Import a dataset
heart_failure_clinical <-read.csv(file.choose(),header = TRUE)
Show whole dataset
heart_failure_clinical
Show data types
str(heart_failure_clinical)
Descriptive Statistic
summary(heart_failure_clinical)
install.packages("LongCART")
library(LongCART)
> heart_failure_clinical <-read.csv(file.choose(),header = TRUE)
> heart_failure_clinical
id age anaemia creatinine_phosphokinase diabetes ejection_fraction
1 1 75 0 582 0 20
2 2 55 0 7861 0 38
3 3 65 0 146 0 20
4 4 50 1 111 0 20
5 5 65 1 160 1 20
6 6 90 1 47 0 40
7 7 75 1 246 0 15
8 8 60 1 315 1 60
9 9 65 0 157 0 65
10 10 80 1 123 0 35
11 11 75 1 81 0 38
12 12 62 0 231 0 25
13 13 45 1 981 0 30
14 14 50 1 168 0 38
15 15 49 1 80 0 30
16 16 82 1 379 0 50
17 17 87 1 149 0 38
18 18 45 0 582 0 14
19 19 70 1 125 0 25
20 20 48 1 582 1 55
21 21 65 1 52 0 25
22 22 65 1 128 1 30
23 23 68 1 220 0 35
24 24 53 0 63 1 60
25 25 75 0 582 1 30
26 26 80 0 148 1 38
27 27 95 1 112 0 40
28 28 70 0 122 1 45
29 29 58 1 60 0 38
30 30 82 0 70 1 30
31 31 94 0 582 1 38
32 32 85 0 23 0 45
33 33 50 1 249 1 35
34 34 50 1 159 1 30
35 35 65 0 94 1 50
36 36 69 0 582 1 35
37 37 90 1 60 1 50
38 38 82 1 855 1 50
39 39 60 0 2656 1 30
40 40 60 0 235 1 38
41 41 70 0 582 0 20
42 42 50 0 124 1 30
43 43 70 0 571 1 45
44 44 72 0 127 1 50
45 45 60 1 588 1 60
46 46 50 0 582 1 38
47 47 51 0 1380 0 25
48 48 60 0 582 1 38
49 49 80 1 553 0 20
50 50 57 1 129 0 30
51 51 68 1 577 0 25
52 52 53 1 91 0 20
53 53 60 0 3964 1 62
54 54 70 1 69 1 50
55 55 60 1 260 1 38
56 56 95 1 371 0 30
57 57 70 1 75 0 35
58 58 60 1 607 0 40
59 59 49 0 789 0 20
60 60 72 0 364 1 20
61 61 45 0 7702 1 25
62 62 50 0 318 0 40
63 63 55 0 109 0 35
64 64 45 0 582 0 35
65 65 45 0 582 0 80
66 66 60 0 68 0 20
67 67 42 1 250 1 15
68 68 72 1 110 0 25
69 69 70 0 161 0 25
70 70 65 0 113 1 25
71 71 41 0 148 0 40
high_blood_pressure platelets serum_creatinine serum_sodium gender smoking time
1 1 265000 1.90 130 1 0 4
2 0 263358 1.10 136 1 0 6
3 0 162000 1.30 129 1 1 7
4 0 210000 1.90 137 1 0 7
5 0 327000 2.70 116 0 0 8
6 1 204000 2.10 132 1 1 8
7 0 127000 1.20 137 1 0 10
8 0 454000 1.10 131 1 1 10
9 0 263358 1.50 138 0 0 10
10 1 388000 9.40 133 1 1 10
11 1 368000 4.00 131 1 1 10
12 1 253000 0.90 140 1 1 10
13 0 136000 1.10 137 1 0 11
14 1 276000 1.10 137 1 0 11
15 1 427000 1.00 138 0 0 12
16 0 47000 1.30 136 1 0 13
17 0 262000 0.90 140 1 0 14
18 0 166000 0.80 127 1 0 14
19 1 237000 1.00 140 0 0 15
20 0 87000 1.90 121 0 0 15
21 1 276000 1.30 137 0 0 16
22 1 297000 1.60 136 0 0 20
23 1 289000 0.90 140 1 1 20
24 0 368000 0.80 135 1 0 22
