Assignment #4
Bryce J. Parsons
3/2/2020
downloading and installing updated course packages from DataViz webpage
#install.packages("dplyr")
#install.packages("nycflights13")
#install.packages("tidyverse")loading associated libraries and packages (‘dplyr’)
library(nycflights13)
library(tidyverse)## ── Attaching packages ───────────────────────────────────────── tidyverse 1.3.0 ──## ✓ ggplot2 3.2.1 ✓ purrr 0.3.3
## ✓ tibble 2.1.3 ✓ dplyr 0.8.4
## ✓ tidyr 1.0.2 ✓ stringr 1.4.0
## ✓ readr 1.3.1 ✓ forcats 0.4.0## ── Conflicts ──────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()previewing all flights and loading nycflights13 data frame
nycflights13::flights## # A tibble: 336,776 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 544 545 -1 1004 1022
## 5 2013 1 1 554 600 -6 812 837
## 6 2013 1 1 554 558 -4 740 728
## 7 2013 1 1 555 600 -5 913 854
## 8 2013 1 1 557 600 -3 709 723
## 9 2013 1 1 557 600 -3 838 846
## 10 2013 1 1 558 600 -2 753 745
## # … with 336,766 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>view(flights)filtering for flights on Jan. 1
second line, saving the result for Jan 1
filter(flights, month == 1, day == 1)## # A tibble: 842 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 544 545 -1 1004 1022
## 5 2013 1 1 554 600 -6 812 837
## 6 2013 1 1 554 558 -4 740 728
## 7 2013 1 1 555 600 -5 913 854
## 8 2013 1 1 557 600 -3 709 723
## 9 2013 1 1 557 600 -3 838 846
## 10 2013 1 1 558 600 -2 753 745
## # … with 832 more rows, and 11 more variables: arr_delay <dbl>, carrier <chr>,
## # flight <int>, tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>,
## # distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>jan1 <- filter(flights, month == 1, day == 1)printing result and saving them to a variable
(dec25 <- filter(flights, month == 12, day == 25))## # A tibble: 719 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 12 25 456 500 -4 649 651
## 2 2013 12 25 524 515 9 805 814
## 3 2013 12 25 542 540 2 832 850
## 4 2013 12 25 546 550 -4 1022 1027
## 5 2013 12 25 556 600 -4 730 745
## 6 2013 12 25 557 600 -3 743 752
## 7 2013 12 25 557 600 -3 818 831
## 8 2013 12 25 559 600 -1 855 856
## 9 2013 12 25 559 600 -1 849 855
## 10 2013 12 25 600 600 0 850 846
## # … with 709 more rows, and 11 more variables: arr_delay <dbl>, carrier <chr>,
## # flight <int>, tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>,
## # distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>filtering for flights based on month 1, 11, 12
shows flights that departed in Jan for first line. Second line shows flights departed in Nov. or Dec.
filter(flights, month == 1)## # A tibble: 27,004 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 544 545 -1 1004 1022
## 5 2013 1 1 554 600 -6 812 837
## 6 2013 1 1 554 558 -4 740 728
## 7 2013 1 1 555 600 -5 913 854
## 8 2013 1 1 557 600 -3 709 723
## 9 2013 1 1 557 600 -3 838 846
## 10 2013 1 1 558 600 -2 753 745
## # … with 26,994 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>filter(flights, month == 11 | month == 12)## # A tibble: 55,403 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 11 1 5 2359 6 352 345
## 2 2013 11 1 35 2250 105 123 2356
## 3 2013 11 1 455 500 -5 641 651
## 4 2013 11 1 539 545 -6 856 827
## 5 2013 11 1 542 545 -3 831 855
## 6 2013 11 1 549 600 -11 912 923
## 7 2013 11 1 550 600 -10 705 659
## 8 2013 11 1 554 600 -6 659 701
## 9 2013 11 1 554 600 -6 826 827
## 10 2013 11 1 554 600 -6 749 751
## # … with 55,393 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>####short hand for selecting flights in either month 11, 12.
