# Load necessary libraries
library(cluster)
## Warning: package 'cluster' was built under R version 4.3.3
library(factoextra)
## Warning: package 'factoextra' was built under R version 4.3.3
## Loading required package: ggplot2
## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(DataExplorer)
## Warning: package 'DataExplorer' was built under R version 4.3.3
data<-read.csv(file.choose())
View(data)
# Assign column names to the 'data' object (assuming it's a data frame or matrix)
names(data) <- c('T_xacc','T_yacc','T_zacc','T_xgyro','T_ygro','T_zgyro','T_xmag','T_ymag','T_zmag',
'RA_xacc','RA_yacc','RA_zacc','RA_xgyro','RA_ygro','RA_zgyro','RA_xmag','RA_ymag','RA_zmag',
'LA_xacc','LA_yacc','LA_zacc','LA_xgyro','LA_ygro','LA_zgyro','LA_xmag','LA_ymag','LA_zmag',
'RL_xacc','RL_yacc','RL_zacc','RL_xgyro','RL_ygro','RL_zgyro','RL_xmag','RL_ymag','RL_zmag',
'LL_xacc','LL_yacc','LL_zacc','LL_xgyro','LL_ygro','LL_zgyro','LL_xmag','LL_ymag','LL_zmag')
head(data)
## T_xacc T_yacc T_zacc T_xgyro T_ygro T_zgyro T_xmag T_ymag T_zmag
## 1 8.1305 1.0202 5.3843 -0.009368 0.023485 0.001953 -0.78717 -0.068275 0.15890
## 2 8.1604 1.0201 5.3622 0.015046 0.014330 0.000204 -0.78664 -0.068277 0.15879
## 3 8.1603 1.0052 5.3770 0.006892 0.018045 0.005649 -0.78529 -0.069849 0.15912
## 4 8.1605 1.0275 5.3473 0.008811 0.030433 -0.005346 -0.78742 -0.068796 0.15916
## 5 8.1454 1.0201 5.3919 0.007001 0.029523 -0.008080 -0.78716 -0.070603 0.15905
## 6 8.1454 1.0495 5.4518 -0.005710 0.014217 -0.021708 -0.78720 -0.067744 0.15836
## RA_xacc RA_yacc RA_zacc RA_xgyro RA_ygro RA_zgyro RA_xmag RA_ymag
## 1 0.71829 5.6005 7.9712 0.012862 -0.005241 -0.003029 -0.57306 -0.55684
## 2 0.69849 5.6612 7.9568 0.021639 -0.010421 0.011992 -0.57357 -0.55788
## 3 0.72799 5.6393 7.9763 0.016440 0.001875 0.002322 -0.60463 -0.56833
## 4 0.71572 5.6441 7.9714 0.000286 -0.003408 0.002425 -0.56864 -0.55990
## 5 0.71323 5.6611 7.9714 0.012768 -0.015835 -0.002188 -0.56927 -0.55966
## 6 0.71813 5.6466 7.9617 0.016329 -0.005132 0.009398 -0.56549 -0.55804
## RA_zmag LA_xacc LA_yacc LA_zacc LA_xgyro LA_ygro LA_zgyro LA_xmag
## 1 -0.21335 3.4340 -8.3708 3.8537 -0.014302 -0.001877 -0.004997 -0.64838
## 2 -0.21336 3.4291 -8.3757 3.8757 0.000126 -0.008308 -0.012062 -0.64821
## 3 -0.24523 3.4437 -8.3271 3.8286 0.000092 0.003542 -0.011145 -0.64841
## 4 -0.21383 3.4486 -8.3709 3.8466 -0.012524 0.003591 -0.004980 -0.64909
## 5 -0.21335 3.4437 -8.3563 3.8609 -0.007098 -0.000094 -0.008514 -0.64811
## 6 -0.21032 3.4389 -8.3903 3.8492 0.000106 -0.014629 -0.010307 -0.64737
## LA_ymag LA_zmag RL_xacc RL_yacc RL_zacc RL_xgyro RL_ygro RL_zgyro
## 1 0.34240 0.074865 -3.5386 9.0812 -0.93332 0.014458 0.002668 -0.011870
## 2 0.34099 0.073155 -3.5385 9.0662 -0.92580 -0.009606 0.010623 -0.008289
## 3 0.34125 0.074143 -3.5385 9.0587 -0.94080 0.000949 0.007971 -0.003015
## 4 0.34152 0.075607 -3.5311 9.0812 -0.93317 -0.009898 -0.002577 0.003975
## 5 0.34200 0.075141 -3.5608 9.0585 -0.91873 0.000952 0.013264 -0.002976
## 6 0.34107 0.074829 -3.5310 9.0662 -0.93315 0.007318 0.006195 -0.010084
## RL_xmag RL_ymag RL_zmag LL_xacc LL_yacc LL_zacc LL_xgyro LL_ygro
## 1 0.73172 -0.25236 -0.034005 -2.8146 -9.0737 2.6218 -0.014784 -0.016477
## 2 0.72914 -0.25249 -0.036489 -2.8221 -9.0886 2.6366 -0.012770 0.005717
## 3 0.73080 -0.25176 -0.036151 -2.8071 -9.0811 2.6070 -0.005725 0.009620
## 4 0.73035 -0.25235 -0.033807 -2.8146 -9.0737 2.6218 -0.003929 -0.008371
## 5 0.72932 -0.25278 -0.035693 -2.8072 -9.0886 2.6070 -0.014559 0.016500
## 6 0.73044 -0.25180 -0.034855 -2.8076 -9.0893 2.6085 -0.012902 0.009463
## LL_zgyro LL_xmag LL_ymag LL_zmag
## 1 0.002789 0.73937 0.30183 -0.057514
## 2 -0.007918 0.73955 0.30052 -0.057219
## 3 0.006555 0.74029 0.30184 -0.057750
## 4 0.002816 0.73845 0.30090 -0.057527
## 5 -0.006040 0.74009 0.30065 -0.056939
## 6 -0.002449 0.73886 0.30164 -0.057682
str(data)
