Distributed Computing R Project

UNIVERSITI TEKNOLOGI
PETRONAS
COURSE:
INFORMATION COMMUNICATION & TECHNOLOGY (ICT)
TDB3063:
DISTRIBUTED COMPUTING
Assignment Topics:
Suicide Rate in Germany
STUDENT’S DETAILS
NO. NAME ID COURSE
1. MUHAMMAD FARHAN ASYRAF ICT
2. NUR FATIN FIRZANAH ICT
ASSIGNMENT DETAIL
DISTRBUTED COMPUTING
1
TABLE OF CONTENT
CONTENT PAGE
1.0 Background 3
2.0 Program 4 – 18
3.0 Result 19 -25
4.0 Appendix 26 - 34
5.0 Reference 35
2
Assignment Topics:
Suicide Rate in Germany
1.0 BACKGROUND
RStudio is an open-source integrated development environment

(IDE) for R. R is a programming language designed for statistical computing and
graphics. Hence, R language is widely used among statisticians and data miners
for developing statistical software and data analysis. Hence, this automation of
analyses will save our time and energy, and lead to proper documentation in
which RStudio help in conducting precise analyses and correcting mistakes.
Hence, the purpose of this project is to find the statistic and analysis
regarding the “Suicide Rate in Germany”. Based on the data, we can analysis
hundreds of data easily. Thus, for our project, R is really beneficial to us as it
helping us in manipulating, analysing, and visualizing hundreds of data.
Based on the data, there are four main dataset that can be simplified
which are the gender (sex), method of suicide, frequency and also age. Hence,
by using RStudio, we can simplified hundreds of data and come out with
summary of dataset – can refer to the “Program & Result” page.
3
2.0 PROGRAM
> setwd("C:/Users/asus pc/Desktop/DC")

> library(readr)
> Suicide <- read_csv("Suicide.csv")
Parsed with column specification:
cols(
Freq = col_integer(),
sex = col_character(),
method = col_character(),
age = col_integer()
)
> View(Suicide)
> install.packages("caret")
Installing package into ëC:/Users/asus pc/Documents/R/win-library/3.5í
(as ëlibí is unspecified)
trying URL
'https://cran.rstudio.com/bin/windows/contrib/3.5/caret_6.0-80.zip'
Content type 'application/zip' length 6114409 bytes (5.8 MB)
downloaded 5.8 MB
package ëcaretí successfully unpacked and MD5 sums checked
The downloaded binary packages are in

C:\Users\asus
pc\AppData\Local\Temp\RtmpKUPZYQ\downloaded_packages
> library("caret")
Loading required package: lattice
Loading required package: ggplot2
> install.packages("lattice")
Error in install.packages : Updating loaded packages
Restarting R session...
4
trying URL
'https://cran.rstudio.com/bin/windows/contrib/3.5/lattice_0.20-35.zip'
downloaded 1.1 MB
package ëlatticeí successfully unpacked and MD5 sums checked

Warning in install.packages :
cannot remove prior installation of package ëlatticeí

C:\Users\asus
pc\AppData\Local\Temp\RtmpI5Y9i0\downloaded_packages
> install.packages("ggplot2")
trying URL
'https://cran.rstudio.com/bin/windows/contrib/3.5/ggplot2_3.0.0.zip'
downloaded 3.4 MB
package ëggplot2í successfully unpacked and MD5 sums checked

