https://can.gitbiopages.ens-lyon.fr/R_basis/
1 Introduction
Until now we have worked with data already formated in a nice way.
In the tidyverse data formated in a nice way are called tidy
The goal of this practical is to understand how to transform an hugly blob of information into a tidy data set.
1.1 Tidydata
There are three interrelated rules which make a dataset tidy:
- Each variable must have its own column.
- Each observation must have its own row.
- Each value must have its own cell.
Doing this kind and transformation is often called data wrangling, due to the felling that we have to wrangle with the data to force them into a tidy format.
But once this step is finish most of the subsequent analysis will be realy fast to do !
As usual we will need the tidyverse library.
Solution
library(tidyverse)For this practical we are going to use the table set of datasets which demonstrate multiple ways to layout the same tabular data.
Use the help to know more about table1 dataset
Solution
?table1
table1, table2, table3, table4a, table4b, and table5 all display the number of TB (Tuberculosis) cases documented by the World Health Organization in Afghanistan, Brazil, and China between 1999 and 2000. The data contains values associated with four variables (country, year, cases, and population), but each table organizes the values in a different layout.
2 Pivoting data
2.1 pivot longer
wide_example <- tibble(X1 = c("A","B"),
X2 = c(1,2),
X3 = c(0.1,0.2),
X4 = c(10,20))If you have a wide dataset, such as wide_example, that you want to make longer, you will use the pivot_longer() function.
You have to specify the names of the columns you want to pivot into longer format (X2,X3,X4):
wide_example %>%
pivot_longer(c(X2,X3,X4))… or the reverse selection (-X1):
wide_example %>% pivot_longer(-X1)You can specify the names of the columns where the data will be tidy (by default, it is names and value):
long_example <- wide_example %>%
pivot_longer(-X1, names_to = "V1", values_to = "V2")2.1.1 Exercice
Visualize the table4a dataset (you can use the View() function).
View(table4a)Is the data tidy ? How would you transform this dataset to make it tidy ?
Solution
We have information about 3 variables in the table4a: country, year and number of cases.
However, the variable information (year) is stored as column names.
We want to pivot the horizontal column year, vertically and make the table longer.
You can use the pivot_longer fonction to make your table longer and have one observation per row and one variable per column.
For this we need to :
- specify which column to select (all except
country). - give the name of the new variable (
year) - give the name of the variable stored in the cells of the columns years (
case)
table4a %>%
pivot_longer(-country,
names_to = "year",
values_to = "case")# A tibble: 6 × 3
country year case
<chr> <chr> <int>
1 Afghanistan 1999 745
2 Afghanistan 2000 2666
3 Brazil 1999 37737
4 Brazil 2000 80488
5 China 1999 212258
6 China 2000 2137662.2 pivot wider
If you have a long dataset, that you want to make wider, you will use the pivot_wider() function.
You have to specify which column contains the name of the output column (names_from), and which column contains the cell values from (values_from).
long_example %>% pivot_wider(names_from = V1,
values_from = V2)2.2.1 Exercice
Visualize the table2 dataset
Is the data tidy ? How would you transform this dataset to make it tidy ? (you can now make also make a guess from the name of the subsection)
Solution
The column count store two types of information: the population size of the country and the number of cases in the country.
You can use the pivot_wider fonction to make your table wider and have one observation per row and one variable per column.
table2 %>%
pivot_wider(names_from = type,
values_from = count)# A tibble: 6 × 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 12804285833 Merging data
3.1 Relational data
To avoid having a huge table and to save space, information is often splited between different tables.
In our flights dataset, information about the carrier or the airports (origin and dest) are saved in a separate table (airlines, airports).
library(nycflights13)
flights# A tibble: 336,776 × 19
year month day dep_time sched_de…¹ dep_d…² arr_t…³ sched…⁴ arr_d…⁵ carrier
<int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr>
1 2013 1 1 517 515 2 830 819 11 UA
2 2013 1 1 533 529 4 850 830 20 UA
3 2013 1 1 542 540 2 923 850 33 AA
4 2013 1 1 544 545 -1 1004 1022 -18 B6
5 2013 1 1 554 600 -6 812 837 -25 DL
6 2013 1 1 554 558 -4 740 728 12 UA
7 2013 1 1 555 600 -5 913 854 19 B6
8 2013 1 1 557 600 -3 709 723 -14 EV
9 2013 1 1 557 600 -3 838 846 -8 B6
10 2013 1 1 558 600 -2 753 745 8 AA
# … with 336,766 more rows, 9 more variables: flight <int>, tailnum <chr>,
# origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
# minute <dbl>, time_hour <dttm>, and abbreviated variable names
# ¹sched_dep_time, ²dep_delay, ³arr_time, ⁴sched_arr_time, ⁵arr_delayairlines# A tibble: 16 × 2
carrier name
<chr> <chr>
1 9E Endeavor Air Inc.