## 'data.frame': 124 obs. of 45 variables:
## $ T_xacc : num 8.13 8.16 8.16 8.16 8.15 ...
## $ T_yacc : num 1.02 1.02 1.01 1.03 1.02 ...
## $ T_zacc : num 5.38 5.36 5.38 5.35 5.39 ...
## $ T_xgyro : num -0.00937 0.01505 0.00689 0.00881 0.007 ...
## $ T_ygro : num 0.0235 0.0143 0.018 0.0304 0.0295 ...
## $ T_zgyro : num 0.001953 0.000204 0.005649 -0.005346 -0.00808 ...
## $ T_xmag : num -0.787 -0.787 -0.785 -0.787 -0.787 ...
## $ T_ymag : num -0.0683 -0.0683 -0.0698 -0.0688 -0.0706 ...
## $ T_zmag : num 0.159 0.159 0.159 0.159 0.159 ...
## $ RA_xacc : num 0.718 0.698 0.728 0.716 0.713 ...
## $ RA_yacc : num 5.6 5.66 5.64 5.64 5.66 ...
## $ RA_zacc : num 7.97 7.96 7.98 7.97 7.97 ...
## $ RA_xgyro: num 0.012862 0.021639 0.01644 0.000286 0.012768 ...
## $ RA_ygro : num -0.00524 -0.01042 0.00187 -0.00341 -0.01583 ...
## $ RA_zgyro: num -0.00303 0.01199 0.00232 0.00243 -0.00219 ...
## $ RA_xmag : num -0.573 -0.574 -0.605 -0.569 -0.569 ...
## $ RA_ymag : num -0.557 -0.558 -0.568 -0.56 -0.56 ...
## $ RA_zmag : num -0.213 -0.213 -0.245 -0.214 -0.213 ...
## $ LA_xacc : num 3.43 3.43 3.44 3.45 3.44 ...
## $ LA_yacc : num -8.37 -8.38 -8.33 -8.37 -8.36 ...
## $ LA_zacc : num 3.85 3.88 3.83 3.85 3.86 ...
## $ LA_xgyro: num -0.014302 0.000126 0.000092 -0.012524 -0.007098 ...
## $ LA_ygro : num -0.001877 -0.008308 0.003542 0.003591 -0.000094 ...
## $ LA_zgyro: num -0.005 -0.01206 -0.01115 -0.00498 -0.00851 ...
## $ LA_xmag : num -0.648 -0.648 -0.648 -0.649 -0.648 ...
## $ LA_ymag : num 0.342 0.341 0.341 0.342 0.342 ...
## $ LA_zmag : num 0.0749 0.0732 0.0741 0.0756 0.0751 ...
## $ RL_xacc : num -3.54 -3.54 -3.54 -3.53 -3.56 ...
## $ RL_yacc : num 9.08 9.07 9.06 9.08 9.06 ...
## $ RL_zacc : num -0.933 -0.926 -0.941 -0.933 -0.919 ...
## $ RL_xgyro: num 0.014458 -0.009606 0.000949 -0.009898 0.000952 ...
## $ RL_ygro : num 0.00267 0.01062 0.00797 -0.00258 0.01326 ...
## $ RL_zgyro: num -0.01187 -0.00829 -0.00301 0.00398 -0.00298 ...
## $ RL_xmag : num 0.732 0.729 0.731 0.73 0.729 ...
## $ RL_ymag : num -0.252 -0.252 -0.252 -0.252 -0.253 ...
## $ RL_zmag : num -0.034 -0.0365 -0.0362 -0.0338 -0.0357 ...
## $ LL_xacc : num -2.81 -2.82 -2.81 -2.81 -2.81 ...
## $ LL_yacc : num -9.07 -9.09 -9.08 -9.07 -9.09 ...
## $ LL_zacc : num 2.62 2.64 2.61 2.62 2.61 ...
## $ LL_xgyro: num -0.01478 -0.01277 -0.00572 -0.00393 -0.01456 ...
## $ LL_ygro : num -0.01648 0.00572 0.00962 -0.00837 0.0165 ...
## $ LL_zgyro: num 0.00279 -0.00792 0.00656 0.00282 -0.00604 ...
## $ LL_xmag : num 0.739 0.74 0.74 0.738 0.74 ...
## $ LL_ymag : num 0.302 0.301 0.302 0.301 0.301 ...
## $ LL_zmag : num -0.0575 -0.0572 -0.0578 -0.0575 -0.0569 ...
summary(data)
