21
## 478 15.02340   0.0 18.10    0 0.6140 5.304  97.3  2.1007  24 666    20.2 349.48
## 479 10.23300   0.0 18.10    0 0.6140 6.185  96.7  2.1705  24 666    20.2 379.70
## 480 14.33370   0.0 18.10    0 0.6140 6.229  88.0  1.9512  24 666    20.2 383.32
## 481  5.82401   0.0 18.10    0 0.5320 6.242  64.7  3.4242  24 666    20.2 396.90
## 482  5.70818   0.0 18.10    0 0.5320 6.750  74.9  3.3317  24 666    20.2 393.07
## 483  5.73116   0.0 18.10    0 0.5320 7.061  77.0  3.4106  24 666    20.2 395.28
## 484  2.81838   0.0 18.10    0 0.5320 5.762  40.3  4.0983  24 666    20.2 392.92
## 485  2.37857   0.0 18.10    0 0.5830 5.871  41.9  3.7240  24 666    20.2 370.73
## 486  3.67367   0.0 18.10    0 0.5830 6.312  51.9  3.9917  24 666    20.2 388.62
## 487  5.69175   0.0 18.10    0 0.5830 6.114  79.8  3.5459  24 666    20.2 392.68
## 488  4.83567   0.0 18.10    0 0.5830 5.905  53.2  3.1523  24 666    20.2 388.22
## 489  0.15086   0.0 27.74    0 0.6090 5.454  92.7  1.8209   4 711    20.1 395.09
## 490  0.18337   0.0 27.74    0 0.6090 5.414  98.3  1.7554   4 711    20.1 344.05
## 491  0.20746   0.0 27.74    0 0.6090 5.093  98.0  1.8226   4 711    20.1 318.43
## 492  0.10574   0.0 27.74    0 0.6090 5.983  98.8  1.8681   4 711    20.1 390.11
## 493  0.11132   0.0 27.74    0 0.6090 5.983  83.5  2.1099   4 711    20.1 396.90
## 494  0.17331   0.0  9.69    0 0.5850 5.707  54.0  2.3817   6 391    19.2 396.90
## 495  0.27957   0.0  9.69    0 0.5850 5.926  42.6  2.3817   6 391    19.2 396.90
## 496  0.17899   0.0  9.69    0 0.5850 5.670  28.8  2.7986   6 391    19.2 393.29
## 497  0.28960   0.0  9.69    0 0.5850 5.390  72.9  2.7986   6 391    19.2 396.90
## 498  0.26838   0.0  9.69    0 0.5850 5.794  70.6  2.8927   6 391    19.2 396.90
## 499  0.23912   0.0  9.69    0 0.5850 6.019  65.3  2.4091   6 391    19.2 396.90
## 500  0.17783   0.0  9.69    0 0.5850 5.569  73.5  2.3999   6 391    19.2 395.77
## 501  0.22438   0.0  9.69    0 0.5850 6.027  79.7  2.4982   6 391    19.2 396.90
## 502  0.06263   0.0 11.93    0 0.5730 6.593  69.1  2.4786   1 273    21.0 391.99
## 503  0.04527   0.0 11.93    0 0.5730 6.120  76.7  2.2875   1 273    21.0 396.90
## 504  0.06076   0.0 11.93    0 0.5730 6.976  91.0  2.1675   1 273    21.0 396.90
## 505  0.10959   0.0 11.93    0 0.5730 6.794  89.3  2.3889   1 273    21.0 393.45
## 506  0.04741   0.0 11.93    0 0.5730 6.030  80.8  2.5050   1 273    21.0 396.90
##     lstat medv
## 1    4.98 24.0
## 2    9.14 21.6
## 3    4.03 34.7
## 4    2.94 33.4
## 5    5.33 36.2
## 6    5.21 28.7
## 7   12.43 22.9
## 8   19.15 27.1
## 9   29.93 16.5
## 10  17.10 18.9
## 11  20.45 15.0
## 12  13.27 18.9
## 13  15.71 21.7
## 14   8.26 20.4
## 15  10.26 18.2
## 16   8.47 19.9
## 17   6.58 23.1
## 18  14.67 17.5
## 19  11.69 20.2
## 20  11.28 18.2
## 21  21.02 13.6
## 22  13.83 19.6
## 23  18.72 15.2
## 24  19.88 14.5
## 25  16.30 15.6
## 26  16.51 13.9
## 27  14.81 16.6
## 28  17.28 14.8
## 29  12.80 18.4
## 30  11.98 21.0
## 31  22.60 12.7
## 32  13.04 14.5
## 33  27.71 13.2
## 34  18.35 13.1
## 35  20.34 13.5
## 36   9.68 18.9
## 37  11.41 20.0
## 38   8.77 21.0
## 39  10.13 24.7
## 40   4.32 30.8
## 41   1.98 34.9
## 42   4.84 26.6
## 43   5.81 25.3
## 44   7.44 24.7
## 45   9.55 21.2
## 46  10.21 19.3
## 47  14.15 20.0
## 48  18.80 16.6
## 49  30.81 14.4
## 50  16.20 19.4
## 51  13.45 19.7
## 52   9.43 20.5
## 53   5.28 25.0
## 54   8.43 23.4
## 55  14.80 18.9
## 56   4.81 35.4
## 57   5.77 24.7
## 58   3.95 31.6
## 59   6.86 23.3
## 60   9.22 19.6
## 61  13.15 18.7
## 62  14.44 16.0
## 63   6.73 22.2
## 64   9.50 25.0
## 65   8.05 33.0
## 66   4.67 23.5
## 67  10.24 19.4
## 68   8.10 22.0
## 69  13.09 17.4
## 70   8.79 20.9
## 71   6.72 24.2
## 72   9.88 21.7
## 73   5.52 22.8
## 74   7.54 23.4
## 75   6.78 24.1
## 76   8.94 21.4
## 77  11.97 20.0
## 78  10.27 20.8
## 79  12.34 21.2
## 80   9.10 20.3
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## 96   6.65 28.4
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## 105 12.33 20.1
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## 107 18.66 19.5
## 108 14.09 20.4
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## 110 15.55 19.4
## 111 13.00 21.7
## 112 10.16 22.8
## 113 16.21 18.8
## 114 17.09 18.7
## 115 10.45 18.5
## 116 15.76 18.3
## 117 12.04 21.2
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## 119 15.37 20.4
## 120 13.61 19.3
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## 131 12.60 19.2
