Load packages

If you are using the package for the first time, you will first have to install it.

# install.packages("survival")

If you have already downloaded this package in the current version of R, you will only have to load the package.

library(survival)

Get the data

Load a data set from a package.
You can use the double colon symbol (:), to return the pbc object from the package survival. We store this data set to an object with the name pbc.

pbc <- survival::pbc

Vectors

Examples of vectors can be seen below.

pbc$age
##   [1] 58.76523 56.44627 70.07255 54.74059 38.10541 66.25873 55.53457 53.05681
##   [9] 42.50787 70.55989 53.71389 59.13758 45.68925 56.22177 64.64613 40.44353
##  [17] 52.18344 53.93018 49.56057 59.95346 64.18891 56.27652 55.96715 44.52019
##  [25] 45.07324 52.02464 54.43943 44.94730 63.87680 41.38535 41.55236 53.99589
##  [33] 51.28268 52.06023 48.61875 56.41068 61.72758 36.62697 55.39220 46.66940
##  [41] 33.63450 33.69473 48.87064 37.58248 41.79329 45.79877 47.42779 49.13621
##  [49] 61.15264 53.50856 52.08761 50.54073 67.40862 39.19781 65.76318 33.61807
##  [57] 53.57153 44.56947 40.39425 58.38193 43.89870 60.70637 46.62834 62.90760
##  [65] 40.20260 46.45311 51.28816 32.61328 49.33881 56.39973 48.84600 32.49281
##  [73] 38.49418 51.92060 43.51814 51.94251 49.82615 47.94524 46.51608 67.41136
##  [81] 63.26352 67.31006 56.01369 55.83025 47.21697 52.75838 37.27858 41.39357
##  [89] 52.44353 33.47570 45.60712 76.70910 36.53388 53.91650 46.39014 48.84600
##  [97] 71.89322 28.88433 48.46817 51.46886 44.95003 56.56947 48.96372 43.01711
## [105] 34.03970 68.50924 62.52156 50.35729 44.06297 38.91034 41.15264 55.45791
## [113] 51.23340 52.82683 42.63929 61.07050 49.65640 48.85421 54.25599 35.15127
## [121] 67.90691 55.43600 45.82067 52.88980 47.18138 53.59890 44.10404 41.94935
## [129] 63.61396 44.22724 62.00137 40.55305 62.64476 42.33539 42.96783 55.96167
## [137] 62.86105 51.24983 46.76249 54.07529 47.03628 55.72621 46.10267 52.28747
## [145] 51.20055 33.86448 75.01164 30.86379 61.80424 34.98700 55.04175 69.94114
## [153] 49.60438 69.37714 43.55647 59.40862 48.75838 36.49281 45.76044 57.37166
## [161] 42.74333 58.81725 53.49760 43.41410 53.30595 41.35524 60.95825 47.75359
## [169] 35.49076 48.66256 52.66804 49.86995 30.27515 55.56742 52.15332 41.60986
## [177] 55.45243 70.00411 43.94251 42.56810 44.56947 56.94456 40.26010 37.60712
## [185] 48.36140 70.83641 35.79192 62.62286 50.64750 54.52704 52.69268 52.72005
## [193] 56.77207 44.39699 29.55510 57.04038 44.62697 35.79740 40.71732 32.23272
## [201] 41.09240 61.63997 37.05681 62.57906 48.97741 61.99042 72.77207 61.29500
## [209] 52.62423 49.76318 52.91444 47.26352 50.20397 69.34702 41.16906 59.16496
## [217] 36.07940 34.59548 42.71321 63.63039 56.62971 46.26420 61.24298 38.62012
## [225] 38.77070 56.69541 58.95140 36.92266 62.41478 34.60917 58.33539 50.18207
## [233] 42.68583 34.37919 33.18275 38.38193 59.76181 66.41205 46.78987 56.07940
## [241] 41.37440 64.57221 67.48802 44.82957 45.77139 32.95003 41.22108 55.41684
## [249] 47.98084 40.79124 56.97467 68.46270 78.43943 39.85763 35.31006 31.44422
## [257] 58.26420 51.48802 59.96988 74.52430 52.36413 42.78713 34.87474 44.13963
## [265] 46.38193 56.30938 70.90760 55.39493 45.08419 26.27789 50.47228 38.39836
## [273] 47.41958 47.98084 38.31622 50.10815 35.08830 32.50376 56.15332 46.15469
## [281] 65.88364 33.94387 62.86105 48.56400 46.34908 38.85284 58.64750 48.93634
## [289] 67.57290 65.98494 40.90075 50.24504 57.19644 60.53662 35.35113 31.38125
## [297] 55.98631 52.72553 38.09172 58.17112 45.21013 37.79877 60.65982 35.53457
## [305] 43.06639 56.39151 30.57358 61.18275 58.29979 62.33265 37.99863 33.15264
