R for Data Science
Ch4: Workflow: basics
Import data
flights## # A tibble: 336,776 × 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
## # ℹ 336,766 more rows
## # ℹ 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 rows
filter(flights, month == 1, day == 1)## # A tibble: 842 × 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
## # ℹ 832 more rows
## # ℹ 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 == 1 & day == 1)## # A tibble: 842 × 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
## # ℹ 832 more rows
## # ℹ 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 == 1 | day == 1)## # A tibble: 37,198 × 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
## # ℹ 37,188 more rows
## # ℹ 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 %in% c(11, 12))## # A tibble: 55,403 × 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
## # ℹ 55,393 more rows
## # ℹ 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 rows
arrange(flights, desc(month), desc(day))## # A tibble: 336,776 × 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 31 13 2359 14 439 437
## 2 2013 12 31 18 2359 19 449 444
## 3 2013 12 31 26 2245 101 129 2353
## 4 2013 12 31 459 500 -1 655 651
## 5 2013 12 31 514 515 -1 814 812
## 6 2013 12 31 549 551 -2 925 900
## 7 2013 12 31 550 600 -10 725 745
## 8 2013 12 31 552 600 -8 811 826
## 9 2013 12 31 553 600 -7 741 754
## 10 2013 12 31 554 550 4 1024 1027
## # ℹ 336,766 more rows
## # ℹ 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>Select columns
select(flights, year:dep_time)## # A tibble: 336,776 × 4
## year month day dep_time
## <int> <int> <int> <int>
## 1 2013 1 1 517
## 2 2013 1 1 533
## 3 2013 1 1 542
## 4 2013 1 1 544
## 5 2013 1 1 554
## 6 2013 1 1 554
## 7 2013 1 1 555
## 8 2013 1 1 557
## 9 2013 1 1 557
## 10 2013 1 1 558
## # ℹ 336,766 more rowsselect(flights, year, month, day, dep_time)## # A tibble: 336,776 × 4
## year month day dep_time
## <int> <int> <int> <int>
## 1 2013 1 1 517
## 2 2013 1 1 533
## 3 2013 1 1 542
## 4 2013 1 1 544
## 5 2013 1 1 554
## 6 2013 1 1 554
## 7 2013 1 1 555
## 8 2013 1 1 557
## 9 2013 1 1 557
## 10 2013 1 1 558
## # ℹ 336,766 more rowsselect(flights, year, month, day, dep_time, dep_delay)## # A tibble: 336,776 × 5
## year month day dep_time dep_delay
## <int> <int> <int> <int> <dbl>
## 1 2013 1 1 517 2
## 2 2013 1 1 533 4
## 3 2013 1 1 542 2
## 4 2013 1 1 544 -1
## 5 2013 1 1 554 -6
## 6 2013 1 1 554 -4
## 7 2013 1 1 555 -5
## 8 2013 1 1 557 -3
## 9 2013 1 1 557 -3
## 10 2013 1 1 558 -2
## # ℹ 336,766 more rowsselect(flights, year, month, day, starts_with("dep"))## # A tibble: 336,776 × 5
## year month day dep_time dep_delay
## <int> <int> <int> <int> <dbl>
## 1 2013 1 1 517 2
## 2 2013 1 1 533 4
## 3 2013 1 1 542 2
## 4 2013 1 1 544 -1
## 5 2013 1 1 554 -6
## 6 2013 1 1 554 -4
## 7 2013 1 1 555 -5
## 8 2013 1 1 557 -3
## 9 2013 1 1 557 -3
## 10 2013 1 1 558 -2
## # ℹ 336,766 more rowsselect(flights, year, month, day, contains("time "))## # A tibble: 336,776 × 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
## # ℹ 336,766 more rowsselect(flights, year, month, day, ends_with("time "))## # A tibble: 336,776 × 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
## # ℹ 336,766 more rowsselect(flights, year, month, day, contains("time "), everything())## # A tibble: 336,776 × 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
## # ℹ 336,766 more rows
## # ℹ 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>glimpse(flights)## Rows: 336,776
## Columns: 19
## $ year <int> 2013, 2013, 2013, 2013, 2013, 2013, 2013, 2013, 2013, 2…
## $ month <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
## $ day <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
## $ dep_time <int> 517, 533, 542, 544, 554, 554, 555, 557, 557, 558, 558, …
## $ sched_dep_time <int> 515, 529, 540, 545, 600, 558, 600, 600, 600, 600, 600, …
## $ dep_delay <dbl> 2, 4, 2, -1, -6, -4, -5, -3, -3, -2, -2, -2, -2, -2, -1…
## $ arr_time <int> 830, 850, 923, 1004, 812, 740, 913, 709, 838, 753, 849,…
## $ sched_arr_time <int> 819, 830, 850, 1022, 837, 728, 854, 723, 846, 745, 851,…
## $ arr_delay <dbl> 11, 20, 33, -18, -25, 12, 19, -14, -8, 8, -2, -3, 7, -1…
## $ carrier <chr> "UA", "UA", "AA", "B6", "DL", "UA", "B6", "EV", "B6", "…
## $ flight <int> 1545, 1714, 1141, 725, 461, 1696, 507, 5708, 79, 301, 4…
## $ tailnum <chr> "N14228", "N24211", "N619AA", "N804JB", "N668DN", "N394…
## $ origin <chr> "EWR", "LGA", "JFK", "JFK", "LGA", "EWR", "EWR", "LGA",…
## $ dest <chr> "IAH", "IAH", "MIA", "BQN", "ATL", "ORD", "FLL", "IAD",…
## $ air_time <dbl> 227, 227, 160, 183, 116, 150, 158, 53, 140, 138, 149, 1…
## $ distance <dbl> 1400, 1416, 1089, 1576, 762, 719, 1065, 229, 944, 733, …
## $ hour <dbl> 5, 5, 5, 5, 6, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 6, 6, 6…
## $ minute <dbl> 15, 29, 40, 45, 0, 58, 0, 0, 0, 0, 0, 0, 0, 0, 0, 59, 0…
## $ time_hour <dttm> 2013-01-01 05:00:00, 2013-01-01 05:00:00, 2013-01-01 0…Add columns
mutate(flights,
gain = dep_delay - arr_delay) %>%
# Select year, month, day, and gain
select(year:day, gain)## # A tibble: 336,776 × 4
## year month day gain
## <int> <int> <int> <dbl>
## 1 2013 1 1 -9
## 2 2013 1 1 -16
## 3 2013 1 1 -31
## 4 2013 1 1 17
## 5 2013 1 1 19
## 6 2013 1 1 -16
## 7 2013 1 1 -24
## 8 2013 1 1 11
## 9 2013 1 1 5
## 10 2013 1 1 -10
## # ℹ 336,766 more rows# Just keep gain
mutate(flights,
gain = dep_delay - arr_delay) %>%
# Select year, month, day, and gain
select(gain)## # A tibble: 336,776 × 1
## gain
## <dbl>
## 1 -9
## 2 -16
## 3 -31
## 4 17
## 5 19
## 6 -16
## 7 -24
## 8 11
## 9 5
## 10 -10
## # ℹ 336,766 more rows# alternative using transmute()
transmute(flights,
gain = dep_delay - arr_delay)## # A tibble: 336,776 × 1
## gain
## <dbl>
## 1 -9
## 2 -16
## 3 -31
## 4 17
## 5 19
## 6 -16
## 7 -24
## 8 11
## 9 5
## 10 -10
## # ℹ 336,766 more rows# lag()
select(flights, dep_time) %>%
mutate(dep_time_lag1 = lag(dep_time)) ## # A tibble: 336,776 × 2
