10/20/24, 12:46 AM expt4

In [6]: library(readr)
library(class)
library(gmodels)
library(dplyr)

In [11]: bcd <- read.csv("WDBC-data.csv")

In [12]: str(bcd)

'data.frame': 569 obs. of 33 variables:

$ id : int 842302 842517 84300903 84348301 84358402 843786
844359 84458202 844981 84501001 ...
$ diagnosis : chr "M" "M" "M" "M" ...
$ radius_mean : num 18 20.6 19.7 11.4 20.3 ...
$ texture_mean : num 10.4 17.8 21.2 20.4 14.3 ...
$ perimeter_mean : num 122.8 132.9 130 77.6 135.1 ...
$ area_mean : num 1001 1326 1203 386 1297 ...
$ smoothness_mean : num 0.1184 0.0847 0.1096 0.1425 0.1003 ...
$ compactness_mean : num 0.2776 0.0786 0.1599 0.2839 0.1328 ...
$ concavity_mean : num 0.3001 0.0869 0.1974 0.2414 0.198 ...
$ concave.points_mean : num 0.1471 0.0702 0.1279 0.1052 0.1043 ...
$ symmetry_mean : num 0.242 0.181 0.207 0.26 0.181 ...
$ fractal_dimension_mean : num 0.0787 0.0567 0.06 0.0974 0.0588 ...
$ radius_se : num 1.095 0.543 0.746 0.496 0.757 ...
$ texture_se : num 0.905 0.734 0.787 1.156 0.781 ...
$ perimeter_se : num 8.59 3.4 4.58 3.44 5.44 ...
$ area_se : num 153.4 74.1 94 27.2 94.4 ...
$ smoothness_se : num 0.0064 0.00522 0.00615 0.00911 0.01149 ...
$ compactness_se : num 0.049 0.0131 0.0401 0.0746 0.0246 ...
$ concavity_se : num 0.0537 0.0186 0.0383 0.0566 0.0569 ...
$ concave.points_se : num 0.0159 0.0134 0.0206 0.0187 0.0188 ...
$ symmetry_se : num 0.03 0.0139 0.0225 0.0596 0.0176 ...
$ fractal_dimension_se : num 0.00619 0.00353 0.00457 0.00921 0.00511 ...
$ radius_worst : num 25.4 25 23.6 14.9 22.5 ...
$ texture_worst : num 17.3 23.4 25.5 26.5 16.7 ...
$ perimeter_worst : num 184.6 158.8 152.5 98.9 152.2 ...
$ area_worst : num 2019 1956 1709 568 1575 ...
$ smoothness_worst : num 0.162 0.124 0.144 0.21 0.137 ...
$ compactness_worst : num 0.666 0.187 0.424 0.866 0.205 ...
$ concavity_worst : num 0.712 0.242 0.45 0.687 0.4 ...
$ concave.points_worst : num 0.265 0.186 0.243 0.258 0.163 ...
$ symmetry_worst : num 0.46 0.275 0.361 0.664 0.236 ...
$ fractal_dimension_worst: num 0.1189 0.089 0.0876 0.173 0.0768 ...
$ X : logi NA NA NA NA NA NA ...

In [13]: bcd <- select(bcd,-id,-X)

In [14]: table(bcd$diagnosis)
round(prop.table(table(bcd$diagnosis)) * 100, digits = 1)

B M
357 212
B M
62.7 37.3

In [15]: ## Missing values

sum(is.na(bcd))

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In [16]: head(bcd)

diagnosis radius_mean texture_mean perimeter_mean area_mean smoothness_mean

<chr> <dbl> <dbl> <dbl> <dbl> <dbl>

1 M 17.99 10.38 122.80 1001.0 0.11840

2 M 20.57 17.77 132.90 1326.0 0.08474

3 M 19.69 21.25 130.00 1203.0 0.10960

4 M 11.42 20.38 77.58 386.1 0.14250

5 M 20.29 14.34 135.10 1297.0 0.10030

6 M 12.45 15.70 82.57 477.1 0.12780

In [17]: ## Corelation
cor(select(bcd,-diagnosis))

