Dataframe Manipulation with dplyr
Overview
Teaching: 40 min
Exercises: 15 minQuestions
How can I manipulate dataframes without repeating myself?
Objectives
To be able to use the six main dataframe manipulation ‘verbs’ with pipes in
dplyr.To understand how
group_by()andsummarize()can be combined to summarize datasets.Be able to analyze a subset of data using logical filtering.
Manipulation of dataframes means many things to many researchers, we often select certain observations (rows) or variables (columns), we often group the data by a certain variable(s), or we even calculate summary statistics. We can do these operations using the normal base R operations:
mean(gapminder[gapminder$continent == "Africa", "gdpPercap"])
[1] 2193.755
mean(gapminder[gapminder$continent == "Americas", "gdpPercap"])
[1] 7136.11
mean(gapminder[gapminder$continent == "Asia", "gdpPercap"])
[1] 7902.15
But this isn’t very nice because there is a fair bit of repetition. Repeating yourself will cost you time, both now and later, and potentially introduce some nasty bugs.
The dplyr package
Luckily, the dplyr
package provides a number of very useful functions for manipulating dataframes
in a way that will reduce the above repetition, reduce the probability of making
errors, and probably even save you some typing. As an added bonus, you might
even find the dplyr grammar easier to read.
Here we’re going to cover 6 of the most commonly used functions as well as using
pipes (%>%) to combine them.
select()filter()group_by()summarize()mutate()count()
If you have have not installed this package earlier, please do so:
install.packages('dplyr')
Now let’s load the package:
library("dplyr")
Using select()
If, for example, we wanted to move forward with only a few of the variables in
our dataframe we could use the select() function. This will keep only the
variables you select.
year_country_gdp <- select(gapminder,year,country,gdpPercap)
If we open up year_country_gdp we’ll see that it only contains the year,
country and gdpPercap. Above we used ‘normal’ grammar, but the strengths of
dplyr lie in combining several functions using pipes. Since the pipes grammar
is unlike anything we’ve seen in R before, let’s repeat what we’ve done above
using pipes.
year_country_gdp <- gapminder %>% select(year,country,gdpPercap)
To help you understand why we wrote that in that way, let’s walk through it step
by step. First we summon the gapminder dataframe and pass it on, using the pipe
symbol %>%, to the next step, which is the select() function. In this case
we don’t specify which data object we use in the select() function since in
gets that from the previous pipe. Fun Fact: There is a good chance you have
encountered pipes before in the shell. In R, a pipe symbol is %>% while in the
shell it is | but the concept is the same!
Using filter()
If we now wanted to move forward with the above, but only with European
countries, we can combine select and filter
year_country_gdp_euro <- gapminder %>%
filter(continent=="Europe") %>%
select(year,country,gdpPercap)
Challenge 1
Write a single command (which can span multiple lines and includes pipes) that will produce a dataframe that has the African values for
lifeExp,countryandyear, but not for other Continents. How many rows does your dataframe have and why?Solution to Challenge 1
year_country_lifeExp_Africa <- gapminder %>% filter(continent=="Africa") %>% select(year,country,lifeExp)
As with last time, first we pass the gapminder dataframe to the filter()
function, then we pass the filtered version of the gapminder dataframe to the
select() function. Note: The order of operations is very important in this
case. If we used ‘select’ first, filter would not be able to find the variable
continent since we would have removed it in the previous step.
Using group_by() and summarize()
Now, we were supposed to be reducing the error prone repetitiveness of what can
be done with base R, but up to now we haven’t done that since we would have to
repeat the above for each continent. Instead of filter(), which will only pass
observations that meet your criteria (in the above: continent=="Europe"), we
can use group_by(), which will essentially use every unique criteria that you
could have used in filter.
str(gapminder)
'data.frame': 1704 obs. of 6 variables:
$ country : Factor w/ 142 levels "Afghanistan",..: 1 1 1 1 1 1 1 1 1 1 ...
$ year : int 1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
$ pop : num 8425333 9240934 10267083 11537966 13079460 ...
$ continent: Factor w/ 5 levels "Africa","Americas",..: 3 3 3 3 3 3 3 3 3 3 ...
$ lifeExp : num 28.8 30.3 32 34 36.1 ...
$ gdpPercap: num 779 821 853 836 740 ...
str(gapminder %>% group_by(continent))
Classes 'grouped_df', 'tbl_df', 'tbl' and 'data.frame': 1704 obs. of 6 variables:
$ country : Factor w/ 142 levels "Afghanistan",..: 1 1 1 1 1 1 1 1 1 1 ...
$ year : int 1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
$ pop : num 8425333 9240934 10267083 11537966 13079460 ...