## dep_time dep_time_lag1
## <int> <int>
## 1 517 NA
## 2 533 517
## 3 542 533
## 4 544 542
## 5 554 544
## 6 554 554
## 7 555 554
## 8 557 555
## 9 557 557
## 10 558 557
## # ℹ 336,766 more rows# cumsum()
select(flights, minute) %>%
mutate(minute_cumsum = cumsum(minute))## # A tibble: 336,776 × 2
## minute minute_cumsum
## <dbl> <dbl>
## 1 15 15
## 2 29 44
## 3 40 84
## 4 45 129
## 5 0 129
## 6 58 187
## 7 0 187
## 8 0 187
## 9 0 187
## 10 0 187
## # ℹ 336,766 more rowsSummarize by groups
Collapsing data to a single row
flights## # A tibble: 336,776 × 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
## # ℹ 336,766 more rows
## # ℹ 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># average departure delay
summarise(flights, mean(dep_delay, na.rm = TRUE))## # A tibble: 1 × 1
## `mean(dep_delay, na.rm = TRUE)`
## <dbl>
## 1 12.6Summarize by group
flights %>%
# Group by airlines
group_by(carrier) %>%
# Calculate average departure delay
summarise(delay = mean(dep_delay, na.rm = TRUE)) %>%
# Sort it
arrange(delay)## # A tibble: 16 × 2
## carrier delay
## <chr> <dbl>
## 1 US 3.78
## 2 HA 4.90
## 3 AS 5.80
## 4 AA 8.59
## 5 DL 9.26
## 6 MQ 10.6
## 7 UA 12.1
## 8 OO 12.6
## 9 VX 12.9
## 10 B6 13.0
## 11 9E 16.7
## 12 WN 17.7
## 13 FL 18.7
## 14 YV 19.0
## 15 EV 20.0
## 16 F9 20.2Delays increase with distance up to ~750 miles and then decrease
flights %>%
group_by(dest) %>%
summarise(count = n(),
dist = mean(distance, na.rm = TRUE),
delay = mean(arr_delay, na.rm = TRUE)) %>%
# Plot
ggplot(mapping = aes(x = dist, y= delay)) +
geom_point(aes(size = count), alpha = 0.3) +
geom_smooth(se = FALSE)## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'## Warning: Removed 1 rows containing non-finite values (`stat_smooth()`).## Warning: Removed 1 rows containing missing values (`geom_point()`).
Missing values
flights %>%
# Remove missing values
filter(is.na(dep_delay))## # A tibble: 8,255 × 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 NA 1630 NA NA 1815
## 2 2013 1 1 NA 1935 NA NA 2240
## 3 2013 1 1 NA 1500 NA NA 1825
## 4 2013 1 1 NA 600 NA NA 901
## 5 2013 1 2 NA 1540 NA NA 1747
## 6 2013 1 2 NA 1620 NA NA 1746
## 7 2013 1 2 NA 1355 NA NA 1459
## 8 2013 1 2 NA 1420 NA NA 1644
## 9 2013 1 2 NA 1321 NA NA 1536
## 10 2013 1 2 NA 1545 NA NA 1910
## # ℹ 8,245 more rows
## # ℹ 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>counts Wow, there are some planes that have an average delay of 5 hours (300 minutes)!
grouping multiple varaibles
flights %>%
group_by(year, month, day) %>%
summarise(count = n()) %>%
ungroup()## `summarise()` has grouped output by 'year', 'month'. You can override using the
## `.groups` argument.## # A tibble: 365 × 4
## year month day count
## <int> <int> <int> <int>
## 1 2013 1 1 842
## 2 2013 1 2 943
## 3 2013 1 3 914
## 4 2013 1 4 915
## 5 2013 1 5 720
## 6 2013 1 6 832
## 7 2013 1 7 933
## 8 2013 1 8 899
## 9 2013 1 9 902
## 10 2013 1 10 932
## # ℹ 355 more rows