## 132 12.26 19.6
## 133 11.12 23.0
## 134 15.03 18.4
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## 139 21.32 13.3
## 140 18.46 17.8
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## 142 34.41 14.4
## 143 26.82 13.4
## 144 26.42 15.6
## 145 29.29 11.8
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## 155 15.12 17.0
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## 157 16.14 13.1
## 158  4.59 41.3
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## 161  5.50 27.0
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## 165 11.64 22.7
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## 171 14.43 17.4
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## 271 13.00 21.1
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## 313 11.72 19.4
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## 316 11.50 16.2
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## 384 24.56 12.3
## 385 30.63  8.8
## 386 30.81  7.2
## 387 28.28 10.5
## 388 31.99  7.4
## 389 30.62 10.2
## 390 20.85 11.5
## 391 17.11 15.1
## 392 18.76 23.2
## 393 25.68  9.7
## 394 15.17 13.8
## 395 16.35 12.7
## 396 17.12 13.1
## 397 19.37 12.5
## 398 19.92  8.5
## 399 30.59  5.0
## 400 29.97  6.3
## 401 26.77  5.6
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## 405 27.38  8.5
## 406 22.98  5.0
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## 409 26.40 17.2
## 410 19.78 27.5
## 411 10.11 15.0
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## 413 34.37 17.9
## 414 20.08 16.3
## 415 36.98  7.0
## 416 29.05  7.2
## 417 25.79  7.5
## 418 26.64 10.4
## 419 20.62  8.8
## 420 22.74  8.4
## 421 15.02 16.7
## 422 15.70 14.2
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## 424 23.29 13.4
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## 426 24.39  8.3
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## 429 21.52 11.0
## 430 24.08  9.5
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## 432 19.69 14.1
## 433 12.03 16.1
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## 435 15.17 11.7
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## 438 26.45  8.7
## 439 34.02  8.4
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## 441 22.11 10.5
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## 444 18.85 15.4
## 445 23.79 10.8
## 446 23.98 11.8
## 447 17.79 14.9
## 448 16.44 12.6
## 449 18.13 14.1
## 450 19.31 13.0
## 451 17.44 13.4
## 452 17.73 15.2
## 453 17.27 16.1
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## 455 18.71 14.9
## 456 18.13 14.1
## 457 19.01 12.7
## 458 16.94 13.5
## 459 16.23 14.9
## 460 14.70 20.0
## 461 16.42 16.4
## 462 14.65 17.7
## 463 13.99 19.5
## 464 10.29 20.2
## 465 13.22 21.4
## 466 14.13 19.9
## 467 17.15 19.0
## 468 21.32 19.1
## 469 18.13 19.1
## 470 14.76 20.1
## 471 16.29 19.9
## 472 12.87 19.6
## 473 14.36 23.2
## 474 11.66 29.8
## 475 18.14 13.8
## 476 24.10 13.3
## 477 18.68 16.7
## 478 24.91 12.0
## 479 18.03 14.6
## 480 13.11 21.4
## 481 10.74 23.0
## 482  7.74 23.7
## 483  7.01 25.0
## 484 10.42 21.8
## 485 13.34 20.6
## 486 10.58 21.2
## 487 14.98 19.1
## 488 11.45 20.6
## 489 18.06 15.2
## 490 23.97  7.0
## 491 29.68  8.1
## 492 18.07 13.6
## 493 13.35 20.1
## 494 12.01 21.8
## 495 13.59 24.5
## 496 17.60 23.1
## 497 21.14 19.7
## 498 14.10 18.3
## 499 12.92 21.2
## 500 15.10 17.5
## 501 14.33 16.8
## 502  9.67 22.4
## 503  9.08 20.6
## 504  5.64 23.9
## 505  6.48 22.0
## 506  7.88 11.9
# Number of rows and columns
dim(Boston)
## [1] 506  14
# Structure and variable descriptions
str(Boston)
## 'data.frame':    506 obs. of  14 variables:
##  $ crim   : num  0.00632 0.02731 0.02729 0.03237 0.06905 ...
##  $ zn     : num  18 0 0 0 0 0 12.5 12.5 12.5 12.5 ...
##  $ indus  : num  2.31 7.07 7.07 2.18 2.18 2.18 7.87 7.87 7.87 7.87 ...
##  $ chas   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ nox    : num  0.538 0.469 0.469 0.458 0.458 0.458 0.524 0.524 0.524 0.524 ...
##  $ rm     : num  6.58 6.42 7.18 7 7.15 ...
##  $ age    : num  65.2 78.9 61.1 45.8 54.2 58.7 66.6 96.1 100 85.9 ...
##  $ dis    : num  4.09 4.97 4.97 6.06 6.06 ...
##  $ rad    : int  1 2 2 3 3 3 5 5 5 5 ...
##  $ tax    : num  296 242 242 222 222 222 311 311 311 311 ...
##  $ ptratio: num  15.3 17.8 17.8 18.7 18.7 18.7 15.2 15.2 15.2 15.2 ...
##  $ black  : num  397 397 393 395 397 ...
##  $ lstat  : num  4.98 9.14 4.03 2.94 5.33 ...
##  $ medv   : num  24 21.6 34.7 33.4 36.2 28.7 22.9 27.1 16.5 18.9 ...
?Boston
## starting httpd help server ... done