2 AA American Airlines Inc.
3 AS Alaska Airlines Inc.
4 B6 JetBlue Airways
5 DL Delta Air Lines Inc.
6 EV ExpressJet Airlines Inc.
7 F9 Frontier Airlines Inc.
8 FL AirTran Airways Corporation
9 HA Hawaiian Airlines Inc.
10 MQ Envoy Air
11 OO SkyWest Airlines Inc.
12 UA United Air Lines Inc.
13 US US Airways Inc.
14 VX Virgin America
15 WN Southwest Airlines Co.
16 YV Mesa Airlines Inc. airports# A tibble: 1,458 × 8
faa name lat lon alt tz dst tzone
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 04G Lansdowne Airport 41.1 -80.6 1044 -5 A America/…
2 06A Moton Field Municipal Airport 32.5 -85.7 264 -6 A America/…
3 06C Schaumburg Regional 42.0 -88.1 801 -6 A America/…
4 06N Randall Airport 41.4 -74.4 523 -5 A America/…
5 09J Jekyll Island Airport 31.1 -81.4 11 -5 A America/…
6 0A9 Elizabethton Municipal Airport 36.4 -82.2 1593 -5 A America/…
7 0G6 Williams County Airport 41.5 -84.5 730 -5 A America/…
8 0G7 Finger Lakes Regional Airport 42.9 -76.8 492 -5 A America/…
9 0P2 Shoestring Aviation Airfield 39.8 -76.6 1000 -5 U America/…
10 0S9 Jefferson County Intl 48.1 -123. 108 -8 A America/…
# … with 1,448 more rowsweather# A tibble: 26,115 × 15
origin year month day hour temp dewp humid wind_dir wind_speed wind_g…¹
<chr> <int> <int> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 EWR 2013 1 1 1 39.0 26.1 59.4 270 10.4 NA
2 EWR 2013 1 1 2 39.0 27.0 61.6 250 8.06 NA
3 EWR 2013 1 1 3 39.0 28.0 64.4 240 11.5 NA
4 EWR 2013 1 1 4 39.9 28.0 62.2 250 12.7 NA
5 EWR 2013 1 1 5 39.0 28.0 64.4 260 12.7 NA
6 EWR 2013 1 1 6 37.9 28.0 67.2 240 11.5 NA
7 EWR 2013 1 1 7 39.0 28.0 64.4 240 15.0 NA
8 EWR 2013 1 1 8 39.9 28.0 62.2 250 10.4 NA
9 EWR 2013 1 1 9 39.9 28.0 62.2 260 15.0 NA
10 EWR 2013 1 1 10 41 28.0 59.6 260 13.8 NA
# … with 26,105 more rows, 4 more variables: precip <dbl>, pressure <dbl>,
# visib <dbl>, time_hour <dttm>, and abbreviated variable name ¹wind_gustflights2 <- flights %>%
select(year:day, hour, origin, dest, tailnum, carrier)3.2 Relational schema
The relationships between tables can be seen in a relational graph. The variables used to connect each pair of tables are called keys. A key is a variable (or set of variables) that uniquely identifies an observation.
3.3 Joints
If you have to combine data from 2 tables in a a new table, you will use joints.
There are several types of joints depending of what you want to get.
Small concrete examples:
3.3.1 inner_joint()
keeps observations in x AND y
flights2 %>%
inner_join(airlines)Joining, by = "carrier"# A tibble: 336,776 × 9
year month day hour origin dest tailnum carrier name
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr>
1 2013 1 1 5 EWR IAH N14228 UA United Air Lines Inc.
2 2013 1 1 5 LGA IAH N24211 UA United Air Lines Inc.
3 2013 1 1 5 JFK MIA N619AA AA American Airlines Inc.
4 2013 1 1 5 JFK BQN N804JB B6 JetBlue Airways
5 2013 1 1 6 LGA ATL N668DN DL Delta Air Lines Inc.