C:\Users\asus
pc\AppData\Local\Temp\RtmpI5Y9i0\downloaded_packages
> library("lattice")
> library("ggplot2")
> library("caret")
Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
5
cannot open compressed file 'C:/Users/asus pc/Documents/R/win-
library/3.5/lattice/DESCRIPTION', probable reason 'No such file or
directory'
> filename <- "Suicide.csv"
>
> dataset <- read.csv(filename, header=TRUE)
>
> validation_index <- createDataPartition(dataset$age, p=0.80, list=FALSE)
>
> validation <- dataset[-validation_index,]
> dataset <- dataset[validation_index,]
> dim(dataset)
[1] 246 4
> head(dataset)
Freq sex method age
1 4 male poison 10
2 0 male cookgas 10
3 0 male toxicgas 10
4 247 male hang 10
5 1 male drown 10
6 17 male gun 10
> summary(dataset)
Freq sex
Min. : 0.00 female:120
1st Qu.: 10.25 male :126
Median : 52.50
Mean : 171.13
3rd Qu.: 162.75
Max. :1381.00
method age
knife :29 Min. :10.00
other :29 1st Qu.:30.00
poison :28 Median :50.00
drown :27 Mean :49.88
gun :27 3rd Qu.:70.00
hang :27 Max. :90.00
(Other):79
6
> control <- trainControl(method="cv", number=10)
> metric <- "Accuracy"
> fit <- train(age~., data=dataset, method="svmRadial", metric=metric,
trControl=control)
Error: Metric Accuracy not applicable for regression models
>
> validation_index <- createDataPartition(dataset$method, p=0.80,
list=FALSE)
> validation <- dataset[-validation_index,]
> dataset <- dataset[validation_index,]
> dim(dataset)
[1] 201 4
> head(dataset)
Freq sex method age
1 4 male poison 10
2 0 male cookgas 10
4 247 male hang 10
8 6 male jump 10
9 0 male other 10
> summary(dataset)
Freq sex
Min. : 0.0 female: 98
1st Qu.: 10.0 male :103
Median : 52.0
Mean : 163.9
3rd Qu.: 161.0
Max. :1381.0
method age
knife :24 Min. :10.00
other :24 1st Qu.:30.00
poison :23 Median :50.00
drown :22 Mean :51.04
gun :22 3rd Qu.:75.00
hang :22 Max. :90.00
(Other):64
> control <- trainControl(method="cv", number=10)
7
> metric <- "Accuracy"
> fit <- train(method~., data=dataset, method="svmRadial", metric=metric,
trControl=control)
> results <- resamples(list(svm=fit))
Error in resamples.default(list(svm = fit)) :
at least two train objects are needed
> fit2 <- train(method~., data=dataset, method="bagFDA", metric=metric,
trControl=control)
Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
> install.packages("e1071")
> install.packages("e1071")
trying URL
'https://cran.rstudio.com/bin/windows/contrib/3.5/e1071_1.6-8.zip'
Content type 'application/zip' length 1013497 bytes (989 KB)
downloaded 989 KB
package ëe1071í successfully unpacked and MD5 sums checked

C:\Users\asus
pc\AppData\Local\Temp\Rtmpgd93bj\downloaded_packages
> results <- resamples(list(svm=fit, fit))
Error in resamples(list(svm = fit, fit)) :
could not find function "resamples"
> results <- resamples(list(svm=fit, fit2))
Error in resamples(list(svm = fit, fit2)) :
could not find function "resamples"
trControl=control)
8
Error in train(method ~ ., data = dataset, method = "bagFDA", metric =
metric, :
could not find function "train"
> library("caret", lib.loc="~/R/win-library/3.5")
Loading required package: lattice
Loading required package: ggplot2
Need help? Try Stackoverflow: https://stackoverflow.com/tags/ggplot2.
> library("e1071", lib.loc="~/R/win-library/3.5")
> library("earth", lib.loc="~/R/win-library/3.5")
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
> library("class", lib.loc="C:/Program Files/R/R-3.5.1/library")
trControl=control)
> results <- resamples(list(svm=fit, fit2))
> summary(results)
Call:
summary.resamples(object = results)
Models: svm, Model2

Number of resamples: 10
Accuracy
Min. 1st Qu. Median
svm 0.1000000 0.1397727 0.2440476
Model2 0.1904762 0.3000000 0.3157895
Mean 3rd Qu. Max. NA's
svm 0.2237324 0.2875000 0.3684211 0
Model2 0.3394839 0.4066986 0.5000000 0
Kappa
Min. 1st Qu. Median
svm -0.02272727 0.02837779 0.1476998
Model2 0.08695652 0.21346463 0.2341067
Mean 3rd Qu. Max. NA's
svm 0.1259243 0.2006152 0.2897196 0
Model2 0.2570373 0.3303799 0.4269341 0
9
>
> Print(fit)
Error in Print(fit) : could not find function "Print"
>
> print(fit)
Support Vector Machines with Radial Basis Function Kernel
201 samples
3 predictor
9 classes: 'cookgas', 'drown', 'gun', 'hang', 'jump', 'knife', 'other', 'poison',
'toxicgas'
No pre-processing
Resampling: Cross-Validated (10 fold)
Summary of sample sizes: 181, 179, 183, 181, 182, 181, ...
Resampling results across tuning parameters:
C Accuracy Kappa
0.25 0.1829035 0.08349059
0.50 0.2038084 0.10531461
1.00 0.2237324 0.12592428
Tuning parameter 'sigma' was held

constant at a value of 1.51453
Accuracy was used to select the
optimal model using the largest value.
The final values used for the model
were sigma = 1.51453 and C = 1.
>
> print(fit2)
Bagged Flexible Discriminant Analysis
201 samples
3 predictor
9 classes: 'cookgas', 'drown', 'gun', 'hang', 'jump', 'knife', 'other', 'poison',
'toxicgas'
No pre-processing
Resampling: Cross-Validated (10 fold)
10
Summary of sample sizes: 180, 182, 182, 180, 181, 179, ...
Resampling results across tuning parameters:
nprune Accuracy Kappa