How many rows are in this Boston data set? How many columns? What do the rows and columns represent?

The Boston housing dataset contains 506 rows and 14 columns. Each row represents a census tract in Boston, while each column represents a variable describing housing characteristics, economic indicators, or demographic factors such as crime rate, property tax rate, average number of rooms, and median home value.

  1. Make some pairwise scatterplots of the predictors (columns) in this data set. Describe your findings.
pairs(Boston)

The pairwise scatterplots show several noticeable relationships among predictors. For example, median home value tends to increase with the number of rooms and decrease as the percentage of lower-status population increases. There also appears to be correlation between tax rate and accessibility to highways. Some variables show potential multicollinearity, meaning that certain predictors may contain overlapping information.

  1. Are any of the predictors associated with per capita crime rate? If so, explain the relationship.
cor(Boston)
##                crim          zn       indus         chas         nox
## crim     1.00000000 -0.20046922  0.40658341 -0.055891582  0.42097171
## zn      -0.20046922  1.00000000 -0.53382819 -0.042696719 -0.51660371
## indus    0.40658341 -0.53382819  1.00000000  0.062938027  0.76365145
## chas    -0.05589158 -0.04269672  0.06293803  1.000000000  0.09120281
## nox      0.42097171 -0.51660371  0.76365145  0.091202807  1.00000000
## rm      -0.21924670  0.31199059 -0.39167585  0.091251225 -0.30218819
## age      0.35273425 -0.56953734  0.64477851  0.086517774  0.73147010
## dis     -0.37967009  0.66440822 -0.70802699 -0.099175780 -0.76923011
## rad      0.62550515 -0.31194783  0.59512927 -0.007368241  0.61144056
## tax      0.58276431 -0.31456332  0.72076018 -0.035586518  0.66802320
## ptratio  0.28994558 -0.39167855  0.38324756 -0.121515174  0.18893268
## black   -0.38506394  0.17552032 -0.35697654  0.048788485 -0.38005064
## lstat    0.45562148 -0.41299457  0.60379972 -0.053929298  0.59087892
## medv    -0.38830461  0.36044534 -0.48372516  0.175260177 -0.42732077
##                  rm         age         dis          rad         tax    ptratio
## crim    -0.21924670  0.35273425 -0.37967009  0.625505145  0.58276431  0.2899456
## zn       0.31199059 -0.56953734  0.66440822 -0.311947826 -0.31456332 -0.3916785
## indus   -0.39167585  0.64477851 -0.70802699  0.595129275  0.72076018  0.3832476
## chas     0.09125123  0.08651777 -0.09917578 -0.007368241 -0.03558652 -0.1215152
## nox     -0.30218819  0.73147010 -0.76923011  0.611440563  0.66802320  0.1889327
## rm       1.00000000 -0.24026493  0.20524621 -0.209846668 -0.29204783 -0.3555015
## age     -0.24026493  1.00000000 -0.74788054  0.456022452  0.50645559  0.2615150
## dis      0.20524621 -0.74788054  1.00000000 -0.494587930 -0.53443158 -0.2324705
## rad     -0.20984667  0.45602245 -0.49458793  1.000000000  0.91022819  0.4647412
## tax     -0.29204783  0.50645559 -0.53443158  0.910228189  1.00000000  0.4608530
## ptratio -0.35550149  0.26151501 -0.23247054  0.464741179  0.46085304  1.0000000
## black    0.12806864 -0.27353398  0.29151167 -0.444412816 -0.44180801 -0.1773833
## lstat   -0.61380827  0.60233853 -0.49699583  0.488676335  0.54399341  0.3740443
## medv     0.69535995 -0.37695457  0.24992873 -0.381626231 -0.46853593 -0.5077867
##               black      lstat       medv
## crim    -0.38506394  0.4556215 -0.3883046
## zn       0.17552032 -0.4129946  0.3604453
## indus   -0.35697654  0.6037997 -0.4837252
## chas     0.04878848 -0.0539293  0.1752602
## nox     -0.38005064  0.5908789 -0.4273208
## rm       0.12806864 -0.6138083  0.6953599
## age     -0.27353398  0.6023385 -0.3769546
## dis      0.29151167 -0.4969958  0.2499287
## rad     -0.44441282  0.4886763 -0.3816262
## tax     -0.44180801  0.5439934 -0.4685359
## ptratio -0.17738330  0.3740443 -0.5077867
## black    1.00000000 -0.3660869  0.3334608
## lstat   -0.36608690  1.0000000 -0.7376627
## medv     0.33346082 -0.7376627  1.0000000
cor(Boston$crim, Boston)
##      crim         zn     indus        chas       nox         rm       age
## [1,]    1 -0.2004692 0.4065834 -0.05589158 0.4209717 -0.2192467 0.3527343
##             dis       rad       tax   ptratio      black     lstat       medv
## [1,] -0.3796701 0.6255051 0.5827643 0.2899456 -0.3850639 0.4556215 -0.3883046

Several predictors appear to be associated with per capita crime rate. Crime rate shows a positive relationship with tax rate and percentage of lower-status population, meaning that higher values of these predictors are associated with higher crime rates. Crime rate shows a negative relationship with median home value and number of rooms, suggesting that areas with higher property values and larger homes tend to have lower crime rates.

  1. Do any of the census tracts of Boston appear to have particularly high crime rates? Tax rates? Comment on the range of each predictor.
range(Boston$crim)
## [1]  0.00632 88.97620
range(Boston$tax)
## [1] 187 711
summary(Boston)
##       crim                zn             indus            chas        
##  Min.   : 0.00632   Min.   :  0.00   Min.   : 0.46   Min.   :0.00000  
##  1st Qu.: 0.08205   1st Qu.:  0.00   1st Qu.: 5.19   1st Qu.:0.00000  
##  Median : 0.25651   Median :  0.00   Median : 9.69   Median :0.00000  
##  Mean   : 3.61352   Mean   : 11.36   Mean   :11.14   Mean   :0.06917  
##  3rd Qu.: 3.67708   3rd Qu.: 12.50   3rd Qu.:18.10   3rd Qu.:0.00000  
##  Max.   :88.97620   Max.   :100.00   Max.   :27.74   Max.   :1.00000  
##       nox               rm             age              dis        
##  Min.   :0.3850   Min.   :3.561   Min.   :  2.90   Min.   : 1.130  
##  1st Qu.:0.4490   1st Qu.:5.886   1st Qu.: 45.02   1st Qu.: 2.100  
##  Median :0.5380   Median :6.208   Median : 77.50   Median : 3.207  
##  Mean   :0.5547   Mean   :6.285   Mean   : 68.57   Mean   : 3.795  
##  3rd Qu.:0.6240   3rd Qu.:6.623   3rd Qu.: 94.08   3rd Qu.: 5.188  
##  Max.   :0.8710   Max.   :8.780   Max.   :100.00   Max.   :12.127  
##       rad              tax           ptratio          black       
##  Min.   : 1.000   Min.   :187.0   Min.   :12.60   Min.   :  0.32  
##  1st Qu.: 4.000   1st Qu.:279.0   1st Qu.:17.40   1st Qu.:375.38  
##  Median : 5.000   Median :330.0   Median :19.05   Median :391.44  
##  Mean   : 9.549   Mean   :408.2   Mean   :18.46   Mean   :356.67  
##  3rd Qu.:24.000   3rd Qu.:666.0   3rd Qu.:20.20   3rd Qu.:396.23  
##  Max.   :24.000   Max.   :711.0   Max.   :22.00   Max.   :396.90  
##      lstat            medv      
##  Min.   : 1.73   Min.   : 5.00  
##  1st Qu.: 6.95   1st Qu.:17.02  
##  Median :11.36   Median :21.20  
##  Mean   :12.65   Mean   :22.53  
##  3rd Qu.:16.95   3rd Qu.:25.00  
##  Max.   :37.97   Max.   :50.00

The dataset shows that crime rates vary widely across census tracts, with some areas experiencing significantly higher crime levels than others.The per capita crime rate ranges from 0.0063 to 88.9762, indicating substantial variability and the presence of extreme outliers. The tax rate ranges from 187 to 711, showing wide variation in local property taxation across towns. Overall, the predictors demonstrate substantial variability, which is useful for predictive modeling because it provides diverse information across observations.

e.How many of the census tracts in this data set bound the Charles river?

table(Boston$chas)
## 
##   0   1 
## 471  35

The Boston housing data set contains 506 census tracts in total. Based on the variable chas, which indicates whether a tract bounds the Charles River, 35 census tracts bound the Charles River, while 471 census tracts do not. This shows that only a small fraction of the census tracts are located along the river.

  1. What is the median pupil-teacher ratio among the towns in this data set?
median(Boston$ptratio)
## [1] 19.05

The median pupil-teacher ratio among towns in the Boston housing data set is 19.05 students per teacher. This value represents the typical pupil-teacher ratio across the census tracts included in the data.