6 2013 1 1 5 EWR ORD N39463 UA United Air Lines Inc.
7 2013 1 1 6 EWR FLL N516JB B6 JetBlue Airways
8 2013 1 1 6 LGA IAD N829AS EV ExpressJet Airlines Inc.
9 2013 1 1 6 JFK MCO N593JB B6 JetBlue Airways
10 2013 1 1 6 LGA ORD N3ALAA AA American Airlines Inc.
# … with 336,766 more rows3.3.2 left_joint()
keeps all observations in x
flights2 %>%
left_join(airlines)Joining, by = "carrier"# A tibble: 336,776 × 9
year month day hour origin dest tailnum carrier name
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr>
1 2013 1 1 5 EWR IAH N14228 UA United Air Lines Inc.
2 2013 1 1 5 LGA IAH N24211 UA United Air Lines Inc.
3 2013 1 1 5 JFK MIA N619AA AA American Airlines Inc.
4 2013 1 1 5 JFK BQN N804JB B6 JetBlue Airways
5 2013 1 1 6 LGA ATL N668DN DL Delta Air Lines Inc.
6 2013 1 1 5 EWR ORD N39463 UA United Air Lines Inc.
7 2013 1 1 6 EWR FLL N516JB B6 JetBlue Airways
8 2013 1 1 6 LGA IAD N829AS EV ExpressJet Airlines Inc.
9 2013 1 1 6 JFK MCO N593JB B6 JetBlue Airways
10 2013 1 1 6 LGA ORD N3ALAA AA American Airlines Inc.
# … with 336,766 more rows3.3.3 right_joint()
keeps all observations in y
flights2 %>%
right_join(airlines)Joining, by = "carrier"# A tibble: 336,776 × 9
year month day hour origin dest tailnum carrier name
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr>
1 2013 1 1 5 EWR IAH N14228 UA United Air Lines Inc.
2 2013 1 1 5 LGA IAH N24211 UA United Air Lines Inc.
3 2013 1 1 5 JFK MIA N619AA AA American Airlines Inc.
4 2013 1 1 5 JFK BQN N804JB B6 JetBlue Airways
5 2013 1 1 6 LGA ATL N668DN DL Delta Air Lines Inc.
6 2013 1 1 5 EWR ORD N39463 UA United Air Lines Inc.
7 2013 1 1 6 EWR FLL N516JB B6 JetBlue Airways
8 2013 1 1 6 LGA IAD N829AS EV ExpressJet Airlines Inc.
9 2013 1 1 6 JFK MCO N593JB B6 JetBlue Airways
10 2013 1 1 6 LGA ORD N3ALAA AA American Airlines Inc.
# … with 336,766 more rows3.3.4 full_joint()
keeps all observations in x and y
flights2 %>%
full_join(airlines)Joining, by = "carrier"# A tibble: 336,776 × 9
year month day hour origin dest tailnum carrier name
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr>
1 2013 1 1 5 EWR IAH N14228 UA United Air Lines Inc.
2 2013 1 1 5 LGA IAH N24211 UA United Air Lines Inc.
3 2013 1 1 5 JFK MIA N619AA AA American Airlines Inc.
4 2013 1 1 5 JFK BQN N804JB B6 JetBlue Airways
5 2013 1 1 6 LGA ATL N668DN DL Delta Air Lines Inc.
6 2013 1 1 5 EWR ORD N39463 UA United Air Lines Inc.
7 2013 1 1 6 EWR FLL N516JB B6 JetBlue Airways
8 2013 1 1 6 LGA IAD N829AS EV ExpressJet Airlines Inc.
9 2013 1 1 6 JFK MCO N593JB B6 JetBlue Airways
10 2013 1 1 6 LGA ORD N3ALAA AA American Airlines Inc.
# … with 336,766 more rows3.4 Defining the key columns
The default, by = NULL, uses all variables that appear in both tables, the so called natural join.