## T_xacc T_yacc T_zacc T_xgyro
## Min. :7.682 Min. :0.9974 Min. :5.317 Min. :-0.039399
## 1st Qu.:7.876 1st Qu.:1.0352 1st Qu.:5.437 1st Qu.:-0.004507
## Median :7.959 Median :1.0838 Median :5.611 Median : 0.005143
## Mean :7.974 Mean :1.0835 Mean :5.608 Mean : 0.005013
## 3rd Qu.:8.108 3rd Qu.:1.1240 3rd Qu.:5.753 3rd Qu.: 0.014096
## Max. :8.161 Max. :1.1832 Max. :6.181 Max. : 0.045403
## T_ygro T_zgyro T_xmag T_ymag
## Min. :-0.08064 Min. :-0.030754 Min. :-0.7955 Min. :-0.07158
## 1st Qu.: 0.01103 1st Qu.:-0.008880 1st Qu.:-0.7932 1st Qu.:-0.06985
## Median : 0.02411 Median :-0.003463 Median :-0.7916 Median :-0.06873
## Mean : 0.02632 Mean :-0.003729 Mean :-0.7908 Mean :-0.06848
## 3rd Qu.: 0.04304 3rd Qu.: 0.001965 3rd Qu.:-0.7875 3rd Qu.:-0.06719
## Max. : 0.21476 Max. : 0.015614 Max. :-0.7853 Max. :-0.06435
## T_zmag RA_xacc RA_yacc RA_zacc
## Min. :0.1096 Min. :0.5854 Min. :5.596 Min. :7.841
## 1st Qu.:0.1198 1st Qu.:0.6491 1st Qu.:5.663 1st Qu.:7.889
## Median :0.1349 Median :0.6886 Median :5.709 Median :7.933
## Mean :0.1357 Mean :0.6790 Mean :5.713 Mean :7.926
## 3rd Qu.:0.1547 3rd Qu.:0.7096 3rd Qu.:5.757 3rd Qu.:7.962
## Max. :0.1592 Max. :0.7593 Max. :5.848 Max. :8.001
## RA_xgyro RA_ygro RA_zgyro RA_xmag
## Min. :-0.014167 Min. :-0.017639 Min. :-0.035780 Min. :-0.6046
## 1st Qu.: 0.006609 1st Qu.:-0.006953 1st Qu.:-0.008205 1st Qu.:-0.5713
## Median : 0.012949 Median : 0.000066 Median :-0.002933 Median :-0.5689
## Mean : 0.012954 Mean :-0.001029 Mean :-0.002965 Mean :-0.5693
## 3rd Qu.: 0.018526 3rd Qu.: 0.003621 3rd Qu.: 0.002403 3rd Qu.:-0.5666
## Max. : 0.038867 Max. : 0.015303 Max. : 0.016870 Max. :-0.5384
## RA_ymag RA_zmag LA_xacc LA_yacc
## Min. :-0.5743 Min. :-0.2452 Min. :3.268 Min. :-8.482
## 1st Qu.:-0.5637 1st Qu.:-0.2132 1st Qu.:3.380 1st Qu.:-8.394
## Median :-0.5611 Median :-0.2114 Median :3.411 Median :-8.371
## Mean :-0.5616 Mean :-0.2111 Mean :3.403 Mean :-8.376
## 3rd Qu.:-0.5596 3rd Qu.:-0.2088 3rd Qu.:3.434 3rd Qu.:-8.356
## Max. :-0.5484 Max. :-0.1840 Max. :3.487 Max. :-8.293
## LA_zacc LA_xgyro LA_ygro LA_zgyro
## Min. :3.794 Min. :-0.045979 Min. :-0.0333500 Min. :-0.036797
## 1st Qu.:3.837 1st Qu.:-0.012329 1st Qu.:-0.0054370 1st Qu.:-0.011178
## Median :3.849 Median :-0.006575 Median : 0.0000160 Median :-0.006770