nov_dec <- filter(flights, month %in% c(11, 12))5.2.4 Exercises
1. Find all flights that had an arrival delay of two or more hours
filter(flights, arr_delay >= 120)## # A tibble: 10,200 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 811 630 101 1047 830
## 2 2013 1 1 848 1835 853 1001 1950
## 3 2013 1 1 957 733 144 1056 853
## 4 2013 1 1 1114 900 134 1447 1222
## 5 2013 1 1 1505 1310 115 1638 1431
## 6 2013 1 1 1525 1340 105 1831 1626
## 7 2013 1 1 1549 1445 64 1912 1656
## 8 2013 1 1 1558 1359 119 1718 1515
## 9 2013 1 1 1732 1630 62 2028 1825
## 10 2013 1 1 1803 1620 103 2008 1750
## # … with 10,190 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>2. Flew to Houston (IAH or HOU)
filter(flights, dest == "IAH" | dest == "HOU")## # A tibble: 9,313 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 623 627 -4 933 932
## 4 2013 1 1 728 732 -4 1041 1038
## 5 2013 1 1 739 739 0 1104 1038
## 6 2013 1 1 908 908 0 1228 1219
## 7 2013 1 1 1028 1026 2 1350 1339
## 8 2013 1 1 1044 1045 -1 1352 1351
## 9 2013 1 1 1114 900 134 1447 1222
## 10 2013 1 1 1205 1200 5 1503 1505
## # … with 9,303 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>3. Were operated by United, American, or Delta
filter(flights, carrier == "UA" | carrier == "DL" | carrier == "AA")## # A tibble: 139,504 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 554 600 -6 812 837
## 5 2013 1 1 554 558 -4 740 728
## 6 2013 1 1 558 600 -2 753 745
## 7 2013 1 1 558 600 -2 924 917
## 8 2013 1 1 558 600 -2 923 937
## 9 2013 1 1 559 600 -1 941 910
## 10 2013 1 1 559 600 -1 854 902
## # … with 139,494 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>4. Departed in summer (July, August, and September)
filter(flights, month == 7 | month == 8 | month == 9)## # A tibble: 86,326 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 7 1 1 2029 212 236 2359
## 2 2013 7 1 2 2359 3 344 344
## 3 2013 7 1 29 2245 104 151 1
## 4 2013 7 1 43 2130 193 322 14
## 5 2013 7 1 44 2150 174 300 100
## 6 2013 7 1 46 2051 235 304 2358
## 7 2013 7 1 48 2001 287 308 2305
## 8 2013 7 1 58 2155 183 335 43
## 9 2013 7 1 100 2146 194 327 30
## 10 2013 7 1 100 2245 135 337 135
## # … with 86,316 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>5. Arrived more than two hours late, but didn’t leave late
filter(flights, arr_delay > 120 & dep_delay <= 0)## # A tibble: 29 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 27 1419 1420 -1 1754 1550
## 2 2013 10 7 1350 1350 0 1736 1526
## 3 2013 10 7 1357 1359 -2 1858 1654
## 4 2013 10 16 657 700 -3 1258 1056
## 5 2013 11 1 658 700 -2 1329 1015
## 6 2013 3 18 1844 1847 -3 39 2219
## 7 2013 4 17 1635 1640 -5 2049 1845
## 8 2013 4 18 558 600 -2 1149 850
## 9 2013 4 18 655 700 -5 1213 950
## 10 2013 5 22 1827 1830 -3 2217 2010
## # … with 19 more rows, and 11 more variables: arr_delay <dbl>, carrier <chr>,
## # flight <int>, tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>,
## # distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>6. Were delayed by at least an hour, but made up over 30 minutes in flight
filter(flights, dep_delay >= 60 & arr_delay <= 30)## # A tibble: 239 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 3 1850 1745 65 2148 2120
## 2 2013 1 3 1950 1845 65 2228 2227
## 3 2013 1 3 2015 1915 60 2135 2111
## 4 2013 1 6 1019 900 79 1558 1530
## 5 2013 1 7 1543 1430 73 1758 1735
## 6 2013 1 11 1020 920 60 1311 1245
## 7 2013 1 12 1706 1600 66 1949 1927
## 8 2013 1 12 1953 1845 68 2154 2137
## 9 2013 1 19 1456 1355 61 1636 1615
## 10 2013 1 21 1531 1430 61 1843 1815
## # … with 229 more rows, and 11 more variables: arr_delay <dbl>, carrier <chr>,
## # flight <int>, tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>,
## # distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>7. Departed between midnight and 6am (inclusive)
filter(flights, dep_time >= 0000 & dep_time <= 600)## # A tibble: 9,344 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 544 545 -1 1004 1022
## 5 2013 1 1 554 600 -6 812 837
## 6 2013 1 1 554 558 -4 740 728
## 7 2013 1 1 555 600 -5 913 854
## 8 2013 1 1 557 600 -3 709 723
## 9 2013 1 1 557 600 -3 838 846
## 10 2013 1 1 558 600 -2 753 745
## # … with 9,334 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>8. Another useful dplyr filtering helper is between(). What does it do? Can you use it to simplify the code needed to answer the previous challenges?
#####Yes, you can use it to simplify the innequalitities. Here is an example:
filter(flights, between(dep_time, 0000, 600))## # A tibble: 9,344 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 517 515 2 830 819
## 2 2013 1 1 533 529 4 850 830
## 3 2013 1 1 542 540 2 923 850
## 4 2013 1 1 544 545 -1 1004 1022
## 5 2013 1 1 554 600 -6 812 837
## 6 2013 1 1 554 558 -4 740 728
## 7 2013 1 1 555 600 -5 913 854
## 8 2013 1 1 557 600 -3 709 723
## 9 2013 1 1 557 600 -3 838 846
## 10 2013 1 1 558 600 -2 753 745
## # … with 9,334 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>9. How many flights have a missing dep_time? What other variables are missing? What might these rows represent?
count(filter(flights, is.na(dep_time)))## # A tibble: 1 x 1
## n
## <int>
## 1 8255#8255 flights w/ a missing dep time. Other varibales that are missing include dep_delay and arr_time. This could indicate that the flight was canceled or mischeduled. 10. Why is NA ^ 0 not missing? Why is NA | TRUE not missing? Why is FALSE & NA not missing? Can you figure out the general rule? (NA * 0 is a tricky counterexample!)
The reason being that if you cant search for something that doesn’t exist, an NA doesn’t exist in the data base rather a blank exists and an NA is returned.