flights2 %>%
left_join(weather)Joining, by = c("year", "month", "day", "hour", "origin")# A tibble: 336,776 × 18
year month day hour origin dest tailnum carrier temp dewp humid
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
1 2013 1 1 5 EWR IAH N14228 UA 39.0 28.0 64.4
2 2013 1 1 5 LGA IAH N24211 UA 39.9 25.0 54.8
3 2013 1 1 5 JFK MIA N619AA AA 39.0 27.0 61.6
4 2013 1 1 5 JFK BQN N804JB B6 39.0 27.0 61.6
5 2013 1 1 6 LGA ATL N668DN DL 39.9 25.0 54.8
6 2013 1 1 5 EWR ORD N39463 UA 39.0 28.0 64.4
7 2013 1 1 6 EWR FLL N516JB B6 37.9 28.0 67.2
8 2013 1 1 6 LGA IAD N829AS EV 39.9 25.0 54.8
9 2013 1 1 6 JFK MCO N593JB B6 37.9 27.0 64.3
10 2013 1 1 6 LGA ORD N3ALAA AA 39.9 25.0 54.8
# … with 336,766 more rows, and 7 more variables: wind_dir <dbl>,
# wind_speed <dbl>, wind_gust <dbl>, precip <dbl>, pressure <dbl>,
# visib <dbl>, time_hour <dttm>If the two tables contain columns with the same names but corresponding to different things (such as year in flights2 and planes) you have to manually define the key or the keys.
flights2 %>%
left_join(planes, by = "tailnum")# A tibble: 336,776 × 16
year.x month day hour origin dest tailnum carrier year.y type manuf…¹
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <int> <chr> <chr>
1 2013 1 1 5 EWR IAH N14228 UA 1999 Fixed w… BOEING
2 2013 1 1 5 LGA IAH N24211 UA 1998 Fixed w… BOEING
3 2013 1 1 5 JFK MIA N619AA AA 1990 Fixed w… BOEING
4 2013 1 1 5 JFK BQN N804JB B6 2012 Fixed w… AIRBUS
5 2013 1 1 6 LGA ATL N668DN DL 1991 Fixed w… BOEING
6 2013 1 1 5 EWR ORD N39463 UA 2012 Fixed w… BOEING
7 2013 1 1 6 EWR FLL N516JB B6 2000 Fixed w… AIRBUS…
8 2013 1 1 6 LGA IAD N829AS EV 1998 Fixed w… CANADA…
9 2013 1 1 6 JFK MCO N593JB B6 2004 Fixed w… AIRBUS
10 2013 1 1 6 LGA ORD N3ALAA AA NA <NA> <NA>
# … with 336,766 more rows, 5 more variables: model <chr>, engines <int>,
# seats <int>, speed <int>, engine <chr>, and abbreviated variable name
# ¹manufacturerIf you want to join by data that are in two columns with different names, you must specify the correspondence with a named character vector: by = c("a" = "b"). This will match variable a in table x to variable b in table y.
flights2 %>%
left_join(airports, c("dest" = "faa"))# A tibble: 336,776 × 15
year month day hour origin dest tailnum carrier name lat lon alt
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
1 2013 1 1 5 EWR IAH N14228 UA Georg… 30.0 -95.3 97
2 2013 1 1 5 LGA IAH N24211 UA Georg… 30.0 -95.3 97
3 2013 1 1 5 JFK MIA N619AA AA Miami… 25.8 -80.3 8
4 2013 1 1 5 JFK BQN N804JB B6 <NA> NA NA NA
5 2013 1 1 6 LGA ATL N668DN DL Harts… 33.6 -84.4 1026
6 2013 1 1 5 EWR ORD N39463 UA Chica… 42.0 -87.9 668
7 2013 1 1 6 EWR FLL N516JB B6 Fort … 26.1 -80.2 9
8 2013 1 1 6 LGA IAD N829AS EV Washi… 38.9 -77.5 313
9 2013 1 1 6 JFK MCO N593JB B6 Orlan… 28.4 -81.3 96
10 2013 1 1 6 LGA ORD N3ALAA AA Chica… 42.0 -87.9 668
# … with 336,766 more rows, and 3 more variables: tz <dbl>, dst <chr>,
# tzone <chr>If 2 columns have identical names in the input tables but are not used in the join, they are automatically renamed with the suffix .x and .y because all column names must be different in the output table.