  1. The soybean data can also be found at the UC Irvine Machine Learning Repository. Data were collected to predict disease in 683 soybeans. The 35 predictors are mostly categorical and include information on the environmental conditions (e.g., temperature, precipitation) and plant conditions (e.g., left spots, mold growth). The outcome labels consist of 19 distinct classes.
data(Soybean)
str(Soybean)
## 'data.frame':    683 obs. of  36 variables:
##  $ Class          : Factor w/ 19 levels "2-4-d-injury",..: 11 11 11 11 11 11 11 11 11 11 ...
##  $ date           : Factor w/ 7 levels "0","1","2","3",..: 7 5 4 4 7 6 6 5 7 5 ...
##  $ plant.stand    : Ord.factor w/ 2 levels "0"<"1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ precip         : Ord.factor w/ 3 levels "0"<"1"<"2": 3 3 3 3 3 3 3 3 3 3 ...
##  $ temp           : Ord.factor w/ 3 levels "0"<"1"<"2": 2 2 2 2 2 2 2 2 2 2 ...
##  $ hail           : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 2 1 1 ...
##  $ crop.hist      : Factor w/ 4 levels "0","1","2","3": 2 3 2 2 3 4 3 2 4 3 ...
##  $ area.dam       : Factor w/ 4 levels "0","1","2","3": 2 1 1 1 1 1 1 1 1 1 ...
##  $ sever          : Factor w/ 3 levels "0","1","2": 2 3 3 3 2 2 2 2 2 3 ...
##  $ seed.tmt       : Factor w/ 3 levels "0","1","2": 1 2 2 1 1 1 2 1 2 1 ...
##  $ germ           : Ord.factor w/ 3 levels "0"<"1"<"2": 1 2 3 2 3 2 1 3 2 3 ...
##  $ plant.growth   : Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
##  $ leaves         : Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
##  $ leaf.halo      : Factor w/ 3 levels "0","1","2": 1 1 1 1 1 1 1 1 1 1 ...
##  $ leaf.marg      : Factor w/ 3 levels "0","1","2": 3 3 3 3 3 3 3 3 3 3 ...
##  $ leaf.size      : Ord.factor w/ 3 levels "0"<"1"<"2": 3 3 3 3 3 3 3 3 3 3 ...
##  $ leaf.shread    : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ leaf.malf      : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ leaf.mild      : Factor w/ 3 levels "0","1","2": 1 1 1 1 1 1 1 1 1 1 ...
##  $ stem           : Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
##  $ lodging        : Factor w/ 2 levels "0","1": 2 1 1 1 1 1 2 1 1 1 ...
##  $ stem.cankers   : Factor w/ 4 levels "0","1","2","3": 4 4 4 4 4 4 4 4 4 4 ...
##  $ canker.lesion  : Factor w/ 4 levels "0","1","2","3": 2 2 1 1 2 1 2 2 2 2 ...
##  $ fruiting.bodies: Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
##  $ ext.decay      : Factor w/ 3 levels "0","1","2": 2 2 2 2 2 2 2 2 2 2 ...
##  $ mycelium       : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ int.discolor   : Factor w/ 3 levels "0","1","2": 1 1 1 1 1 1 1 1 1 1 ...
##  $ sclerotia      : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ fruit.pods     : Factor w/ 4 levels "0","1","2","3": 1 1 1 1 1 1 1 1 1 1 ...
##  $ fruit.spots    : Factor w/ 4 levels "0","1","2","4": 4 4 4 4 4 4 4 4 4 4 ...
##  $ seed           : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ mold.growth    : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ seed.discolor  : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ seed.size      : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ shriveling     : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ roots          : Factor w/ 3 levels "0","1","2": 1 1 1 1 1 1 1 1 1 1 ...
summary(Soybean)
##                  Class          date     plant.stand  precip      temp    
##  brown-spot         : 92   5      :149   0   :354    0   : 74   0   : 80  
##  alternarialeaf-spot: 91   4      :131   1   :293    1   :112   1   :374  
##  frog-eye-leaf-spot : 91   3      :118   NA's: 36    2   :459   2   :199  
##  phytophthora-rot   : 88   2      : 93               NA's: 38   NA's: 30  
##  anthracnose        : 44   6      : 90                                    
##  brown-stem-rot     : 44   (Other):101                                    
##  (Other)            :233   NA's   :  1                                    
##    hail     crop.hist  area.dam    sever     seed.tmt     germ     plant.growth
##  0   :435   0   : 65   0   :123   0   :195   0   :305   0   :165   0   :441    
##  1   :127   1   :165   1   :227   1   :322   1   :222   1   :213   1   :226    
##  NA's:121   2   :219   2   :145   2   : 45   2   : 35   2   :193   NA's: 16    
##             3   :218   3   :187   NA's:121   NA's:121   NA's:112               
##             NA's: 16   NA's:  1                                                
##                                                                                
##                                                                                
##  leaves  leaf.halo  leaf.marg  leaf.size  leaf.shread leaf.malf  leaf.mild 
##  0: 77   0   :221   0   :357   0   : 51   0   :487    0   :554   0   :535  
##  1:606   1   : 36   1   : 21   1   :327   1   : 96    1   : 45   1   : 20  
##          2   :342   2   :221   2   :221   NA's:100    NA's: 84   2   : 20  
##          NA's: 84   NA's: 84   NA's: 84                          NA's:108  
##                                                                            