5.3.1
1 How could you use arrange() to sort all missing values to the start? (Hint: use is.na()).
arrange(flights, dep_time)%>%
tail()## # A tibble: 6 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 9 30 NA 1842 NA NA 2019
## 2 2013 9 30 NA 1455 NA NA 1634
## 3 2013 9 30 NA 2200 NA NA 2312
## 4 2013 9 30 NA 1210 NA NA 1330
## 5 2013 9 30 NA 1159 NA NA 1344
## 6 2013 9 30 NA 840 NA NA 1020
## # … with 11 more variables: arr_delay <dbl>, carrier <chr>, flight <int>,
## # tailnum <chr>, origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
## # hour <dbl>, minute <dbl>, time_hour <dttm>#2 Sort flights to find the most delayed flights. Find the flights that left earliest.
arrange(flights, desc(dep_delay))## # A tibble: 336,776 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 9 641 900 1301 1242 1530
## 2 2013 6 15 1432 1935 1137 1607 2120
## 3 2013 1 10 1121 1635 1126 1239 1810
## 4 2013 9 20 1139 1845 1014 1457 2210
## 5 2013 7 22 845 1600 1005 1044 1815
## 6 2013 4 10 1100 1900 960 1342 2211
## 7 2013 3 17 2321 810 911 135 1020
## 8 2013 6 27 959 1900 899 1236 2226
## 9 2013 7 22 2257 759 898 121 1026
## 10 2013 12 5 756 1700 896 1058 2020
## # … with 336,766 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>#3 Sort flights to find the fastest (highest speed) flights.
arrange(flights, (air_time))## # A tibble: 336,776 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 16 1355 1315 40 1442 1411
## 2 2013 4 13 537 527 10 622 628
## 3 2013 12 6 922 851 31 1021 954
## 4 2013 2 3 2153 2129 24 2247 2224
## 5 2013 2 5 1303 1315 -12 1342 1411
## 6 2013 2 12 2123 2130 -7 2211 2225
## 7 2013 3 2 1450 1500 -10 1547 1608
## 8 2013 3 8 2026 1935 51 2131 2056
## 9 2013 3 18 1456 1329 87 1533 1426
## 10 2013 3 19 2226 2145 41 2305 2246
## # … with 336,766 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>#4 Which flights travelled the farthest? Which travelled the shortest?
arrange(flights, (distance))## # A tibble: 336,776 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 7 27 NA 106 NA NA 245
## 2 2013 1 3 2127 2129 -2 2222 2224
## 3 2013 1 4 1240 1200 40 1333 1306
## 4 2013 1 4 1829 1615 134 1937 1721
## 5 2013 1 4 2128 2129 -1 2218 2224
## 6 2013 1 5 1155 1200 -5 1241 1306
## 7 2013 1 6 2125 2129 -4 2224 2224
## 8 2013 1 7 2124 2129 -5 2212 2224
## 9 2013 1 8 2127 2130 -3 2304 2225
## 10 2013 1 9 2126 2129 -3 2217 2224
## # … with 336,766 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>arrange(flights, desc(distance))## # A tibble: 336,776 x 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time
## <int> <int> <int> <int> <int> <dbl> <int> <int>
## 1 2013 1 1 857 900 -3 1516 1530
## 2 2013 1 2 909 900 9 1525 1530
## 3 2013 1 3 914 900 14 1504 1530
## 4 2013 1 4 900 900 0 1516 1530
## 5 2013 1 5 858 900 -2 1519 1530
## 6 2013 1 6 1019 900 79 1558 1530
## 7 2013 1 7 1042 900 102 1620 1530
## 8 2013 1 8 901 900 1 1504 1530
## 9 2013 1 9 641 900 1301 1242 1530
## 10 2013 1 10 859 900 -1 1449 1530
## # … with 336,766 more rows, and 11 more variables: arr_delay <dbl>,
## # carrier <chr>, flight <int>, tailnum <chr>, origin <chr>, dest <chr>,
## # air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>, time_hour <dttm>5.4.1
#1. Brainstorm as many ways as possible to select dep_time, dep_delay, arr_time, and arr_delay from flights.
select(flights, dep_time, dep_delay, arr_time, arr_delay)## # A tibble: 336,776 x 4
## dep_time dep_delay arr_time arr_delay
## <int> <dbl> <int> <dbl>
## 1 517 2 830 11
## 2 533 4 850 20
## 3 542 2 923 33
## 4 544 -1 1004 -18
## 5 554 -6 812 -25
## 6 554 -4 740 12
## 7 555 -5 913 19
## 8 557 -3 709 -14
## 9 557 -3 838 -8
## 10 558 -2 753 8
## # … with 336,766 more rows#2 What happens if you include the name of a variable multiple times in a select() call?
select(flights, year, month, day, year, year)## # A tibble: 336,776 x 3
## year month day
## <int> <int> <int>
## 1 2013 1 1
## 2 2013 1 1
## 3 2013 1 1
## 4 2013 1 1
## 5 2013 1 1
## 6 2013 1 1
## 7 2013 1 1
## 8 2013 1 1
## 9 2013 1 1
## 10 2013 1 1
## # … with 336,766 more rows#3 What does the one_of() function do? Why might it be helpful in conjunction with this vector?
vars <- c("year", "month", "day", "dep_delay", "arr_delay")
select(flights, one_of(vars))## # A tibble: 336,776 x 5
## year month day dep_delay arr_delay
## <int> <int> <int> <dbl> <dbl>
## 1 2013 1 1 2 11
## 2 2013 1 1 4 20
## 3 2013 1 1 2 33
## 4 2013 1 1 -1 -18
## 5 2013 1 1 -6 -25
## 6 2013 1 1 -4 12
## 7 2013 1 1 -5 19
## 8 2013 1 1 -3 -14
## 9 2013 1 1 -3 -8
## 10 2013 1 1 -2 8
## # … with 336,766 more rows#4 Does the result of running the following code surprise you? How do the select helpers deal with case by default? How can you change that default?