## [313] 60.00000 64.99932 54.00137 75.00068 62.00137 43.00068 46.00137 44.00000
## [321] 60.99932 64.00000 40.00000 63.00068 34.00137 52.00000 48.99932 54.00137
## [329] 63.00068 54.00137 46.00137 52.99932 56.00000 56.00000 55.00068 64.99932
## [337] 56.00000 47.00068 60.00000 52.99932 54.00137 50.00137 48.00000 36.00000
## [345] 48.00000 70.00137 51.00068 52.00000 54.00137 48.00000 66.00137 52.99932
## [353] 62.00137 59.00068 39.00068 67.00068 58.00137 64.00000 46.00137 64.00000
## [361] 40.99932 48.99932 44.00000 59.00068 63.00068 60.99932 64.00000 48.99932
## [369] 42.00137 50.00137 51.00068 36.99932 62.00137 51.00068 52.00000 44.00000
## [377] 32.99932 60.00000 63.00068 32.99932 40.99932 51.00068 36.99932 59.00068
## [385] 55.00068 54.00137 48.99932 40.00000 67.00068 68.00000 40.99932 68.99932
## [393] 52.00000 56.99932 36.00000 50.00137 64.00000 62.00137 42.00137 44.00000
## [401] 68.99932 52.00000 66.00137 40.00000 52.00000 46.00137 54.00137 51.00068
## [409] 43.00068 39.00068 51.00068 67.00068 35.00068 67.00068 39.00068 56.99932
## [417] 58.00137 52.99932
pbc$time
##   [1]  400 4500 1012 1925 1504 2503 1832 2466 2400   51 3762  304 3577 1217 3584
##  [16] 3672  769  131 4232 1356 3445  673  264 4079 4127 1444   77  549 4509  321
##  [31] 3839 4523 3170 3933 2847 3611  223 3244 2297 4467 1350 4453 4556 3428 4025
##  [46] 2256 2576 4427  708 2598 3853 2386 1000 1434 1360 1847 3282 4459 2224 4365
##  [61] 4256 3090  859 1487 3992 4191 2769 4039 1170 3458 4196 4184 4190 1827 1191
##  [76]   71  326 1690 3707  890 2540 3574 4050 4032 3358 1657  198 2452 1741 2689
##  [91]  460  388 3913  750  130 3850  611 3823 3820  552 3581 3099  110 3086 3092
## [106] 3222 3388 2583 2504 2105 2350 3445  980 3395 3422 3336 1083 2288  515 2033
## [121]  191 3297  971 3069 2468  824 3255 1037 3239 1413  850 2944 2796 3149 3150
## [136] 3098 2990 1297 2106 3059 3050 2419  786  943 2976 2615 2995 1427  762 2891
## [151] 2870 1152 2863  140 2666  853 2835 2475 1536 2772 2797  186 2055  264 1077
## [166] 2721 1682 2713 1212 2692 2574 2301 2657 2644 2624 1492 2609 2580 2573 2563
## [181] 2556 2555 2241  974 2527 1576  733 2332 2456 2504  216 2443  797 2449 2330
## [196] 2363 2365 2357 1592 2318 2294 2272 2221 2090 2081 2255 2171  904 2216 2224
## [211] 2195 2176 2178 1786 1080 2168  790 2170 2157 1235 2050  597  334 1945 2022
## [226] 1978  999 1967  348 1979 1165 1951 1932 1776 1882 1908 1882 1874  694 1831
## [241]  837 1810  930 1690 1790 1435  732 1785 1783 1769 1457 1770 1765  737 1735
## [256] 1701 1614 1702 1615 1656 1677 1666 1301 1542 1084 1614  179 1191 1363 1568
## [271] 1569 1525 1558 1447 1349 1481 1434 1420 1433 1412   41 1455 1030 1418 1401
## [286] 1408 1234 1067  799 1363  901 1329 1320 1302  877 1321  533 1300 1293  207
## [301] 1295 1271 1250 1230 1216 1216 1149 1153  994  939  839  788 4062 3561 2844
## [316] 2071 3030 1680   41 2403 1170 2011 3523 3468 4795 1236 4214 2111 1462 1746
## [331]   94  785 1518  466 3527 2635 2286  791 3492 3495  111 3231  625 3157 3021
## [346]  559 2812 2834 2855  662  727 2716 2698  990 2338 1616 2563 2537 2534  778
## [361]  617 2267 2249  359 1925  249 2202   43 1197 1095  489 2149 2103 1980 1347
## [376] 1478 1987 1168  597 1725 1899  221 1022 1639 1635 1654 1653 1560 1581 1419
## [391] 1443 1368  193 1367 1329 1343 1328 1375 1260 1223  935  943 1141 1092 1150
## [406]  703 1129 1086 1067 1072 1119 1097  989  681 1103 1055  691  976
  • Create vectors with continuous data.
vec1 <- c(1:100)
vec2 <- c(2, 32, 14, 23, 54, 13, 45)
  • Create a vector with categorical data.
vec3 <- c("male", "female", "female", "male", "female", "female")
  • Create a vector with logical data.
vec4 <- c(TRUE, TRUE, FALSE)