##                                                                            
##                                                                            
##    stem     lodging    stem.cankers canker.lesion fruiting.bodies ext.decay 
##  0   :296   0   :520   0   :379     0   :320      0   :473        0   :497  
##  1   :371   1   : 42   1   : 39     1   : 83      1   :104        1   :135  
##  NA's: 16   NA's:121   2   : 36     2   :177      NA's:106        2   : 13  
##                        3   :191     3   : 65                      NA's: 38  
##                        NA's: 38     NA's: 38                                
##                                                                             
##                                                                             
##  mycelium   int.discolor sclerotia  fruit.pods fruit.spots   seed    
##  0   :639   0   :581     0   :625   0   :407   0   :345    0   :476  
##  1   :  6   1   : 44     1   : 20   1   :130   1   : 75    1   :115  
##  NA's: 38   2   : 20     NA's: 38   2   : 14   2   : 57    NA's: 92  
##             NA's: 38                3   : 48   4   :100              
##                                     NA's: 84   NA's:106              
##                                                                      
##                                                                      
##  mold.growth seed.discolor seed.size  shriveling  roots    
##  0   :524    0   :513      0   :532   0   :539   0   :551  
##  1   : 67    1   : 64      1   : 59   1   : 38   1   : 86  
##  NA's: 92    NA's:106      NA's: 92   NA's:106   2   : 15  
##                                                  NA's: 31  
##                                                            
##                                                            
## 
  1. Investigate the frequency distributions for the categorical predictors. Are any of the distributions degenerate in the ways discussed earlier in this chapter?
# Frequency for each predictor
lapply(Soybean, table)
## $Class
## 
##                2-4-d-injury         alternarialeaf-spot 
##                          16                          91 
##                 anthracnose            bacterial-blight 
##                          44                          20 
##           bacterial-pustule                  brown-spot 
##                          20                          92 
##              brown-stem-rot                charcoal-rot 
##                          44                          20 
##               cyst-nematode diaporthe-pod-&-stem-blight 
##                          14                          15 
##       diaporthe-stem-canker                downy-mildew 
##                          20                          20 
##          frog-eye-leaf-spot            herbicide-injury 
##                          91                           8 
##      phyllosticta-leaf-spot            phytophthora-rot 
##                          20                          88 
##              powdery-mildew           purple-seed-stain 
##                          20                          20 
##        rhizoctonia-root-rot 
##                          20 
## 
## $date
## 
##   0   1   2   3   4   5   6 
##  26  75  93 118 131 149  90 
## 
## $plant.stand
## 
##   0   1 
## 354 293 
## 
## $precip
## 
##   0   1   2 
##  74 112 459 
## 
## $temp
## 
##   0   1   2 
##  80 374 199 
## 
## $hail
## 
##   0   1 
## 435 127 
## 
## $crop.hist
## 
##   0   1   2   3 
##  65 165 219 218 
## 
## $area.dam
## 
##   0   1   2   3 
## 123 227 145 187 
## 
## $sever
## 
##   0   1   2 
## 195 322  45 
## 
## $seed.tmt
## 
##   0   1   2 
## 305 222  35 
## 
## $germ
## 
##   0   1   2 
## 165 213 193 
## 
## $plant.growth
## 
##   0   1 
## 441 226 
## 
## $leaves
## 
##   0   1 
##  77 606 
## 
## $leaf.halo
## 
##   0   1   2 
## 221  36 342 
## 
## $leaf.marg
## 
##   0   1   2 
## 357  21 221 
## 
## $leaf.size
## 
##   0   1   2 
##  51 327 221 
## 
## $leaf.shread
## 
##   0   1 
## 487  96 
## 
## $leaf.malf
## 
##   0   1 
## 554  45 
## 
## $leaf.mild
## 
##   0   1   2 
## 535  20  20 
## 
## $stem
## 
##   0   1 
## 296 371 
## 
## $lodging
## 
##   0   1 
## 520  42 
## 
## $stem.cankers
## 
##   0   1   2   3 
## 379  39  36 191 
## 
## $canker.lesion
## 
##   0   1   2   3 
## 320  83 177  65 
## 
## $fruiting.bodies
## 
##   0   1 
## 473 104 
## 
## $ext.decay
## 
##   0   1   2 
## 497 135  13 
## 
## $mycelium
## 
##   0   1 
## 639   6 
## 
## $int.discolor
## 
##   0   1   2 
## 581  44  20 
## 
## $sclerotia
## 
##   0   1 
## 625  20 
## 
## $fruit.pods
## 
##   0   1   2   3 
## 407 130  14  48 
## 
## $fruit.spots
## 
##   0   1   2   4 
## 345  75  57 100 
## 
## $seed
## 
##   0   1 
## 476 115 
## 
## $mold.growth
## 
##   0   1 
## 524  67 
## 
## $seed.discolor
## 
##   0   1 
## 513  64 
## 
## $seed.size
## 
##   0   1 
## 532  59 
## 
## $shriveling
## 
##   0   1 
## 539  38 
## 
## $roots
## 
##   0   1   2 
## 551  86  15