select(flights, contains("TIME"))## # A tibble: 336,776 x 6
## dep_time sched_dep_time arr_time sched_arr_time air_time time_hour
## <int> <int> <int> <int> <dbl> <dttm>
## 1 517 515 830 819 227 2013-01-01 05:00:00
## 2 533 529 850 830 227 2013-01-01 05:00:00
## 3 542 540 923 850 160 2013-01-01 05:00:00
## 4 544 545 1004 1022 183 2013-01-01 05:00:00
## 5 554 600 812 837 116 2013-01-01 06:00:00
## 6 554 558 740 728 150 2013-01-01 05:00:00
## 7 555 600 913 854 158 2013-01-01 06:00:00
## 8 557 600 709 723 53 2013-01-01 06:00:00
## 9 557 600 838 846 140 2013-01-01 06:00:00
## 10 558 600 753 745 138 2013-01-01 06:00:00
## # … with 336,766 more rows5.5 Add New variable w/ Mutate()
mutate() always adds new columns at the end of your dataset
flights_sml <- select(flights,
year:day,
ends_with("delay"),
distance,
air_time
)
mutate(flights_sml,
gain = dep_delay - arr_delay,
speed = distance / air_time * 60
)## # A tibble: 336,776 x 9
## year month day dep_delay arr_delay distance air_time gain speed
## <int> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 2013 1 1 2 11 1400 227 -9 370.
## 2 2013 1 1 4 20 1416 227 -16 374.
## 3 2013 1 1 2 33 1089 160 -31 408.
## 4 2013 1 1 -1 -18 1576 183 17 517.
## 5 2013 1 1 -6 -25 762 116 19 394.
## 6 2013 1 1 -4 12 719 150 -16 288.
## 7 2013 1 1 -5 19 1065 158 -24 404.
## 8 2013 1 1 -3 -14 229 53 11 259.
## 9 2013 1 1 -3 -8 944 140 5 405.
## 10 2013 1 1 -2 8 733 138 -10 319.
## # … with 336,766 more rowstransmute(flights,
dep_time,
hour = dep_time %/% 100,
minute = dep_time %% 100
)## # A tibble: 336,776 x 3
## dep_time hour minute
## <int> <dbl> <dbl>
## 1 517 5 17
## 2 533 5 33
## 3 542 5 42
## 4 544 5 44
## 5 554 5 54
## 6 554 5 54
## 7 555 5 55
## 8 557 5 57
## 9 557 5 57
## 10 558 5 58
## # … with 336,766 more rows5.5.2
1. Currently dep_time and sched_dep_time are convenient to look at, but hard to compute with because they’re not really continuous numbers. Convert them to a more convenient representation of number of minutes since midnight.
1504 %/% 100## [1] 152. Compare air_time with arr_time - dep_time. What do you expect to see? What do you see? What do you need to do to fix it?
flights_airtime <-
mutate(flights,
dep_time = (dep_time %/% 100 * 60 + dep_time %% 100) %% 1440,
arr_time = (arr_time %/% 100 * 60 + arr_time %% 100) %% 1440,
air_time_diff = air_time - arr_time + dep_time
)4. Find the 10 most delayed flights using a ranking function. How do you want to handle ties? Carefully read the documentation for min_rank().
rankme <- tibble(
x = c(10, 5, 1, 5, 5)
)
rankme <- mutate(rankme,
x_row_number = row_number(x),
x_min_rank = min_rank(x),
x_dense_rank = dense_rank(x)
)
arrange(rankme, x)## # A tibble: 5 x 4
## x x_row_number x_min_rank x_dense_rank
## <dbl> <int> <int> <int>
## 1 1 1 1 1
## 2 5 2 2 2
## 3 5 3 2 2
## 4 5 4 2 2
## 5 10 5 5 35. What does 1:3 + 1:10 return? Why?
1:3 + 1:10## Warning in 1:3 + 1:10: longer object length is not a multiple of shorter object
## length## [1] 2 4 6 5 7 9 8 10 12 11# The code also produces a warning that the shorter vector is not a multiple of the longer vector. A warning is provided since often, but not always, this indicates a bug in the code.6. What trigonometric functions does R provide?
All trigonometric functions are all described in a single help page, named Trig. You can open the documentation for these functions with ?Trig or by using ? with any of the following functions, for example:?sin. R provides functions for the three primary trigonometric functions: sine (sin())), cosine (cos()), and tangent (tan()). The input angles to all these functions are in radians.
5.6 Grouped summaries with summarise()
summarise(flights, delay = mean(dep_delay, na.rm = TRUE))## # A tibble: 1 x 1
## delay
## <dbl>
## 1 12.65.6.1 (GGPlot, I just did one example since we didn’t have to do it all.)
by_dest <- group_by(flights, dest)
delay <- summarise(by_dest,
count = n(),
dist = mean(distance, na.rm = TRUE),
delay = mean(arr_delay, na.rm = TRUE)
)
delay <- filter(delay, count > 20, dest != "HNL")
ggplot(data = delay, mapping = aes(x = dist, y = delay)) +
geom_point(aes(size = count), alpha = 1/3) +
geom_smooth(se = FALSE)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
- Group flights by destination.
- Summarise to compute distance, average delay, and number of flights.