## Mean :3.852 Mean :-0.004886 Mean : 0.0000467 Mean :-0.007540
## 3rd Qu.:3.864 3rd Qu.: 0.003567 3rd Qu.: 0.0057930 3rd Qu.:-0.001463
## Max. :3.922 Max. : 0.020662 Max. : 0.0238160 Max. : 0.016169
## LA_xmag LA_ymag LA_zmag RL_xacc
## Min. :-0.6503 Min. :0.3375 Min. :0.06794 Min. :-3.607
## 1st Qu.:-0.6485 1st Qu.:0.3409 1st Qu.:0.07090 1st Qu.:-3.547
## Median :-0.6479 Median :0.3418 Median :0.07238 Median :-3.538
## Mean :-0.6479 Mean :0.3418 Mean :0.07226 Mean :-3.536
## 3rd Qu.:-0.6471 3rd Qu.:0.3431 3rd Qu.:0.07357 3rd Qu.:-3.524
## Max. :-0.6456 Max. :0.3456 Max. :0.07637 Max. :-3.472
## RL_yacc RL_zacc RL_xgyro RL_ygro
## Min. :9.028 Min. :-1.0010 Min. :-0.0236640 Min. :-0.0131380
## 1st Qu.:9.058 1st Qu.:-0.9548 1st Qu.:-0.0042617 1st Qu.: 0.0008448
## Median :9.066 Median :-0.9331 Median : 0.0004570 Median : 0.0078635
## Mean :9.063 Mean :-0.9345 Mean : 0.0004088 Mean : 0.0077402
## 3rd Qu.:9.066 3rd Qu.:-0.9186 3rd Qu.: 0.0046515 3rd Qu.: 0.0131898
## Max. :9.095 Max. :-0.8803 Max. : 0.0187880 Max. : 0.0307700
## RL_zgyro RL_xmag RL_ymag RL_zmag
## Min. :-0.0257220 Min. :0.7280 Min. :-0.2538 Min. :-0.03935
## 1st Qu.:-0.0099825 1st Qu.:0.7297 1st Qu.:-0.2527 1st Qu.:-0.03661
## Median :-0.0038675 Median :0.7303 Median :-0.2521 Median :-0.03574
## Mean :-0.0042643 Mean :0.7302 Mean :-0.2521 Mean :-0.03589
## 3rd Qu.:-0.0002062 3rd Qu.:0.7307 3rd Qu.:-0.2516 3rd Qu.:-0.03524
## Max. : 0.0191430 Max. :0.7324 Max. :-0.2500 Max. :-0.03311
## LL_xacc LL_yacc LL_zacc LL_xgyro
## Min. :-2.868 Min. :-9.112 Min. :2.571 Min. :-0.0246850
## 1st Qu.:-2.823 1st Qu.:-9.089 1st Qu.:2.608 1st Qu.:-0.0096597
## Median :-2.815 Median :-9.089 Median :2.622 Median :-0.0056750
## Mean :-2.815 Mean :-9.085 Mean :2.618 Mean :-0.0050744
## 3rd Qu.:-2.808 3rd Qu.:-9.075 3rd Qu.:2.625 3rd Qu.:-0.0002395
## Max. :-2.748 Max. :-9.044 Max. :2.670 Max. : 0.0158530
## LL_ygro LL_zgyro LL_xmag LL_ymag
## Min. :-0.019207 Min. :-0.021531 Min. :0.7375 Min. :0.2997
## 1st Qu.:-0.002989 1st Qu.:-0.007927 1st Qu.:0.7390 1st Qu.:0.3007
## Median : 0.001615 Median :-0.002556 Median :0.7396 Median :0.3013
## Mean : 0.002281 Mean :-0.003144 Mean :0.7396 Mean :0.3013
## 3rd Qu.: 0.007602 3rd Qu.: 0.001637 3rd Qu.:0.7402 3rd Qu.:0.3018
## Max. : 0.020288 Max. : 0.013777 Max. :0.7424 Max. :0.3034
## LL_zmag
## Min. :-0.05924
## 1st Qu.:-0.05758
## Median :-0.05721
## Mean :-0.05711
## 3rd Qu.:-0.05650
## Max. :-0.05496
sum(is.na(data))
## [1] 0
data <- data %>% select_if(is.numeric)