The soybean data set from the UC Irvine Machine Learning Repository contains 683 observations, 35 categorical predictors, and 19 disease classes. Examination of the frequency tables shows that several predictors have highly imbalanced distributions. For example, mycelium has 639 observations in category 0 and only 6 in category 1, sclerotia has 625 observations in category 0 and 20 in category 1, and shriveling has 539 observations in category 0 and only 38 in category 1. These predictors are considered degenerate because one level dominates the data, providing very limited information for distinguishing among disease classes.

  1. Roughly 18 % of the data are missing. Are there particular predictors that are more likely to be missing? Is the pattern of missing data related to the classes?
# Count missing values per variable
colSums(is.na(Soybean))
##           Class            date     plant.stand          precip            temp 
##               0               1              36              38              30 
##            hail       crop.hist        area.dam           sever        seed.tmt 
##             121              16               1             121             121 
##            germ    plant.growth          leaves       leaf.halo       leaf.marg 
##             112              16               0              84              84 
##       leaf.size     leaf.shread       leaf.malf       leaf.mild            stem 
##              84             100              84             108              16 
##         lodging    stem.cankers   canker.lesion fruiting.bodies       ext.decay 
##             121              38              38             106              38 
##        mycelium    int.discolor       sclerotia      fruit.pods     fruit.spots 
##              38              38              38              84             106 
##            seed     mold.growth   seed.discolor       seed.size      shriveling 
##              92              92             106              92             106 
##           roots 
##              31
# Missing by class
aggregate(is.na(Soybean), by=list(Class = Soybean$Class), sum)
##                          Class Class date plant.stand precip temp hail
## 1                 2-4-d-injury     0    1          16     16   16   16
## 2          alternarialeaf-spot     0    0           0      0    0    0
## 3                  anthracnose     0    0           0      0    0    0
## 4             bacterial-blight     0    0           0      0    0    0
## 5            bacterial-pustule     0    0           0      0    0    0
## 6                   brown-spot     0    0           0      0    0    0
## 7               brown-stem-rot     0    0           0      0    0    0
## 8                 charcoal-rot     0    0           0      0    0    0
## 9                cyst-nematode     0    0          14     14   14   14
## 10 diaporthe-pod-&-stem-blight     0    0           6      0    0   15
## 11       diaporthe-stem-canker     0    0           0      0    0    0
## 12                downy-mildew     0    0           0      0    0    0
## 13          frog-eye-leaf-spot     0    0           0      0    0    0
## 14            herbicide-injury     0    0           0      8    0    8
## 15      phyllosticta-leaf-spot     0    0           0      0    0    0
## 16            phytophthora-rot     0    0           0      0    0   68
## 17              powdery-mildew     0    0           0      0    0    0
## 18           purple-seed-stain     0    0           0      0    0    0
## 19        rhizoctonia-root-rot     0    0           0      0    0    0
##    crop.hist area.dam sever seed.tmt germ plant.growth leaves leaf.halo
## 1         16        1    16       16   16           16      0         0
## 2          0        0     0        0    0            0      0         0
## 3          0        0     0        0    0            0      0         0
## 4          0        0     0        0    0            0      0         0
## 5          0        0     0        0    0            0      0         0
## 6          0        0     0        0    0            0      0         0
## 7          0        0     0        0    0            0      0         0
## 8          0        0     0        0    0            0      0         0
## 9          0        0    14       14   14            0      0        14
## 10         0        0    15       15    6            0      0        15
## 11         0        0     0        0    0            0      0         0
## 12         0        0     0        0    0            0      0         0
## 13         0        0     0        0    0            0      0         0
## 14         0        0     8        8    8            0      0         0
## 15         0        0     0        0    0            0      0         0
## 16         0        0    68       68   68            0      0        55
## 17         0        0     0        0    0            0      0         0
## 18         0        0     0        0    0            0      0         0
## 19         0        0     0        0    0            0      0         0
##    leaf.marg leaf.size leaf.shread leaf.malf leaf.mild stem lodging
## 1          0         0          16         0        16   16      16
## 2          0         0           0         0         0    0       0
## 3          0         0           0         0         0    0       0
## 4          0         0           0         0         0    0       0
## 5          0         0           0         0         0    0       0
## 6          0         0           0         0         0    0       0
## 7          0         0           0         0         0    0       0
## 8          0         0           0         0         0    0       0
## 9         14        14          14        14        14    0      14
## 10        15        15          15        15        15    0      15
## 11         0         0           0         0         0    0       0
## 12         0         0           0         0         0    0       0
## 13         0         0           0         0         0    0       0
## 14         0         0           0         0         8    0       8
## 15         0         0           0         0         0    0       0
## 16        55        55          55        55        55    0      68
## 17         0         0           0         0         0    0       0
## 18         0         0           0         0         0    0       0
## 19         0         0           0         0         0    0       0
##    stem.cankers canker.lesion fruiting.bodies ext.decay mycelium int.discolor
## 1            16            16              16        16       16           16
## 2             0             0               0         0        0            0
## 3             0             0               0         0        0            0
## 4             0             0               0         0        0            0
## 5             0             0               0         0        0            0
## 6             0             0               0         0        0            0
## 7             0             0               0         0        0            0
## 8             0             0               0         0        0            0
## 9            14            14              14        14       14           14
## 10            0             0               0         0        0            0
## 11            0             0               0         0        0            0
## 12            0             0               0         0        0            0
## 13            0             0               0         0        0            0
## 14            8             8               8         8        8            8
## 15            0             0               0         0        0            0
## 16            0             0              68         0        0            0
## 17            0             0               0         0        0            0
## 18            0             0               0         0        0            0
## 19            0             0               0         0        0            0
##    sclerotia fruit.pods fruit.spots seed mold.growth seed.discolor seed.size
## 1         16         16          16   16          16            16        16
## 2          0          0           0    0           0             0         0
## 3          0          0           0    0           0             0         0
## 4          0          0           0    0           0             0         0
## 5          0          0           0    0           0             0         0
## 6          0          0           0    0           0             0         0
## 7          0          0           0    0           0             0         0
## 8          0          0           0    0           0             0         0
## 9         14          0          14    0           0            14         0
## 10         0          0           0    0           0             0         0
## 11         0          0           0    0           0             0         0
## 12         0          0           0    0           0             0         0
## 13         0          0           0    0           0             0         0
## 14         8          0           8    8           8             8         8
## 15         0          0           0    0           0             0         0
## 16         0         68          68   68          68            68        68
## 17         0          0           0    0           0             0         0
## 18         0          0           0    0           0             0         0
## 19         0          0           0    0           0             0         0
##    shriveling roots
## 1          16    16
## 2           0     0
## 3           0     0
## 4           0     0
## 5           0     0
## 6           0     0
## 7           0     0
## 8           0     0
## 9          14     0
## 10          0    15
## 11          0     0
## 12          0     0
## 13          0     0
## 14          8     0
## 15          0     0
## 16         68     0
## 17          0     0
## 18          0     0
## 19          0     0

Approximately 18% of the data contains missing values. Some predictors contain significantly more missing observations than others, indicating uneven missingness across variables. The pattern of missing data appears to vary by disease class, For example, the 2-4-d-injury class alone contains 16 missing values for several early predictors, while other classes have none. This uneven distribution suggests that the missing data pattern is related to the disease class and is therefore not completely random, which may impact classification performance.

  1. Develop a strategy for handling missing data, either by eliminating predictors or imputation.
# Remove predictors with too many missing values
Soybean_clean <- Soybean[, colSums(is.na(Soybean)) < 0.5*nrow(Soybean)]

# Imputation example (most frequent category)
library(caret)
preProcess(Soybean, method = "medianImpute")
## Warning in pre_process_options(method, column_types): The following
## pre-processing methods were eliminated: 'medianImpute'
## Created from 562 samples and 36 variables
## 
## Pre-processing:
##   - ignored (36)

A practical way to handle the missing data is to drop predictors with a large amount of missing values (for example, more than 50%, or over 341 observations) and impute the remaining missing entries using the most common category. This keeps most of the 683 observations in the data while limiting noise and helping the model remain stable.

  1. Chapter 5 introduces Quantitative Structure-Activity Relationship (QSAR) modeling where the characteristics of a chemical compound are used to predict other chemical properties. The caret package contains a QSAR data set from Mente and Lombardo (2005). Here, the ability of a chemical to permeate the blood-brain barrier was experimentally determined for 208 compounds. 134 descriptors were measured for each compound

a.Start R and use these commands to load the data: The numeric outcome is contained in the vector logBBB while the predictors are in the data frame bbbDescr.

data(BloodBrain)