- Filter to remove noisy points and Honolulu airport, which is almost twice as far away as the next closest airport.
delays <- flights %>%
group_by(dest) %>%
summarise(
count = n(),
dist = mean(distance, na.rm = TRUE),
delay = mean(arr_delay, na.rm = TRUE)
) %>%
filter(count > 20, dest != "HNL")5.6.2 MISSING VALUES
Example of how using the na.rm fucntion. na.rm removes missing values prior to computing.
flights %>%
group_by(year, month, day) %>%
summarise(mean = mean(dep_delay, na.rm = TRUE))## # A tibble: 365 x 4
## # Groups: year, month [12]
## year month day mean
## <int> <int> <int> <dbl>
## 1 2013 1 1 11.5
## 2 2013 1 2 13.9
## 3 2013 1 3 11.0
## 4 2013 1 4 8.95
## 5 2013 1 5 5.73
## 6 2013 1 6 7.15
## 7 2013 1 7 5.42
## 8 2013 1 8 2.55
## 9 2013 1 9 2.28
## 10 2013 1 10 2.84
## # … with 355 more rows5.6.3 Counts
Whenever you do any aggregation, it’s always a good idea to include either a count (n()), or a count of non-missing values (sum(!is.na(x))). That way you can check that you’re not drawing conclusions based on very small amounts of data.
5.6.4 Useful summary functions
Just using means, counts, and sum can get you a long way, but R provides many other useful summary functions:
Measures of location: we’ve used mean(x), but median(x) is also useful. The mean is the sum divided by the length; the median is a value where 50% of x is above it, and 50% is below it. It’s sometimes useful to combine aggregation with logical subsetting. We haven’t talked about this sort of subsetting yet, but you’ll learn more about it in subsetting.
##5.6.7 Exercises
Brainstorm at least 5 different ways to assess the typical delay characteristics of a group of flights. Consider the following scenarios:
* A flight is 15 minutes early 50% of the time, and 15 minutes late 50% of the time.
* A flight is always 10 minutes late.
* A flight is 30 minutes early 50% of the time, and 30 minutes late 50% of the time.
* 99% of the time a flight is on time. 1% of the time it’s 2 hours late.
#In many scenarios, arrival delay is more important. In most cases, being arriving late is more costly to the passenger since it could disrupt the next stages of their travel, such as connecting flights or scheduled meetings.
#If a departure is delayed without affecting the arrival time, this delay will not have those affects plans nor does it affect the total time spent traveling. This delay could be beneficial, if less time is spent in the cramped confines of the airplane itself, or a negative, if that delayed time is still spent in the cramped confines of the airplane on the runway.
#Variation in arrival time is worse than consistency. If a flight is always 30 minutes late and that delay is known, then it is as if the arrival time is that delayed time. The traveler could easily plan for this. But higher variation in flight times makes it harder to plan.Which is more important: arrival delay or departure delay?
##### - Arrival Delay is more important becasue it is harder to remedy an arrival delay.
Come up with another approach that will give you the same output as not_cancelled %>% count(dest) and not_cancelled %>% count(tailnum, wt = distance) (without using count()).
not_cancelled <- flights %>%
filter(!is.na(dep_delay), !is.na(arr_delay))Which carrier has the worst delays? Challenge: can you disentangle the effects of bad airports vs. bad carriers? Why/why not? (Hint: think about flights %>% group_by(carrier, dest) %>% summarise(n()))
flights %>%
group_by(carrier) %>%
summarise(arr_delay = mean(arr_delay, na.rm = TRUE)) %>%
arrange(desc(arr_delay))## # A tibble: 16 x 2
## carrier arr_delay
## <chr> <dbl>
## 1 F9 21.9
## 2 FL 20.1
## 3 EV 15.8
## 4 YV 15.6
## 5 OO 11.9
## 6 MQ 10.8
## 7 WN 9.65
## 8 B6 9.46
## 9 9E 7.38
## 10 UA 3.56
## 11 US 2.13
## 12 VX 1.76
## 13 DL 1.64
## 14 AA 0.364
## 15 HA -6.92
## 16 AS -9.93What does the sort argument to count() do. When might you use it?
- The sort argument to count() sorts the results in order of n. You could use this anytime you would run count() followed by arrange().
##5.7 Grouped mutates (and filters) ###Exercise 5.7.1 ####Summary functions (mean()), offset functions (lead(), lag()), ranking functions (min_rank(), row_number()), operate within each group when used with group_by() in mutate() or filter(). Arithmetic operators (+, -), logical operators (<, ==), modular arithmetic operators (%%, %/%), logarithmic functions (log) are not affected by group_by. ####Summary functions like mean(), median(), sum(), std() and others covered in the section Useful Summary Functions calculate their values within each group when used with mutate() or filter() and group_by().
