wbcd <- read.csv("C:\\Users\\RISHI RAHUL\\Desktop\\Dataset\\3 Data Sets\\12 KNN\\wbcd.csv")
str(wbcd)
## 'data.frame': 569 obs. of 32 variables:
## $ id : int 87139402 8910251 905520 868871 9012568 906539 925291 87880 862989 89827 ...
## $ diagnosis : Factor w/ 2 levels "B","M": 1 1 1 1 1 1 1 2 1 1 ...
## $ radius_mean : num 12.3 10.6 11 11.3 15.2 ...
## $ texture_mean : num 12.4 18.9 16.8 13.4 13.2 ...
## $ perimeter_mean : num 78.8 69.3 70.9 73 97.7 ...
## $ area_mean : num 464 346 373 385 712 ...
## $ smoothness_mean : num 0.1028 0.0969 0.1077 0.1164 0.0796 ...
## $ compactness_mean : num 0.0698 0.1147 0.078 0.1136 0.0693 ...
## $ concavity_mean : num 0.0399 0.0639 0.0305 0.0464 0.0339 ...
## $ points_mean : num 0.037 0.0264 0.0248 0.048 0.0266 ...
## $ symmetry_mean : num 0.196 0.192 0.171 0.177 0.172 ...
## $ dimension_mean : num 0.0595 0.0649 0.0634 0.0607 0.0554 ...
## $ radius_se : num 0.236 0.451 0.197 0.338 0.178 ...
## $ texture_se : num 0.666 1.197 1.387 1.343 0.412 ...
## $ perimeter_se : num 1.67 3.43 1.34 1.85 1.34 ...
## $ area_se : num 17.4 27.1 13.5 26.3 17.7 ...
## $ smoothness_se : num 0.00805 0.00747 0.00516 0.01127 0.00501 ...
## $ compactness_se : num 0.0118 0.03581 0.00936 0.03498 0.01485 ...
## $ concavity_se : num 0.0168 0.0335 0.0106 0.0219 0.0155 ...
## $ points_se : num 0.01241 0.01365 0.00748 0.01965 0.00915 ...
## $ symmetry_se : num 0.0192 0.035 0.0172 0.0158 0.0165 ...
## $ dimension_se : num 0.00225 0.00332 0.0022 0.00344 0.00177 ...
## $ radius_worst : num 13.5 11.9 12.4 11.9 16.2 ...
## $ texture_worst : num 15.6 22.9 26.4 15.8 15.7 ...
## $ perimeter_worst : num 87 78.3 79.9 76.5 104.5 ...
## $ area_worst : num 549 425 471 434 819 ...
## $ smoothness_worst : num 0.139 0.121 0.137 0.137 0.113 ...
## $ compactness_worst: num 0.127 0.252 0.148 0.182 0.174 ...
## $ concavity_worst : num 0.1242 0.1916 0.1067 0.0867 0.1362 ...
## $ points_worst : num 0.0939 0.0793 0.0743 0.0861 0.0818 ...
## $ symmetry_worst : num 0.283 0.294 0.3 0.21 0.249 ...
## $ dimension_worst : num 0.0677 0.0759 0.0788 0.0678 0.0677 ...
dim(wbcd)
## [1] 569 32
wbcd <- wbcd[-1]
dim(wbcd)
## [1] 569 31
table(wbcd$diagnosis)
##
## B M
## 357 212
wbcd$diagnosis <- factor(wbcd$diagnosis, levels = c("B", "M"), labels = c("Benign", "Malignant"))
table(wbcd$diagnosis)
##
## Benign Malignant
## 357 212
round(prop.table(table(wbcd$diagnosis))*100, digits = 1)
##
## Benign Malignant
## 62.7 37.3
summary(wbcd[c("radius_mean","area_mean","smoothness_mean")])
## radius_mean area_mean smoothness_mean
## Min. : 6.981 Min. : 143.5 Min. :0.05263
## 1st Qu.:11.700 1st Qu.: 420.3 1st Qu.:0.08637
## Median :13.370 Median : 551.1 Median :0.09587
## Mean :14.127 Mean : 654.9 Mean :0.09636
## 3rd Qu.:15.780 3rd Qu.: 782.7 3rd Qu.:0.10530
## Max. :28.110 Max. :2501.0 Max. :0.16340
normalize_data <- function(x){
return((x-min(x))/(max(x)-min(x)))
}
wbcd_n <- as.data.frame(lapply(wbcd[2:31], normalize_data))
summary(wbcd_n[c("radius_mean","area_mean","smoothness_mean")])
## radius_mean area_mean smoothness_mean
## Min. :0.0000 Min. :0.0000 Min. :0.0000
## 1st Qu.:0.2233 1st Qu.:0.1174 1st Qu.:0.3046
## Median :0.3024 Median :0.1729 Median :0.3904
## Mean :0.3382 Mean :0.2169 Mean :0.3948
## 3rd Qu.:0.4164 3rd Qu.:0.2711 3rd Qu.:0.4755
## Max. :1.0000 Max. :1.0000 Max. :1.0000
wbcd_train <- wbcd_n[1:469,]
wbcd_test <- wbcd_n[470:569,]
wbcd_train_labels <- wbcd[1:469,1]
#wbcd_train_labels <- as.factor(wbcd_train_labels[[1]])
wbcd_test_labels <- wbcd[470:569,1]
#wbcd_test_labels <- as.factor(wbcd_test_labels[[1]])
# EDA part ends here
library(class)
wbcd_pred <- knn(train = wbcd_train, test = wbcd_test, cl = wbcd_train_labels, k=21)
library(gmodels)
## Warning: package 'gmodels' was built under R version 3.5.1
CrossTable(wbcd_test_labels, wbcd_pred)
##
##
## Cell Contents
## |-------------------------|
## | N |
## | Chi-square contribution |
## | N / Row Total |
## | N / Col Total |
## | N / Table Total |
## |-------------------------|
##
##
## Total Observations in Table: 100
##
##
## | wbcd_pred
## wbcd_test_labels | Benign | Malignant | Row Total |
## -----------------|-----------|-----------|-----------|
## Benign | 61 | 0 | 61 |
## | 13.255 | 22.570 | |
## | 1.000 | 0.000 | 0.610 |
## | 0.968 | 0.000 | |
## | 0.610 | 0.000 | |
## -----------------|-----------|-----------|-----------|
## Malignant | 2 | 37 | 39 |
## | 20.733 | 35.302 | |
## | 0.051 | 0.949 | 0.390 |
## | 0.032 | 1.000 | |
## | 0.020 | 0.370 | |
## -----------------|-----------|-----------|-----------|
## Column Total | 63 | 37 | 100 |
## | 0.630 | 0.370 | |
## -----------------|-----------|-----------|-----------|
##
##