Matrices

  • Create a matrix using the time variable/vector from the pbc data set.
matrix(data = pbc$time[1:9], nrow = 3, ncol = 3)
##      [,1] [,2] [,3]
## [1,]  400 1925 1832
## [2,] 4500 1504 2466
## [3,] 1012 2503 2400

Useful functions to easily combine columns or rows are the cbind() and rbind() functions.
We can combine multiple columns as shown below.

age_time <- cbind(pbc$age, pbc$time)

We can combine multiple rows as shown below.

age_time <- rbind(pbc$age, pbc$time)

TAKE CARE when using these functions.

Columns_com <- cbind(c(1:4), c(1:8))

Since the first column has shorter length, R is recycling the numbers.  
* Create other matrices.
Assume a vector with the elements 1 to 4 and assume 2 rows and 2 columns.
By default the matrix will be filled in by column.

matrix(data = 1:4, nrow = 2, ncol = 2)
##      [,1] [,2]
## [1,]    1    3
## [2,]    2    4

Fill matrix in by row.

matrix(data = 1:4, nrow = 2, ncol = 2, byrow = TRUE)
##      [,1] [,2]
## [1,]    1    2
## [2,]    3    4

Arrays

  • Create an array with 3 rows, 3 columns and 2 matrices.
array(data = 1:18, dim = c(3, 3, 2))
## , , 1
## 
##      [,1] [,2] [,3]
## [1,]    1    4    7
## [2,]    2    5    8
## [3,]    3    6    9
## 
## , , 2
## 
##      [,1] [,2] [,3]
## [1,]   10   13   16
## [2,]   11   14   17
## [3,]   12   15   18
  • Create an array with 6 rows, 2 columns and 3 matrices.
array(data = 1:12, dim = c(6, 2, 3))
## , , 1
## 
##      [,1] [,2]
## [1,]    1    7
## [2,]    2    8
## [3,]    3    9
## [4,]    4   10
## [5,]    5   11
## [6,]    6   12
## 
## , , 2
## 
##      [,1] [,2]
## [1,]    1    7
## [2,]    2    8
## [3,]    3    9
## [4,]    4   10
## [5,]    5   11
## [6,]    6   12
## 
## , , 3
## 
##      [,1] [,2]
## [1,]    1    7
## [2,]    2    8
## [3,]    3    9
## [4,]    4   10
## [5,]    5   11
## [6,]    6   12

Notice that all matrices are the same. R is repeating the elements 1 to 12.

Data frames

  • Create a data frame using the pbc data set.
age_time_sex <- data.frame(pbc$age, pbc$time, pbc$sex)

Add names to the columns of the data frame.

age_time_sex <- data.frame(age = pbc$age, time = pbc$time, sex = pbc$sex)
  • Create other data frames.
DF <- data.frame(Age = c(30, 20, 50),
                 Sex = c("male", "female", "female"),
                 Drug = c("yes", "yes", "no"))
DF
DF <- data.frame(Age = runif(30, 1, 80),
                 Sex = sample(1:2, 30, replace = TRUE),
                 Drug = sample(1:3, 30, replace = TRUE))
DF

Lists

  • Create a list using the pbc data set.
list_pbc <- list(pbc$id, pbc$time)
  • Create other lists.
myList <- list(c(1:20), c("male", "female")) 
myList
## [[1]]
##  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20
## 
## [[2]]
## [1] "male"   "female"

Now add the names x to the first element and sex to the second element.

myList <- list(x = c(1:20), sex = c("male", "female")) 
myList
## $x
##  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20
## 
## $sex
## [1] "male"   "female"

Another example.

mylist = list(names = c("Jack","Mary"), child.ages = c(4,7,9,10,11))
mylist
## $names
## [1] "Jack" "Mary"
## 
## $child.ages
## [1]  4  7  9 10 11