tibble(
x = 1:9,
group = rep(c("a", "b", "c"), each = 3)
) %>%
mutate(x_mean = mean(x)) %>%
group_by(group) %>%
mutate(x_mean_2 = mean(x))## # A tibble: 9 x 4
## # Groups: group [3]
## x group x_mean x_mean_2
## <int> <chr> <dbl> <dbl>
## 1 1 a 5 2
## 2 2 a 5 2
## 3 3 a 5 2
## 4 4 b 5 5
## 5 5 b 5 5
## 6 6 b 5 5
## 7 7 c 5 8
## 8 8 c 5 8
## 9 9 c 5 8tibble(
x = 1:9,
group = rep(c("a", "b", "c"), each = 3)
) %>%
mutate(y = x + 2) %>%
group_by(group) %>%
mutate(z = x + 2)## # A tibble: 9 x 4
## # Groups: group [3]
## x group y z
## <int> <chr> <dbl> <dbl>
## 1 1 a 3 3
## 2 2 a 4 4
## 3 3 a 5 5
## 4 4 b 6 6
## 5 5 b 7 7
## 6 6 b 8 8
## 7 7 c 9 9
## 8 8 c 10 10
## 9 9 c 11 11EXERCISE 5.7.2
1. Which plane (tailnum) has the worst on-time record?
flights %>%
filter(!is.na(tailnum)) %>%
mutate(on_time = !is.na(arr_time) & (arr_delay <= 0)) %>%
group_by(tailnum) %>%
summarise(on_time = mean(on_time), n = n()) %>%
filter(min_rank(on_time) == 1)## # A tibble: 110 x 3
## tailnum on_time n
## <chr> <dbl> <int>
## 1 N121DE 0 2
## 2 N136DL 0 1
## 3 N143DA 0 1
## 4 N17627 0 2
## 5 N240AT 0 5
## 6 N26906 0 1
## 7 N295AT 0 4
## 8 N302AS 0 1
## 9 N303AS 0 1
## 10 N32626 0 1
## # … with 100 more rowsEXERCISE 5.7.3
What time of day should you fly if you want to avoid delays as much as possible?
#flights %>%
#group_by(hour) %>%
#summarise(arr_delay = mean(arr_delay, na.rm = TRUE)) %>%EXERCISE 5.7.4
For each destination, compute the total minutes of delay. For each flight, compute the proportion of the total delay for its destination.
flights %>%
filter(arr_delay > 0) %>%
group_by(dest) %>%
mutate(
arr_delay_total = sum(arr_delay),
arr_delay_prop = arr_delay / arr_delay_total
) %>%
select(
dest, month, day, dep_time, carrier, flight,
arr_delay, arr_delay_prop
) %>%
arrange(dest, desc(arr_delay_prop))## # A tibble: 133,004 x 8
## # Groups: dest [103]
## dest month day dep_time carrier flight arr_delay arr_delay_prop
## <chr> <int> <int> <int> <chr> <int> <dbl> <dbl>
## 1 ABQ 7 22 2145 B6 1505 153 0.0341
## 2 ABQ 12 14 2223 B6 65 149 0.0332
## 3 ABQ 10 15 2146 B6 65 138 0.0308
## 4 ABQ 7 23 2206 B6 1505 137 0.0305
## 5 ABQ 12 17 2220 B6 65 136 0.0303
## 6 ABQ 7 10 2025 B6 1505 126 0.0281
## 7 ABQ 7 30 2212 B6 1505 118 0.0263
## 8 ABQ 7 28 2038 B6 1505 117 0.0261
## 9 ABQ 12 8 2049 B6 65 114 0.0254
## 10 ABQ 9 2 2212 B6 1505 109 0.0243
## # … with 132,994 more rows5.7.5
####Delays are typically temporally correlated: even once the problem that caused the initial delay has been resolved, later flights are delayed to allow earlier flights to leave. Using lag() explore how the delay of a flight is related to the delay of the immediately preceding flight.
lagged_delays <- flights %>%
arrange(origin, month, day, dep_time) %>%
group_by(origin) %>%
mutate(dep_delay_lag = lag(dep_delay)) %>%
filter(!is.na(dep_delay), !is.na(dep_delay_lag))Exercise 5.7.6
Look at each destination. Can you find flights that are suspiciously fast? (i.e. flights that represent a potential data entry error). Compute the air time of a flight relative to the shortest flight to that destination. Which flights were most delayed in the air?
standardized_flights <- flights %>%
filter(!is.na(air_time)) %>%
group_by(dest, origin) %>%
mutate(
air_time_mean = mean(air_time),
air_time_sd = sd(air_time),
n = n()
) %>%
ungroup() %>%
mutate(air_time_standard = (air_time - air_time_mean) / (air_time_sd + 1))EXERCISE 5.7.7
Find all destinations that are flown by at least two carriers. Use that information to rank the carriers.
flights %>%
# find all airports with > 1 carrier
group_by(dest) %>%
mutate(n_carriers = n_distinct(carrier)) %>%
filter(n_carriers > 1) %>%
# rank carriers by numer of destinations
group_by(carrier) %>%
summarize(n_dest = n_distinct(dest)) %>%
arrange(desc(n_dest))## # A tibble: 16 x 2
## carrier n_dest
## <chr> <int>
## 1 EV 51
## 2 9E 48
## 3 UA 42
## 4 DL 39
## 5 B6 35
## 6 AA 19
## 7 MQ 19
## 8 WN 10
## 9 OO 5
## 10 US 5
## 11 VX 4
## 12 YV 3
## 13 FL 2
## 14 AS 1
## 15 F9 1
## 16 HA 1Exercise 5.7.8
For each plane, count the number of flights before the first delay of greater than 1 hour.