$ continent: Factor w/ 5 levels "Africa","Americas",..: 3 3 3 3 3 3 3 3 3 3 ...
$ lifeExp : num 28.8 30.3 32 34 36.1 ...
$ gdpPercap: num 779 821 853 836 740 ...
- attr(*, "vars")= chr "continent"
- attr(*, "drop")= logi TRUE
- attr(*, "indices")=List of 5
..$ : int 24 25 26 27 28 29 30 31 32 33 ...
..$ : int 48 49 50 51 52 53 54 55 56 57 ...
..$ : int 0 1 2 3 4 5 6 7 8 9 ...
..$ : int 12 13 14 15 16 17 18 19 20 21 ...
..$ : int 60 61 62 63 64 65 66 67 68 69 ...
- attr(*, "group_sizes")= int 624 300 396 360 24
- attr(*, "biggest_group_size")= int 624
- attr(*, "labels")='data.frame': 5 obs. of 1 variable:
..$ continent: Factor w/ 5 levels "Africa","Americas",..: 1 2 3 4 5
..- attr(*, "vars")= chr "continent"
..- attr(*, "drop")= logi TRUE
You will notice that the structure of the dataframe where we used group_by()
(grouped_df) is not the same as the original gapminder (data.frame). A
grouped_df can be thought of as a list where each item in the listis a
data.frame which contains only the rows that correspond to the a particular
value continent (at least in the example above).
Using summarize()
The above was a bit on the uneventful side but group_by() is much more
exciting in conjunction with summarize(). This will allow us to create new
variable(s) by using functions that repeat for each of the continent-specific
data frames. That is to say, using the group_by() function, we split our
original dataframe into multiple pieces, then we can run functions
(e.g. mean() or sd()) within summarize().
gdp_bycontinents <- gapminder %>%
group_by(continent) %>%
summarize(mean_gdpPercap=mean(gdpPercap))
gdp_bycontinents
continent mean_gdpPercap
<fctr> <dbl>
1 Africa 2193.755
2 Americas 7136.110
3 Asia 7902.150
4 Europe 14469.476
5 Oceania 18621.609
That allowed us to calculate the mean gdpPercap for each continent, but it gets even better.
Challenge 2
Calculate the average life expectancy per country. Which has the longest average life expectancy and which has the shortest average life expectancy?
Solution to Challenge 2
One solution is as follows:
First let’s build a dataframe with a summary of the average life expectancy per country:
lifeExp_bycountry <- gapminder %>% group_by(country) %>% summarize(mean_lifeExp=mean(lifeExp))Now that we have the data we need, we can use the
minandmaxcommands to determine which country had the longest and shortest life expectancy:min(lifeExp_bycountry$mean_lifeExp)[1] 36.76917max(lifeExp_bycountry$mean_lifeExp)[1] 76.51142Or, you can combine the use of
min()andmax()with filter to obtain both results at once:lifeExp_bycountry <- gapminder %>% group_by(country) %>% summarize(mean_lifeExp=mean(lifeExp)) lifeExp_bycountry %>% filter(mean_lifeExp == min(mean_lifeExp) | mean_lifeExp == max(mean_lifeExp))# A tibble: 2 x 2 country mean_lifeExp <fctr> <dbl> 1 Iceland 76.51142 2 Sierra Leone 36.76917Another way to do this is to use the
dplyrfunctionarrange(), which arranges the rows in a data frame according to the order of one or more variables from the data frame. It has similar syntax to other functions from thedplyrpackage. You can usedesc()insidearrange()to sort in descending order.lifeExp_bycountry %>% arrange(mean_lifeExp) %>% head(1)# A tibble: 1 x 2 country mean_lifeExp <fctr> <dbl> 1 Sierra Leone 36.76917lifeExp_bycountry %>% arrange(desc(mean_lifeExp)) %>% head(1)# A tibble: 1 x 2 country mean_lifeExp <fctr> <dbl> 1 Iceland 76.51142
The function group_by() allows us to group by multiple variables. Let’s group by year and continent.
gdp_bycontinents_byyear <- gapminder %>%
group_by(continent,year) %>%
summarize(mean_gdpPercap=mean(gdpPercap))
That is already quite powerful, but it gets even better! You’re not limited to defining 1 new variable in summarize().
gdp_pop_bycontinents_byyear <- gapminder %>%
group_by(continent,year) %>%
summarize(mean_gdpPercap=mean(gdpPercap),
sd_gdpPercap=sd(gdpPercap),
mean_pop=mean(pop),
sd_pop=sd(pop))
count() and n()
A very common operation is to count the number of observations for each
group. The dplyr package comes with two related functions that help with this.