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radius_mean texture_mean perimeter_mean area_mean smoo

radius_mean 1.000000000 0.323781891 0.997855281 0.987357170

texture_mean 0.323781891 1.000000000 0.329533059 0.321085696

perimeter_mean 0.997855281 0.329533059 1.000000000 0.986506804

area_mean 0.987357170 0.321085696 0.986506804 1.000000000

smoothness_mean 0.170581187 -0.023388516 0.207278164 0.177028377

compactness_mean 0.506123578 0.236702222 0.556936211 0.498501682

concavity_mean 0.676763550 0.302417828 0.716135650 0.685982829

concave.points_mean 0.822528522 0.293464051 0.850977041 0.823268869

symmetry_mean 0.147741242 0.071400980 0.183027212 0.151293079

fractal_dimension_mean -0.311630826 -0.076437183 -0.261476908 -0.283109812

radius_se 0.679090388 0.275868676 0.691765014 0.732562227

texture_se -0.097317443 0.386357623 -0.086761078 -0.066280214

perimeter_se 0.674171616 0.281673115 0.693134890 0.726628328

area_se 0.735863663 0.259844987 0.744982694 0.800085921

smoothness_se -0.222600125 0.006613777 -0.202694026 -0.166776667

compactness_se 0.205999980 0.191974611 0.250743681 0.212582551

concavity_se 0.194203623 0.143293077 0.228082345 0.207660060

concave.points_se 0.376168956 0.163851025 0.407216916 0.372320282

symmetry_se -0.104320881 0.009127168 -0.081629327 -0.072496588

fractal_dimension_se -0.042641269 0.054457520 -0.005523391 -0.019886963

radius_worst 0.969538973 0.352572947 0.969476363 0.962746086

texture_worst 0.297007644 0.912044589 0.303038372 0.287488627

perimeter_worst 0.965136514 0.358039575 0.970386887 0.959119574

area_worst 0.941082460 0.343545947 0.941549808 0.959213326

smoothness_worst 0.119616140 0.077503359 0.150549404 0.123522939

compactness_worst 0.413462823 0.277829592 0.455774228 0.390410309

concavity_worst 0.526911462 0.301025224 0.563879263 0.512605920

concave.points_worst 0.744214198 0.295315843 0.771240789 0.722016626

symmetry_worst 0.163953335 0.105007910 0.189115040 0.143569914

fractal_dimension_worst 0.007065886 0.119205351 0.051018530 0.003737597

In [18]: summary(bcd)

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diagnosis radius_mean texture_mean perimeter_mean

Length:569 Min. : 6.981 Min. : 9.71 Min. : 43.79
Class :character 1st Qu.:11.700 1st Qu.:16.17 1st Qu.: 75.17
Mode :character Median :13.370 Median :18.84 Median : 86.24
Mean :14.127 Mean :19.29 Mean : 91.97
3rd Qu.:15.780 3rd Qu.:21.80 3rd Qu.:104.10
Max. :28.110 Max. :39.28 Max. :188.50
area_mean smoothness_mean compactness_mean concavity_mean
Min. : 143.5 Min. :0.05263 Min. :0.01938 Min. :0.00000
1st Qu.: 420.3 1st Qu.:0.08637 1st Qu.:0.06492 1st Qu.:0.02956
Median : 551.1 Median :0.09587 Median :0.09263 Median :0.06154
Mean : 654.9 Mean :0.09636 Mean :0.10434 Mean :0.08880
3rd Qu.: 782.7 3rd Qu.:0.10530 3rd Qu.:0.13040 3rd Qu.:0.13070
Max. :2501.0 Max. :0.16340 Max. :0.34540 Max. :0.42680
concave.points_mean symmetry_mean fractal_dimension_mean radius_se
Min. :0.00000 Min. :0.1060 Min. :0.04996 Min. :0.1115
1st Qu.:0.02031 1st Qu.:0.1619 1st Qu.:0.05770 1st Qu.:0.2324
Median :0.03350 Median :0.1792 Median :0.06154 Median :0.3242
Mean :0.04892 Mean :0.1812 Mean :0.06280 Mean :0.4052
3rd Qu.:0.07400 3rd Qu.:0.1957 3rd Qu.:0.06612 3rd Qu.:0.4789
Max. :0.20120 Max. :0.3040 Max. :0.09744 Max. :2.8730
texture_se perimeter_se area_se smoothness_se
Min. :0.3602 Min. : 0.757 Min. : 6.802 Min. :0.001713
1st Qu.:0.8339 1st Qu.: 1.606 1st Qu.: 17.850 1st Qu.:0.005169
Median :1.1080 Median : 2.287 Median : 24.530 Median :0.006380
Mean :1.2169 Mean : 2.866 Mean : 40.337 Mean :0.007041
3rd Qu.:1.4740 3rd Qu.: 3.357 3rd Qu.: 45.190 3rd Qu.:0.008146
Max. :4.8850 Max. :21.980 Max. :542.200 Max. :0.031130
compactness_se concavity_se concave.points_se symmetry_se
Min. :0.002252 Min. :0.00000 Min. :0.000000 Min. :0.007882
1st Qu.:0.013080 1st Qu.:0.01509 1st Qu.:0.007638 1st Qu.:0.015160
Median :0.020450 Median :0.02589 Median :0.010930 Median :0.018730
Mean :0.025478 Mean :0.03189 Mean :0.011796 Mean :0.020542
3rd Qu.:0.032450 3rd Qu.:0.04205 3rd Qu.:0.014710 3rd Qu.:0.023480
Max. :0.135400 Max. :0.39600 Max. :0.052790 Max. :0.078950
fractal_dimension_se radius_worst texture_worst perimeter_worst
Min. :0.0008948 Min. : 7.93 Min. :12.02 Min. : 50.41
1st Qu.:0.0022480 1st Qu.:13.01 1st Qu.:21.08 1st Qu.: 84.11
Median :0.0031870 Median :14.97 Median :25.41 Median : 97.66
Mean :0.0037949 Mean :16.27 Mean :25.68 Mean :107.26
3rd Qu.:0.0045580 3rd Qu.:18.79 3rd Qu.:29.72 3rd Qu.:125.40
Max. :0.0298400 Max. :36.04 Max. :49.54 Max. :251.20
area_worst smoothness_worst compactness_worst concavity_worst
Min. : 185.2 Min. :0.07117 Min. :0.02729 Min. :0.0000
1st Qu.: 515.3 1st Qu.:0.11660 1st Qu.:0.14720 1st Qu.:0.1145
Median : 686.5 Median :0.13130 Median :0.21190 Median :0.2267
Mean : 880.6 Mean :0.13237 Mean :0.25427 Mean :0.2722
3rd Qu.:1084.0 3rd Qu.:0.14600 3rd Qu.:0.33910 3rd Qu.:0.3829
Max. :4254.0 Max. :0.22260 Max. :1.05800 Max. :1.2520
concave.points_worst symmetry_worst fractal_dimension_worst
Min. :0.00000 Min. :0.1565 Min. :0.05504
1st Qu.:0.06493 1st Qu.:0.2504 1st Qu.:0.07146
Median :0.09993 Median :0.2822 Median :0.08004
Mean :0.11461 Mean :0.2901 Mean :0.08395
3rd Qu.:0.16140 3rd Qu.:0.3179 3rd Qu.:0.09208
Max. :0.29100 Max. :0.6638 Max. :0.20750