flights %>%
# sort in increasing order
select(tailnum, year, month, day, dep_delay) %>%
filter(!is.na(dep_delay)) %>%
arrange(tailnum, year, month, day) %>%
group_by(tailnum) %>%
# cumulative number of flights delayed over one hour
mutate(cumulative_hr_delays = cumsum(dep_delay > 60)) %>%
# count the number of flights == 0
summarise(total_flights = sum(cumulative_hr_delays < 1)) %>%
arrange(total_flights)## # A tibble: 4,037 x 2
## tailnum total_flights
## <chr> <int>
## 1 D942DN 0
## 2 N10575 0
## 3 N11106 0
## 4 N11109 0
## 5 N11187 0
## 6 N11199 0
## 7 N12967 0
## 8 N13550 0
## 9 N136DL 0
## 10 N13903 0
## # … with 4,027 more rows12 Tidy Data
table1## # A tibble: 6 x 4
## country year cases population
## <chr> <int> <int> <int>
## 1 Afghanistan 1999 745 19987071
## 2 Afghanistan 2000 2666 20595360
## 3 Brazil 1999 37737 172006362
## 4 Brazil 2000 80488 174504898
## 5 China 1999 212258 1272915272
## 6 China 2000 213766 1280428583table2## # A tibble: 12 x 4
## country year type count
## <chr> <int> <chr> <int>
## 1 Afghanistan 1999 cases 745
## 2 Afghanistan 1999 population 19987071
## 3 Afghanistan 2000 cases 2666
## 4 Afghanistan 2000 population 20595360
## 5 Brazil 1999 cases 37737
## 6 Brazil 1999 population 172006362
## 7 Brazil 2000 cases 80488
## 8 Brazil 2000 population 174504898
## 9 China 1999 cases 212258
## 10 China 1999 population 1272915272
## 11 China 2000 cases 213766
## 12 China 2000 population 1280428583table3## # A tibble: 6 x 3
## country year rate
## * <chr> <int> <chr>
## 1 Afghanistan 1999 745/19987071
## 2 Afghanistan 2000 2666/20595360
## 3 Brazil 1999 37737/172006362
## 4 Brazil 2000 80488/174504898
## 5 China 1999 212258/1272915272
## 6 China 2000 213766/1280428583table4a## # A tibble: 3 x 3
## country `1999` `2000`
## * <chr> <int> <int>
## 1 Afghanistan 745 2666
## 2 Brazil 37737 80488
## 3 China 212258 213766table4b## # A tibble: 3 x 3
## country `1999` `2000`
## * <chr> <int> <int>
## 1 Afghanistan 19987071 20595360
## 2 Brazil 172006362 174504898
## 3 China 1272915272 1280428583Exercise 12.2.2
Extract the number of TB cases per country per year.
Extract the matching population per country per year. Divide cases by population, and multiply by 10000. Store back in the appropriate place.
t2_cases <- filter(table2, type == "cases") %>%
rename(cases = count) %>%
arrange(country, year)
t2_population <- filter(table2, type == "population") %>%
rename(population = count) %>%
arrange(country, year)t2_cases_per_cap <- tibble(
year = t2_cases$year,
country = t2_cases$country,
cases = t2_cases$cases,
population = t2_population$population
) %>%
mutate(cases_per_cap = (cases / population) * 10000) %>%
select(country, year, cases_per_cap)t2_cases_per_cap <- t2_cases_per_cap %>%
mutate(type = "cases_per_cap") %>%
rename(count = cases_per_cap)bind_rows(table2, t2_cases_per_cap) %>%
arrange(country, year, type, count)## # A tibble: 18 x 4
## country year type count
## <chr> <int> <chr> <dbl>
## 1 Afghanistan 1999 cases 7.45e+2
## 2 Afghanistan 1999 cases_per_cap 3.73e-1
## 3 Afghanistan 1999 population 2.00e+7
## 4 Afghanistan 2000 cases 2.67e+3
## 5 Afghanistan 2000 cases_per_cap 1.29e+0
## 6 Afghanistan 2000 population 2.06e+7
## 7 Brazil 1999 cases 3.77e+4
## 8 Brazil 1999 cases_per_cap 2.19e+0
## 9 Brazil 1999 population 1.72e+8
## 10 Brazil 2000 cases 8.05e+4
## 11 Brazil 2000 cases_per_cap 4.61e+0
## 12 Brazil 2000 population 1.75e+8
## 13 China 1999 cases 2.12e+5
## 14 China 1999 cases_per_cap 1.67e+0
## 15 China 1999 population 1.27e+9
## 16 China 2000 cases 2.14e+5
## 17 China 2000 cases_per_cap 1.67e+0
## 18 China 2000 population 1.28e+9table4c <-
tibble(
country = table4a$country,
`1999` = table4a[["1999"]] / table4b[["1999"]] * 10000,
`2000` = table4a[["2000"]] / table4b[["2000"]] * 10000
)
table4c## # A tibble: 3 x 3
## country `1999` `2000`
## <chr> <dbl> <dbl>
## 1 Afghanistan 0.373 1.29
## 2 Brazil 2.19 4.61
## 3 China 1.67 1.67Excecise 12.2.3
table2 %>%
filter(type == "cases") %>%
ggplot(aes(year, count)) +
geom_line(aes(group = country), colour = "grey50") +
geom_point(aes(colour = country)) +
scale_x_continuous(breaks = unique(table2$year)) +
ylab("cases")
Exercise 12.3.1
stocks <- tibble(
year = c(2015, 2015, 2016, 2016),
half = c(1, 2, 1, 2),
return = c(1.88, 0.59, 0.92, 0.17)
)
stocks %>%
spread(year, return) %>%
gather(`2015`:`2016`, key = "year", value = "return")## # A tibble: 4 x 3
## half year return
## <dbl> <chr> <dbl>
## 1 1 2015 1.88
## 2 2 2015 0.59
## 3 1 2016 0.92
## 4 2 2016 0.17#The functions spread() and gather() are not perfectly symmetrical because column type information is lost. When we use gather() on a data frame, it discards the original column types.stocks %>%
spread(year, return)## # A tibble: 2 x 3
## half `2015` `2016`
## <dbl> <dbl> <dbl>
## 1 1 1.88 0.92
## 2 2 0.59 0.17# In this example, the column year is numeric. After running spread() and gather(), the year column is a character vector. After spread(), the years are column names.stocks %>%
spread(year, return) %>%
gather(`2015`:`2016`, key = "year", value = "return")## # A tibble: 4 x 3
## half year return
## <dbl> <chr> <dbl>
## 1 1 2015 1.88
## 2 2 2015 0.59
## 3 1 2016 0.92
## 4 2 2016 0.17#The following use of gather() will create a column, year, from the column names.12.4 Separating & Uniting
Exercise 12.4.1
What do the extra and fill arguments do in separate()? Experiment with the various options for the following two toy datasets.