flights2 %>%
left_join(airports, c("dest" = "faa")) %>%
left_join(airports, c("origin" = "faa"))# A tibble: 336,776 × 22
year month day hour origin dest tailnum carrier name.x lat.x lon.x alt.x
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
1 2013 1 1 5 EWR IAH N14228 UA Georg… 30.0 -95.3 97
2 2013 1 1 5 LGA IAH N24211 UA Georg… 30.0 -95.3 97
3 2013 1 1 5 JFK MIA N619AA AA Miami… 25.8 -80.3 8
4 2013 1 1 5 JFK BQN N804JB B6 <NA> NA NA NA
5 2013 1 1 6 LGA ATL N668DN DL Harts… 33.6 -84.4 1026
6 2013 1 1 5 EWR ORD N39463 UA Chica… 42.0 -87.9 668
7 2013 1 1 6 EWR FLL N516JB B6 Fort … 26.1 -80.2 9
8 2013 1 1 6 LGA IAD N829AS EV Washi… 38.9 -77.5 313
9 2013 1 1 6 JFK MCO N593JB B6 Orlan… 28.4 -81.3 96
10 2013 1 1 6 LGA ORD N3ALAA AA Chica… 42.0 -87.9 668
# … with 336,766 more rows, and 10 more variables: tz.x <dbl>, dst.x <chr>,
# tzone.x <chr>, name.y <chr>, lat.y <dbl>, lon.y <dbl>, alt.y <dbl>,
# tz.y <dbl>, dst.y <chr>, tzone.y <chr>You can change the suffix using the option suffix
flights2 %>%
left_join(airports, by = c("dest" = "faa")) %>%
left_join(airports, by = c("origin" = "faa"), suffix = c(".dest",".origin"))# A tibble: 336,776 × 22
year month day hour origin dest tailnum carrier name.d…¹ lat.d…² lon.d…³
<int> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
1 2013 1 1 5 EWR IAH N14228 UA George … 30.0 -95.3
2 2013 1 1 5 LGA IAH N24211 UA George … 30.0 -95.3
3 2013 1 1 5 JFK MIA N619AA AA Miami I… 25.8 -80.3
4 2013 1 1 5 JFK BQN N804JB B6 <NA> NA NA
5 2013 1 1 6 LGA ATL N668DN DL Hartsfi… 33.6 -84.4
6 2013 1 1 5 EWR ORD N39463 UA Chicago… 42.0 -87.9
7 2013 1 1 6 EWR FLL N516JB B6 Fort La… 26.1 -80.2
8 2013 1 1 6 LGA IAD N829AS EV Washing… 38.9 -77.5
9 2013 1 1 6 JFK MCO N593JB B6 Orlando… 28.4 -81.3
10 2013 1 1 6 LGA ORD N3ALAA AA Chicago… 42.0 -87.9
# … with 336,766 more rows, 11 more variables: alt.dest <dbl>, tz.dest <dbl>,
# dst.dest <chr>, tzone.dest <chr>, name.origin <chr>, lat.origin <dbl>,
# lon.origin <dbl>, alt.origin <dbl>, tz.origin <dbl>, dst.origin <chr>,
# tzone.origin <chr>, and abbreviated variable names ¹name.dest, ²lat.dest,
# ³lon.dest3.5 Filtering joins
Filtering joins match observations in the same way as mutating joins, but affect the observations, not the variables. There are two types:
semi_join(x, y)keeps all observations inxthat have a match iny.anti_join(x, y)drops all observations inxthat have a match iny.
top_dest <- flights %>%
count(dest, sort = TRUE) %>%
head(10)
flights %>%
semi_join(top_dest)Joining, by = "dest"# A tibble: 141,145 × 19
year month day dep_time sched_de…¹ dep_d…² arr_t…³ sched…⁴ arr_d…⁵ carrier
<int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr>
1 2013 1 1 542 540 2 923 850 33 AA
2 2013 1 1 554 600 -6 812 837 -25 DL
3 2013 1 1 554 558 -4 740 728 12 UA
4 2013 1 1 555 600 -5 913 854 19 B6
5 2013 1 1 557 600 -3 838 846 -8 B6
6 2013 1 1 558 600 -2 753 745 8 AA
7 2013 1 1 558 600 -2 924 917 7 UA
8 2013 1 1 558 600 -2 923 937 -14 UA
9 2013 1 1 559 559 0 702 706 -4 B6
10 2013 1 1 600 600 0 851 858 -7 B6
# … with 141,135 more rows, 9 more variables: flight <int>, tailnum <chr>,
# origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
# minute <dbl>, time_hour <dttm>, and abbreviated variable names
# ¹sched_dep_time, ²dep_delay, ³arr_time, ⁴sched_arr_time, ⁵arr_delay3.6 Set operations
These expect the x and y inputs to have the same variables, and treat the observations like sets:
intersect(x, y): return only observations in bothxandy.union(x, y): return unique observations inxandy.setdiff(x, y): return observations inx, but not iny.