str(logBBB)
##  num [1:208] 1.08 -0.4 0.22 0.14 0.69 0.44 -0.43 1.38 0.75 0.88 ...
str(bbbDescr)
## 'data.frame':    208 obs. of  134 variables:
##  $ tpsa                : num  12 49.3 50.5 37.4 37.4 ...
##  $ nbasic              : int  1 0 1 0 1 1 1 1 1 1 ...
##  $ negative            : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ vsa_hyd             : num  167.1 92.6 295.2 319.1 299.7 ...
##  $ a_aro               : int  0 6 15 15 12 11 6 12 12 6 ...
##  $ weight              : num  156 151 366 383 326 ...
##  $ peoe_vsa.0          : num  76.9 38.2 58.1 62.2 74.8 ...
##  $ peoe_vsa.1          : num  43.4 25.5 124.7 124.7 118 ...
##  $ peoe_vsa.2          : num  0 0 21.7 13.2 33 ...
##  $ peoe_vsa.3          : num  0 8.62 8.62 21.79 0 ...
##  $ peoe_vsa.4          : num  0 23.3 17.4 0 0 ...
##  $ peoe_vsa.5          : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ peoe_vsa.6          : num  17.24 0 8.62 8.62 8.62 ...
##  $ peoe_vsa.0.1        : num  18.7 49 83.8 83.8 83.8 ...
##  $ peoe_vsa.1.1        : num  43.5 0 49 68.8 36.8 ...
##  $ peoe_vsa.2.1        : num  0 0 0 0 0 ...
##  $ peoe_vsa.3.1        : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ peoe_vsa.4.1        : num  0 0 5.68 5.68 5.68 ...
##  $ peoe_vsa.5.1        : num  0 13.567 2.504 0 0.137 ...
##  $ peoe_vsa.6.1        : num  0 7.9 2.64 2.64 2.5 ...
##  $ a_acc               : int  0 2 2 2 2 2 2 2 0 2 ...
##  $ a_acid              : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ a_base              : int  1 0 1 1 1 1 1 1 1 1 ...
##  $ vsa_acc             : num  0 13.57 8.19 8.19 8.19 ...
##  $ vsa_acid            : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ vsa_base            : num  5.68 0 0 0 0 ...
##  $ vsa_don             : num  5.68 5.68 5.68 5.68 5.68 ...
##  $ vsa_other           : num  0 28.1 43.6 28.3 19.6 ...
##  $ vsa_pol             : num  0 13.6 0 0 0 ...
##  $ slogp_vsa0          : num  18 25.4 14.1 14.1 14.1 ...
##  $ slogp_vsa1          : num  0 23.3 34.8 34.8 34.8 ...
##  $ slogp_vsa2          : num  3.98 23.86 0 0 0 ...
##  $ slogp_vsa3          : num  0 0 76.2 76.2 76.2 ...
##  $ slogp_vsa4          : num  4.41 0 3.19 3.19 3.19 ...
##  $ slogp_vsa5          : num  32.9 0 9.51 0 0 ...
##  $ slogp_vsa6          : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ slogp_vsa7          : num  0 70.6 148.1 144 140.7 ...
##  $ slogp_vsa8          : num  113.2 0 75.5 75.5 75.5 ...
##  $ slogp_vsa9          : num  33.3 41.3 28.3 55.5 26 ...
##  $ smr_vsa0            : num  0 23.86 12.63 3.12 3.12 ...
##  $ smr_vsa1            : num  18 25.4 27.8 27.8 27.8 ...
##  $ smr_vsa2            : num  4.41 0 0 0 0 ...
##  $ smr_vsa3            : num  3.98 5.24 8.43 8.43 8.43 ...
##  $ smr_vsa4            : num  0 20.8 29.6 21.4 20.3 ...
##  $ smr_vsa5            : num  113.2 70.6 235.1 235.1 234.6 ...
##  $ smr_vsa6            : num  0 5.26 76.25 76.25 76.25 ...
##  $ smr_vsa7            : num  66.2 33.3 0 31.3 0 ...
##  $ tpsa.1              : num  16.6 49.3 51.7 38.6 38.6 ...
##  $ logp.o.w.           : num  2.948 0.889 4.439 5.254 3.8 ...
##  $ frac.anion7.        : num  0 0.001 0 0 0 0 0.001 0 0 0 ...
##  $ frac.cation7.       : num  0.999 0 0.986 0.986 0.986 0.986 0.996 0.946 0.999 0.976 ...
##  $ andrewbind          : num  3.4 -3.3 12.8 12.8 10.3 10 10.4 15.9 12.9 9.5 ...
##  $ rotatablebonds      : int  3 2 8 8 8 8 8 7 4 5 ...
##  $ mlogp               : num  2.5 1.06 4.66 3.82 3.27 ...
##  $ clogp               : num  2.97 0.494 5.137 5.878 4.367 ...
##  $ mw                  : num  155 151 365 382 325 ...
##  $ nocount             : int  1 3 5 4 4 4 4 3 2 4 ...
##  $ hbdnr               : int  1 2 1 1 1 1 2 1 1 0 ...
##  $ rule.of.5violations : int  0 0 1 1 0 0 0 0 1 0 ...
##  $ alert               : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ prx                 : int  0 1 6 2 2 2 1 0 0 4 ...
##  $ ub                  : num  0 3 5.3 5.3 4.2 3.6 3 4.7 4.2 3 ...
##  $ pol                 : int  0 2 3 3 2 2 2 3 4 1 ...
##  $ inthb               : int  0 0 0 0 0 0 1 0 0 0 ...
##  $ adistm              : num  0 395 1365 703 746 ...
##  $ adistd              : num  0 10.9 25.7 10 10.6 ...
##  $ polar_area          : num  21.1 117.4 82.1 65.1 66.2 ...
##  $ nonpolar_area       : num  379 248 638 668 602 ...
##  $ psa_npsa            : num  0.0557 0.4743 0.1287 0.0974 0.11 ...
##  $ tcsa                : num  0.0097 0.0134 0.0111 0.0108 0.0118 0.0111 0.0123 0.0099 0.0106 0.0115 ...
##  $ tcpa                : num  0.1842 0.0417 0.0972 0.1218 0.1186 ...
##  $ tcnp                : num  0.0103 0.0198 0.0125 0.0119 0.013 0.0125 0.0162 0.011 0.0109 0.0122 ...
##  $ ovality             : num  1.1 1.12 1.3 1.3 1.27 ...
##  $ surface_area        : num  400 365 720 733 668 ...
##  $ volume              : num  656 555 1224 1257 1133 ...
##  $ most_negative_charge: num  -0.617 -0.84 -0.801 -0.761 -0.857 ...
##  $ most_positive_charge: num  0.307 0.497 0.541 0.48 0.455 ...
##  $ sum_absolute_charge : num  3.89 4.89 7.98 7.93 7.85 ...
##  $ dipole_moment       : num  1.19 4.21 3.52 3.15 3.27 ...
##  $ homo                : num  -9.67 -8.96 -8.63 -8.56 -8.67 ...
##  $ lumo                : num  3.4038 0.1942 0.0589 -0.2651 0.3149 ...
##  $ hardness            : num  6.54 4.58 4.34 4.15 4.49 ...
##  $ ppsa1               : num  349 223 518 508 509 ...
##  $ ppsa2               : num  679 546 2066 2013 1999 ...
##  $ ppsa3               : num  31 42.3 64 61.7 61.6 ...
##  $ pnsa1               : num  51.1 141.8 202 225.4 158.8 ...
##  $ pnsa2               : num  -99.3 -346.9 -805.9 -894 -623.3 ...
##  $ pnsa3               : num  -10.5 -44 -43.8 -42 -39.8 ...
##  $ fpsa1               : num  0.872 0.611 0.719 0.692 0.762 ...
##  $ fpsa2               : num  1.7 1.5 2.87 2.75 2.99 ...
##  $ fpsa3               : num  0.0774 0.1159 0.0888 0.0842 0.0922 ...
##  $ fnsa1               : num  0.128 0.389 0.281 0.307 0.238 ...
##  $ fnsa2               : num  -0.248 -0.951 -1.12 -1.22 -0.933 ...
##  $ fnsa3               : num  -0.0262 -0.1207 -0.0608 -0.0573 -0.0596 ...
##  $ wpsa1               : num  139.7 81.4 372.7 372.1 340.1 ...
##  $ wpsa2               : num  272 199 1487 1476 1335 ...
##  $ wpsa3               : num  12.4 15.4 46 45.2 41.1 ...
##  $ wnsa1               : num  20.4 51.8 145.4 165.3 106 ...
##  $ wnsa2               : num  -39.8 -126.6 -580.1 -655.3 -416.3 ...
##   [list output truncated]
  1. Do any of the individual predictors have degenerate distributions?
nearZeroVar(bbbDescr)
## [1]  3 16 17 22 25 50 60

Several predictors exhibit near-zero variance, meaning they take almost the same value across most of the 208 compounds. Specifically, 7 predictors were identified as near-zero variance variables. These predictors contribute little useful information for modeling and can be safely removed to simplify the model and improve computational efficiency.