tibble(x = c("a,b,c", "d,e,f,g", "h,i,j")) %>%
separate(x, c("one", "two", "three"))## Warning: Expected 3 pieces. Additional pieces discarded in 1 rows [2].## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e f
## 3 h i jtibble(x = c("a,b,c", "d,e", "f,g,i")) %>%
separate(x, c("one", "two", "three"))## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 1 rows [2].## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e <NA>
## 3 f g itibble(x = c("a,b,c", "d,e,f,g", "h,i,j")) %>%
separate(x, c("one", "two", "three"))## Warning: Expected 3 pieces. Additional pieces discarded in 1 rows [2].## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e f
## 3 h i jtibble(x = c("a,b,c", "d,e,f,g", "h,i,j")) %>%
separate(x, c("one", "two", "three"), extra = "drop")## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e f
## 3 h i jtibble(x = c("a,b,c", "d,e,f,g", "h,i,j")) %>%
separate(x, c("one", "two", "three"), extra = "merge")## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e f,g
## 3 h i jtibble(x = c("a,b,c", "d,e", "f,g,i")) %>%
separate(x, c("one", "two", "three"))## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 1 rows [2].## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e <NA>
## 3 f g itibble(x = c("a,b,c", "d,e", "f,g,i")) %>%
separate(x, c("one", "two", "three"), fill = "right")## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 d e <NA>
## 3 f g itibble(x = c("a,b,c", "d,e", "f,g,i")) %>%
separate(x, c("one", "two", "three"), fill = "left")## # A tibble: 3 x 3
## one two three
## <chr> <chr> <chr>
## 1 a b c
## 2 <NA> d e
## 3 f g iExercise 12.4.2
Both unite() and separate() have a remove argument. What does it do? Why would you set it to FALSE?
#The remove argument discards input columns in the result data frame. You would set it to FALSE if you want to create a new variable, but keep the old one.Exercise 12.4.3
Compare and contrast separate() and extract(), Why are there three variations of separation (by position, by separator, and with groups), but only one unite?
#The function separate(), splits a column into multiple columns by separator, if the sep argument is a character vector, or by character positions, if sep is numeric.12.5 Missing values
Exercise 12.5.1
Compare and contrast the fill arguments to spread() and complete().
#In spread(), the fill argument explicitly sets the value to replace NAs. In complete(), the fill argument also sets a value to replace NAs but it is named list, allowing for different values for different variables. Also, both cases replace both implicit and explicit missing values.Exercise 12.5.2
What does the direction argument to fill() do?
#With fill, the direction determines whether NA values should be replaced by the previous non-missing value ("down") or the next non-missing value ("up").12.6 Case Study
Exercise 12.6.1
In this case study, I set na.rm = TRUE just to make it easier to check that we had the correct values. Is this reasonable? Think about how missing values are represented in this dataset. Are there implicit missing values? What’s the difference between an NA and zero?
#The reasonableness of using na.rm = TRUE depends on how missing values are represented in this dataset. The main concern is whether a missing value means that there were no cases of TB or whether it means that the WHO does not have data on the number of TB cases. Here are some things we should look for to help distinguish between these cases.
#If there are no 0 values in the data, then missing values may be used to indicate no cases.
#If there are both explicit and implicit missing values, then it suggests that missing values are being used differently. In that case, it is likely that explicit missing values would mean no cases, and implicit missing values would mean no data on the number of cases.
who %>%
pivot_longer(
cols = new_sp_m014:newrel_f65,
names_to = "key",
values_to = "cases",
values_drop_na = TRUE
) %>%
mutate(
key = stringr::str_replace(key, "newrel", "new_rel")
) %>%
separate(key, c("new", "var", "sexage")) %>%
select(-new, -iso2, -iso3) %>%
separate(sexage, c("sex", "age"), sep = 1)## # A tibble: 76,046 x 6
## country year var sex age cases
## <chr> <int> <chr> <chr> <chr> <int>
## 1 Afghanistan 1997 sp m 014 0
## 2 Afghanistan 1997 sp m 1524 10
## 3 Afghanistan 1997 sp m 2534 6
## 4 Afghanistan 1997 sp m 3544 3
## 5 Afghanistan 1997 sp m 4554 5
## 6 Afghanistan 1997 sp m 5564 2
## 7 Afghanistan 1997 sp m 65 0
## 8 Afghanistan 1997 sp f 014 5
## 9 Afghanistan 1997 sp f 1524 38
## 10 Afghanistan 1997 sp f 2534 36
## # … with 76,036 more rows