data_scaled <- scale(data)
set.seed(123)
kmeans_result <- kmeans(data_scaled, centers = 3, nstart = 25)
fviz_cluster(kmeans_result, data = data_scaled)
dist_matrix <- dist(data_scaled)
hc <- hclust(dist_matrix, method = "ward.D2")
plot(hc)
library(dendextend)
## Warning: package 'dendextend' was built under R version 4.3.3
##
## ---------------------
## Welcome to dendextend version 1.17.1
## Type citation('dendextend') for how to cite the package.
##
## Type browseVignettes(package = 'dendextend') for the package vignette.
## The github page is: https://github.com/talgalili/dendextend/
##
## Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
## You may ask questions at stackoverflow, use the r and dendextend tags:
## https://stackoverflow.com/questions/tagged/dendextend
##
## To suppress this message use: suppressPackageStartupMessages(library(dendextend))
## ---------------------
##
## Attaching package: 'dendextend'
## The following object is masked from 'package:stats':
##
## cutree
res.dist2<-dist(data, method = "euclidean")
res.hcr<-hclust(d = res.dist2, method = "ward.D2")
fviz_dend(res.hcr, cex = 0.5)
## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
## of ggplot2 3.3.4.
## ℹ The deprecated feature was likely used in the factoextra package.
## Please report the issue at <https://github.com/kassambara/factoextra/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
res.hcr1<- hclust(res.dist2, method= "average")
cor(res.dist2, cophenetic(res.hcr1))
## [1] 0.7566942
fviz_dend(res.hcr, cex = 0.5, k_colors=c('brown','yellow','green','blue'), rect = TRUE)
library(dendextend)
res.dsitr<-dist(data, method = "euclidean")
hcr<-hclust(res.dsitr, method = "average")
hcr1<-hclust(res.dsitr, method = "ward.D2")
denr<- as.dendrogram(hcr)
denr2<- as.dendrogram(hcr1)
dend_listr<- dendlist(denr, denr2)
tanglegram(denr, denr2)
dim(data)
## [1] 124 45
sa1<- sample(1:124, 20)
sports<- data[sa1, ]
sports.scaled<- scale(sports)
dim(sports)
## [1] 20 45
res.dsits<- dist(sports, method = "euclidean")
hcs<- hclust(res.dsits, method = "average")
hcss<- hclust(res.dsits, method = "ward.D2")
den34<- as.dendrogram(hcs)
den35<- as.dendrogram(hcss)
dend_lists<- dendlist(den34, den35)
dend_lists
## [[1]]
## 'dendrogram' with 2 branches and 20 members total, at height 0.6251281
##
## [[2]]
## 'dendrogram' with 2 branches and 20 members total, at height 1.303784
##
## attr(,"class")
## [1] "dendlist"
tanglegram(den34, den35)