  1. Generally speaking, are there strong relationships between the predictor data? If so, how could correlations in the predictor set be reduced? Does this have a dramatic effect on the number of predictors available for modeling?
cor_matrix <- cor(bbbDescr)
highCorr <- findCorrelation(cor_matrix)
length(highCorr)
## [1] 36

The predictor variables show strong correlations among certain descriptors, which suggests redundancy in the dataset. These correlations can be reduced by removing predictors that exceed a specified correlation threshold. Applying correlation filtering substantially reduces the number of predictors while retaining most of the relevant information, helping to reduce multicollinearity without dramatically harming model performance.

  1. Brodnjak-Vonina et al. (2005) develop a methodology for food laboratories to determine the type of oil from a sample. In their procedure, they used a gas chromatograph (an instrument that separates chemicals in a sample) to measure seven different fatty acids in an oil. These measurements would then be used to predict the type of oil in food samples. To create their model, they used 96 samples2 of seven types of oils. These data can be found in the caret package using data(oil). The oil types are contained in a factor variable called oilType. The types are pumpkin (coded as A), sunflower (B), peanut (C), olive (D), soybean (E), rapeseed (F) and corn (G). In R,
data(oil)

str(oilType)
##  Factor w/ 7 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
table(oilType)
## oilType
##  A  B  C  D  E  F  G 
## 37 26  3  7 11 10  2
  1. Use the sample function in base R to create a completely random sample of 60 oils. How closely do the frequencies of the random sample match the original samples? Repeat this procedure several times of understand the variation in the sampling process.
set.seed(123)
randomSample <- sample(seq_along(oilType), 60)

table(oilType[randomSample])
## 
##  A  B  C  D  E  F  G 
## 24 17  3  3  6  5  2

A completely random sample of 60 out of 96 oils does not preserve the original oil-type proportions. For example, pumpkin oil drops from 37 to 24 samples, while olive oil drops from 7 to 3. Repeating the sampling shows noticeable variation in class counts due to randomness, especially for rare oils like corn (2 total samples).

  1. Use the caret package function createDataPartition to create a stratified random sample. How does this compare to completely random samples?
stratSample <- createDataPartition(oilType, p = 60/length(oilType), list = FALSE)

table(oilType[stratSample])
## 
##  A  B  C  D  E  F  G 
## 24 17  2  5  7  7  2

Using createDataPartition from the caret produces a stratified sample of 60 oils that closely matches the original distribution. For instance, pumpkin oil remains at 24 samples, and sunflower oil at 17, making the sample more representative and reducing sampling bias compared to random sampling.

  1. With such a small samples size, what are the options for determining performance of the model? Should a test set be used?

With a small dataset, using a separate test set may significantly reduce the amount of data available for model training. Alternative methods such as cross-validation, bootstrapping, or leave-one-out cross-validation (LOOCV) are often preferred. These techniques allow the model to be evaluated multiple times using different training and validation splits, which improves reliability while preserving limited data.

  1. One method for understanding the uncertainty of a test set is to use a confidence interval. To obtain a confidence interval for the overall accuracy, the based R function binom.test can be used. It requires the user to input the number of samples and the number correctly classified to calculate the interval. For example, suppose a test set sample of 20 oil samples was set aside and 76 were used for model training. For this test set size and a model that is about 80 % accurate (16 out of 20 correct), the confidence interval would be computed using
binom.test(16, 20)
## 
##  Exact binomial test
## 
## data:  16 and 20
## number of successes = 16, number of trials = 20, p-value = 0.01182
## alternative hypothesis: true probability of success is not equal to 0.5
## 95 percent confidence interval:
##  0.563386 0.942666
## sample estimates:
## probability of success 
##                    0.8

In this case, the width of the 95% confidence interval is 37.9 %. Try different samples sizes and accuracy rates to understand the trade-off between the uncertainty in the results, the model performance, and the test set size.

binom.test(32, 40)
## 
##  Exact binomial test
## 
## data:  32 and 40
## number of successes = 32, number of trials = 40, p-value = 0.0001822
## alternative hypothesis: true probability of success is not equal to 0.5
## 95 percent confidence interval:
##  0.6435220 0.9094776
## sample estimates:
## probability of success 
##                    0.8
binom.test(45, 50)
## 
##  Exact binomial test
## 
## data:  45 and 50
## number of successes = 45, number of trials = 50, p-value = 4.21e-09
## alternative hypothesis: true probability of success is not equal to 0.5
## 95 percent confidence interval:
##  0.7818646 0.9667249
## sample estimates:
## probability of success 
##                    0.9

Confidence intervals show how certain we are about a model’s accuracy. When the test set is small, the confidence interval is wide, meaning the accuracy estimate is less reliable. For example, 80% accuracy on 20 samples (16/20) gives a wide 95% CI of 56.3%–94.3%. As the test set gets larger, the interval becomes narrower: 40 samples (32/40) gives 64.4%–90.9%, and 50 samples (45/50) gives 78.2%–96.7%. Larger test sets reduce uncertainty, but they leave less data for training, so there is a trade-off.

  1. Briefly discuss the bias–variance tradeoff in statistics and predictive modeling. According to your discussions, please draw a conceptual bias–variance tradeoff plot with x-axis being model complexity and y-axis being error.
complexity <- seq(1, 10, length = 100)

bias <- 1/(complexity)
variance <- complexity/10
total_error <- bias + variance

plot(complexity, bias, type="l", lty=2, ylim=c(0,2),
     ylab="Error", xlab="Model Complexity")
lines(complexity, variance, lty=3)
lines(complexity, total_error, lty=1)
legend("topright",
       legend=c("Bias","Variance","Total Error"),
       lty=c(2,3,1))

The bias-variance tradeoff describes how model complexity impacts prediction error. Models with low complexity tend to have high bias because they oversimplify relationships in the data. Highly complex models have low bias but high variance because they may overfit the training data.In the visualization, the bias curve decreases as model complexity increases, while the variance curve increases. The total error curve is U-shaped and reaches its minimum showing the optimal model complexity. This point represents the best balance between bias and variance.