2 0.2542436 0.1559828
6 0.3194372 0.2345348
11 0.3394839 0.2570373
Tuning parameter 'degree' was

held constant at a value of 1
Accuracy was used to select the
optimal model using the largest value.
The final values used for the model
were degree = 1 and nprune = 11.
>
> predictions <- predict(fit, validation)
>
> confusionMatrix(predictions, validation$method)
Confusion Matrix and Statistics
Reference
Prediction cookgas drown gun hang jump
cookgas 1 2 0 0 0
drown 0 1 0 0 0
gun 3 1 1 1 1
hang 0 0 0 3 0
jump 0 0 1 0 0
knife 1 0 0 0 0
other 0 0 1 0 3
poison 0 0 0 1 0
toxicgas 0 1 2 0 1
Reference
Prediction knife other poison toxicgas
cookgas 1 0 0 0
drown 1 2 0 3
gun 0 1 0 2
hang 0 0 3 0
11
jump 2 1 0 0
knife 0 0 0 0
other 1 0 0 0
poison 0 0 2 0
toxicgas 0 1 0 0
Overall Statistics
Accuracy : 0.1778
95% CI : (0.08, 0.3205)
No Information Rate : 0.1111
P-Value [Acc > NIR] : 0.1208
Kappa : 0.075
Mcnemar's Test P-Value : NA
Statistics by Class:
Class: cookgas
Sensitivity 0.20000
Specificity 0.92500
Pos Pred Value 0.25000
Neg Pred Value 0.90244
Prevalence 0.11111
Detection Rate 0.02222
Detection Prevalence 0.08889
Balanced Accuracy 0.56250
Class: drown
Sensitivity 0.20000
Specificity 0.85000
Prevalence 0.11111
12
Class: gun
Sensitivity 0.20000
Specificity 0.77500
Prevalence 0.11111
Class: hang
Sensitivity 0.60000
Specificity 0.92500
Prevalence 0.11111
Class: jump
Sensitivity 0.00000
Specificity 0.90000
Prevalence 0.11111
Class: knife
Sensitivity 0.00000
Specificity 0.97500
Prevalence 0.11111
13
Class: other
Sensitivity 0.0000
Specificity 0.8750
Prevalence 0.1111
Class: poison
Sensitivity 0.40000
Specificity 0.97500
Prevalence 0.11111
Class: toxicgas
Sensitivity 0.0000
Specificity 0.8750
Prevalence 0.1111
>
>
> predictions2 <- predict(fit2, validation)
>
> confusionMatrix(predictions2, validation$method)
Confusion Matrix and Statistics
14
Reference
Prediction cookgas drown gun hang jump
cookgas 4 3 1 0 0
drown 0 1 0 0 0
gun 0 0 2 0 0
hang 0 0 0 2 0
jump 0 0 0 0 3
knife 1 0 0 1 1
other 0 0 0 0 1
poison 0 1 2 2 0
toxicgas 0 0 0 0 0
Reference
Prediction knife other poison toxicgas
cookgas 1 0 0 0
drown 0 0 0 1
gun 1 0 0 1
hang 0 0 3 0
jump 0 4 0 0
knife 3 0 0 3
other 0 0 0 0
poison 0 1 2 0
toxicgas 0 0 0 0
Overall Statistics
Accuracy : 0.3778
95% CI : (0.2377, 0.5346)
No Information Rate : 0.1111
P-Value [Acc > NIR] : 3.02e-06
Kappa : 0.3
Mcnemar's Test P-Value : NA
Statistics by Class:
Class: cookgas
15
Sensitivity 0.80000
Specificity 0.87500
Prevalence 0.11111
Class: drown
Sensitivity 0.20000
Specificity 0.97500
Prevalence 0.11111
Class: gun
Sensitivity 0.40000
Specificity 0.95000
Prevalence 0.11111
Class: hang
Sensitivity 0.40000
Specificity 0.92500
Prevalence 0.11111
16
Class: jump
Sensitivity 0.60000
Specificity 0.90000
Prevalence 0.11111
Class: knife
Sensitivity 0.60000
Specificity 0.85000
Prevalence 0.11111
Class: other
Sensitivity 0.00000
Specificity 0.97500
Prevalence 0.11111
Class: poison
Sensitivity 0.40000
Specificity 0.85000
Prevalence 0.11111
17
Class: toxicgas
Sensitivity 0.0000
Specificity 1.0000
Pos Pred Value NaN
Prevalence 0.1111
>
>
>
18
3.0 RESULT
Head & Summary Dataset
Summary
19
Fit1
Fit2
20
Statistics
21
Prediction Fit2
22
Overall Statistics
23
24
25
4.0 APPENDIX
List of Dataset
No Freq sex method age