25 1 263358 1.83 134 0 0 23
26 0 149000 1.90 144 1 1 23
27 1 196000 1.00 138 0 0 24
28 1 284000 1.30 136 1 1 26
29 0 153000 5.80 134 1 0 26
30 0 200000 1.20 132 1 1 26
31 1 263358 1.83 134 1 0 27
32 0 360000 3.00 132 1 0 28
33 1 319000 1.00 128 0 0 28
34 0 302000 1.20 138 0 0 29
35 1 188000 1.00 140 1 0 29
36 0 228000 3.50 134 1 0 30
37 0 226000 1.00 134 1 0 30
38 1 321000 1.00 145 0 0 30
39 0 305000 2.30 137 1 0 30
40 0 329000 3.00 142 0 0 30
41 1 263358 1.83 134 1 1 31
42 1 153000 1.20 136 0 1 32
43 1 185000 1.20 139 1 1 33
44 1 218000 1.00 134 1 0 33
45 0 194000 1.10 142 0 0 33
46 0 310000 1.90 135 1 1 35
47 1 271000 0.90 130 1 0 38
48 1 451000 0.60 138 1 1 40
49 1 140000 4.40 133 1 0 41
50 0 395000 1.00 140 0 0 42
51 1 166000 1.00 138 1 0 43
52 1 418000 1.40 139 0 0 43
53 0 263358 6.80 146 0 0 43
54 1 351000 1.00 134 0 0 44
55 0 255000 2.20 132 0 1 45
56 0 461000 2.00 132 1 0 50
57 0 223000 2.70 138 1 1 54
58 0 216000 0.60 138 1 1 54
59 1 319000 1.10 136 1 1 55
60 1 254000 1.30 136 1 1 59
61 1 390000 1.00 139 1 0 60
62 1 216000 2.30 131 0 0 60
63 0 254000 1.10 139 1 1 60
64 0 385000 1.00 145 1 0 61
65 0 263358 1.18 137 0 0 63
66 0 119000 2.90 127 1 1 64
67 0 213000 1.30 136 0 0 65
68 0 274000 1.00 140 1 1 65
69 0 244000 1.20 142 0 0 66
70 0 497000 1.83 135 1 0 67
71 0 374000 0.80 140 1 1 68
DEATH_EVENT
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 0
16 1
17 1
18 1
19 1
20 1
21 0
22 1
23 1
24 0
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 0
35 1
36 1
37 1
38 1
39 0
40 1
41 1
42 1
43 1
44 0
45 1
46 1
47 1
48 1
49 1
50 1
51 1
52 1
53 1
54 1
55 1
56 1
57 0
58 0
59 1
60 1
61 1
62 1
63 0
64 1
65 0
66 1
67 1
68 1
69 1
70 1
71 0
[ reached 'max' / getOption("max.print") -- omitted 228 rows ]
>
> # Show data types
> str(heart_failure_clinical)
'data.frame': 299 obs. of 14 variables:
$ id : int 1 2 3 4 5 6 7 8 9 10 ...
$ age : int 75 55 65 50 65 90 75 60 65 80 ...
$ anaemia : int 0 0 0 1 1 1 1 1 0 1 ...
$ creatinine_phosphokinase: int 582 7861 146 111 160 47 246 315 157 123 ...
$ diabetes : int 0 0 0 0 1 0 0 1 0 0 ...
$ ejection_fraction : int 20 38 20 20 20 40 15 60 65 35 ...
$ high_blood_pressure : int 1 0 0 0 0 1 0 0 0 1 ...
$ platelets : num 265000 263358 162000 210000 327000 ...
$ serum_creatinine : num 1.9 1.1 1.3 1.9 2.7 2.1 1.2 1.1 1.5 9.4 ...
$ serum_sodium : int 130 136 129 137 116 132 137 131 138 133 ...
$ gender : int 1 1 1 1 0 1 1 1 0 1 ...
$ smoking : int 0 0 1 0 0 1 0 1 0 1 ...
$ time : int 4 6 7 7 8 8 10 10 10 10 ...
$ DEATH_EVENT : int 1 1 1 1 1 1 1 1 1 1 ...