In [19]: normalize <- function(x) {

return ((x - min(x)) / (max(x) - min(x)))
}

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new_bcd <- as.data.frame(lapply(select(bcd,-diagnosis), normalize))

summary(select(new_bcd,radius_mean,smoothness_mean))

radius_mean smoothness_mean
Min. :0.0000 Min. :0.0000
1st Qu.:0.2233 1st Qu.:0.3046
Median :0.3024 Median :0.3904
Mean :0.3382 Mean :0.3948
3rd Qu.:0.4164 3rd Qu.:0.4755
Max. :1.0000 Max. :1.0000

In [20]: #Data Preparation

bcd_train <- new_bcd[1:429,]
bcd_test <- new_bcd[430:569,]
bcd_train_labels <- bcd[1:429, 1]
bcd_test_labels <- bcd[430:569, 1]
#Train Model
bcd_test_pred <- knn(train = bcd_train, test = bcd_test, cl = bcd_train_labels,k
#Model Performance
cm = CrossTable(x = bcd_test_labels, y = bcd_test_pred, prop.chisq = FALSE)
cm

Cell Contents
|-------------------------|
| N |
| N / Row Total |
| N / Col Total |
| N / Table Total |
|-------------------------|

Total Observations in Table: 140

| bcd_test_pred
bcd_test_labels | B | M | Row Total |
----------------|-----------|-----------|-----------|
B | 105 | 0 | 105 |
| 1.000 | 0.000 | 0.750 |
| 0.981 | 0.000 | |
| 0.750 | 0.000 | |
----------------|-----------|-----------|-----------|
M | 2 | 33 | 35 |
| 0.057 | 0.943 | 0.250 |
| 0.019 | 1.000 | |
| 0.014 | 0.236 | |
----------------|-----------|-----------|-----------|
Column Total | 107 | 33 | 140 |
| 0.764 | 0.236 | |
----------------|-----------|-----------|-----------|

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$t
y
x B M
B 105 0
M 2 33

$prop.row
y
x B M
B 1.00000000 0.00000000
M 0.05714286 0.94285714

$prop.col
y
x B M
B 0.98130841 0.00000000
M 0.01869159 1.00000000

$prop.tbl
y
x B M
B 0.75000000 0.00000000
M 0.01428571 0.23571429

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