1 4 male poison 10
2 0 male cookgas 10
4 247 male hang 10
5 1 male drown 10
6 17 male gun 10
7 1 male knife 10
8 6 male jump 10
9 0 male other 10
10 348 male poison 15
11 7 male cookgas 15
13 578 male hang 15
14 22 male drown 15
15 179 male gun 15
16 11 male knife 15
17 74 male jump 15
18 175 male other 15
22 699 male hang 20
23 44 male drown 20
24 316 male gun 20
25 35 male knife 20
26 109 male jump 20
31 648 male hang 25
32 52 male drown 25
26
33 268 male gun 25
34 38 male knife 25
35 109 male jump 25
40 825 male hang 30
41 74 male drown 30
42 291 male gun 30
43 52 male knife 30
44 123 male jump 30
49 1278 male hang 35
50 87 male drown 35
51 293 male gun 35
52 49 male knife 35
53 134 male jump 35
59 89 male drown 40
60 299 male gun 40
61 53 male knife 40
62 78 male jump 40
68 71 male drown 45
69 347 male gun 45
27
70 68 male knife 45
71 103 male jump 45
77 87 male drown 50
78 229 male gun 50
79 62 male knife 50
80 63 male jump 50
85 972 male hang 55
86 49 male drown 55
87 151 male gun 55
88 46 male knife 55
89 66 male jump 55
90 77 male other 55
95 83 male drown 60
96 162 male gun 60
97 52 male knife 60
98 92 male jump 60
103 1360 male hang 65
104 75 male drown 65
105 164 male gun 65
106 56 male knife 65
28
107 115 male jump 65
112 1268 male hang 70
114 121 male gun 70
116 119 male jump 70
123 78 male gun 75
125 79 male jump 75
132 18 male gun 80
134 46 male jump 80
141 10 male gun 85
142 9 male knife 85
143 18 male jump 85
29
148 76 male hang 90
149 4 male drown 90
150 2 male gun 90
151 4 male knife 90
152 6 male jump 90
153 2 male other 90
154 28 female poison 10
155 0 female cookgas 10
156 3 female toxicgas 10
157 20 female hang 10
158 0 female drown 10
159 1 female gun 10
160 0 female knife 10
161 10 female jump 10
162 6 female other 10
168 15 female gun 15
177 9 female gun 20
30
31
32
258 4 female gun 65
267 1 female gun 70
276 2 female gun 75
285 0 female gun 80
33
294 0 female gun 85
303 0 female gun 90
34
5.0 REFERENCE
Choi, G., Lee, K., Seo, D., Kim, S., Kim, D., & Lee, Y. (2015). Analysis of medical
data using the big data and R. In Advances in Computer Science and Ubiquitous
Computing (pp. 867-873). Springer, Singapore.
Gandrud, C. (2016). Reproducible research with R and R studio. Chapman and

Hall/CRC.
Horton, N. J., & Kleinman, K. (2015). Using R and RStudio for data management,
statistical analysis, and graphics. Chapman and Hall/CRC.
Racine, J. S. (2012). RStudio: A Platform‐Independent IDE for R and Sweave.

Journal of Applied Econometrics, 27(1), 167-172.
35

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UNIVERSITI TEKNOLOGI

3.0 Result 19 -25

RStudio is an open-source integrated development environment

> setwd("C:/Users/asus pc/Desktop/DC")

package ëcaretí successfully unpacked and MD5 sums checked

The downloaded binary packages are in

package ëlatticeí successfully unpacked and MD5 sums checked

The downloaded binary packages are in

package ëggplot2í successfully unpacked and MD5 sums checked

The downloaded binary packages are in

package ëe1071í successfully unpacked and MD5 sums checked

The downloaded binary packages are in

Models: svm, Model2

Tuning parameter 'sigma' was held

nprune Accuracy Kappa

Tuning parameter 'degree' was

Head & Summary Dataset

No Freq sex method age

Gandrud, C. (2016). Reproducible research with R and R studio. Chapman and

Racine, J. S. (2012). RStudio: A Platform‐Independent IDE for R and Sweave.

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