>
> # Descriptive Statistic
> summary(heart_failure_clinical)
id age anaemia creatinine_phosphokinase
Min. : 1.0 Min. :40.00 Min. :0.0000 Min. : 23.0
1st Qu.: 75.5 1st Qu.:51.00 1st Qu.:0.0000 1st Qu.: 116.5
Median :150.0 Median :60.00 Median :0.0000 Median : 250.0
Mean :150.0 Mean :60.84 Mean :0.4314 Mean : 581.8
3rd Qu.:224.5 3rd Qu.:70.00 3rd Qu.:1.0000 3rd Qu.: 582.0
Max. :299.0 Max. :95.00 Max. :1.0000 Max. :7861.0
diabetes ejection_fraction high_blood_pressure platelets
Min. :0.0000 Min. :14.00 Min. :0.0000 Min. : 25100
1st Qu.:0.0000 1st Qu.:30.00 1st Qu.:0.0000 1st Qu.:212500
Median :0.0000 Median :38.00 Median :0.0000 Median :262000
Mean :0.4181 Mean :38.08 Mean :0.3512 Mean :263358
3rd Qu.:1.0000 3rd Qu.:45.00 3rd Qu.:1.0000 3rd Qu.:303500
Max. :1.0000 Max. :80.00 Max. :1.0000 Max. :850000
serum_creatinine serum_sodium gender smoking time
Min. :0.500 Min. :113.0 Min. :0.0000 Min. :0.0000 Min. : 4.0
1st Qu.:0.900 1st Qu.:134.0 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.: 73.0
Median :1.100 Median :137.0 Median :1.0000 Median :0.0000 Median :115.0
Mean :1.394 Mean :136.6 Mean :0.6488 Mean :0.3211 Mean :130.3
3rd Qu.:1.400 3rd Qu.:140.0 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:203.0
Max. :9.400 Max. :148.0 Max. :1.0000 Max. :1.0000 Max. :285.0
DEATH_EVENT
Min. :0.0000
1st Qu.:0.0000
Median :0.0000
Mean :0.3211
3rd Qu.:1.0000
Max. :1.0000
>
>
> install.packages("LongCART")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘cli’, ‘lifecycle’, ‘rlang’, ‘scales’, ‘vctrs’, ‘ggplot2’, ‘survminer’
There are binary versions available but the source versions are later:
binary source needs_compilation
cli 3.2.0 3.6.3 TRUE
lifecycle 1.0.1 1.0.4 FALSE
rlang 1.0.2 1.1.5 TRUE
scales 1.2.0 1.3.0 TRUE
vctrs 0.4.1 0.6.5 TRUE
ggplot2 3.3.5 3.5.1 FALSE
survminer 0.4.9 0.5.0 FALSE
LongCART 3.1 3.2 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cli_3.2.0.zip'
Content type 'application/zip' length 1255499 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_1.0.2.zip'
Content type 'application/zip' length 1718546 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/scales_1.2.0.zip'
Content type 'application/zip' length 616764 bytes (602 KB)
downloaded 602 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/vctrs_0.4.1.zip'
Content type 'application/zip' length 1569486 bytes (1.5 MB)
downloaded 1.5 MB
package ‘cli’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘scales’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\RtmpADfYel\downloaded_packages
installing the source packages ‘lifecycle’, ‘ggplot2’, ‘survminer’, ‘LongCART’
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.4.tar.gz'
Content type 'application/x-gzip' length 107656 bytes (105 KB)
downloaded 105 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.5.1.tar.gz'
Content type 'application/x-gzip' length 3604371 bytes (3.4 MB)
downloaded 3.4 MB
trying URL 'https://cran.rstudio.com/src/contrib/survminer_0.5.0.tar.gz'
Content type 'application/x-gzip' length 2882134 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'https://cran.rstudio.com/src/contrib/LongCART_3.2.tar.gz'
Content type 'application/x-gzip' length 121365 bytes (118 KB)
downloaded 118 KB
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 1.0.2 is being loaded, but >= 1.1.0 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'lifecycle'
* removing 'C:/Users/user/Documents/R/win-library/4.0/lifecycle'
* restoring previous 'C:/Users/user/Documents/R/win-library/4.0/lifecycle'
Warning in install.packages :
installation of package ‘lifecycle’ had non-zero exit status
* installing *source* package 'ggplot2' ...
** package 'ggplot2' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 1.0.2 is being loaded, but >= 1.1.0 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'ggplot2'
* removing 'C:/Users/user/Documents/R/win-library/4.0/ggplot2'
* restoring previous 'C:/Users/user/Documents/R/win-library/4.0/ggplot2'
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
* installing *source* package 'survminer' ...
** package 'survminer' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package 'ggplot2' 3.3.5 was found, but >= 3.4.0 is required by 'survminer'
Execution halted
ERROR: lazy loading failed for package 'survminer'
* removing 'C:/Users/user/Documents/R/win-library/4.0/survminer'
Warning in install.packages :
installation of package ‘survminer’ had non-zero exit status
ERROR: dependency 'survminer' is not available for package 'LongCART'
* removing 'C:/Users/user/Documents/R/win-library/4.0/LongCART'
Warning in install.packages :
installation of package ‘LongCART’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\user\AppData\Local\Temp\RtmpADfYel\downloaded_packages’
> library(LongCART)
Error in library(LongCART) : there is no package called ‘LongCART’