For instance, if we wanted to check the number of countries included in the
dataset for the year 2002, we can use the count() function. It takes the name
of one or more columns that contain the groups we are interested in, and we can
optionally sort the results in descending order by adding sort=TRUE:
gapminder %>%
filter(year == 2002) %>%
count(continent, sort = TRUE)
# A tibble: 5 x 2
continent n
<fctr> <int>
1 Africa 52
2 Asia 33
3 Europe 30
4 Americas 25
5 Oceania 2
If we need to use the number of observations in calculations, the n() function
is useful. For instance, if we wanted to get the standard error of the life
expectency per continent:
gapminder %>%
group_by(continent) %>%
summarize(se_le = sd(lifeExp)/sqrt(n()))
# A tibble: 5 x 2
continent se_pop
<fctr> <dbl>
1 Africa 0.3663016
2 Americas 0.5395389
3 Asia 0.5962151
4 Europe 0.2863536
5 Oceania 0.7747759
Note that n() works the same way as count() but allows us to use it within other functions since as summarize(), mutate(), and filter().
You can also chain together several summary operations; in this case calculating the minimum, maximum, mean and se of each continent’s per-country life-expectancy:
gapminder %>%
group_by(continent) %>%
summarize(
mean_le = mean(lifeExp),
min_le = min(lifeExp),
max_le = max(lifeExp),
se_le = sd(lifeExp)/sqrt(n()))
# A tibble: 5 x 5
continent mean_le min_le max_le se_le
<fctr> <dbl> <dbl> <dbl> <dbl>
1 Africa 48.86533 23.599 76.442 0.3663016
2 Americas 64.65874 37.579 80.653 0.5395389
3 Asia 60.06490 28.801 82.603 0.5962151
4 Europe 71.90369 43.585 81.757 0.2863536
5 Oceania 74.32621 69.120 81.235 0.7747759
Using mutate()
We can also create new variables prior to (or even after) summarizing information using mutate().
gdp_pop_bycontinents_byyear <- gapminder %>%
mutate(gdp_billion=gdpPercap*pop/10^9) %>%
group_by(continent,year) %>%
summarize(mean_gdpPercap=mean(gdpPercap),
sd_gdpPercap=sd(gdpPercap),
mean_pop=mean(pop),
sd_pop=sd(pop),
mean_gdp_billion=mean(gdp_billion),
sd_gdp_billion=sd(gdp_billion))
Challenge 3
Calculate the average life expectancy in 2002 for each continent.
Solution to Challenge 3
lifeExp_bycontinents <- gapminder %>% filter(year==2002) %>% group_by(continent) %>% summarize(mean_lifeExp=mean(lifeExp))
Challenge 4 - Advanced
Modify your code from Challenge 3 to randomly select 2 countries from each continent before calculating the average life expectancy and then arrange the continent names in reverse order.
Hint: Use the
dplyrfunctionsarrangeandsample_n, they have similar syntax to other dplyr functions. Be sure to check out the help documentation for the new functions by typing?arrangeor?sample_nif you run into difficulties.Solution to Challenge 4
lifeExp_2countries_bycontinents <- gapminder %>% filter(year==2002) %>% group_by(continent) %>% sample_n(2) %>% summarize(mean_lifeExp=mean(lifeExp)) %>% arrange(desc(mean_lifeExp))
Combining dplyr and ggplot2
In the plotting lesson we looked at how to make a multi-panel figure by adding
a layer of facet panels using ggplot2. Here is the code we used (with some
extra comments):
# Get the start letter of each country
starts.with <- substr(gapminder$country, start = 1, stop = 1)
# Filter countries that start with "A" or "Z"
az.countries <- gapminder[starts.with %in% c("A", "Z"), ]
# Make the plot
ggplot(data = az.countries, aes(x = year, y = lifeExp, color = continent)) +
geom_line() + facet_wrap( ~ country)
This code makes the right plot but it also creates some variables (starts.with
and az.countries) that we might not have any other uses for. Just as we used
%>% to pipe data along a chain of dplyr functions we can use it to pass data
to ggplot(). Because %>% replaces the first argument in a function we don’t
need to specify the data = argument in the ggplot() function. By combining
dplyr and ggplot2 functions we can make the same figure without creating any
new variables or modifying the data.
gapminder %>%
# Get the start letter of each country
mutate(startsWith = substr(country, start = 1, stop = 1)) %>%
# Filter countries that start with "A" or "Z"
filter(startsWith %in% c("A", "Z")) %>%
# Make the plot
ggplot(aes(x = year, y = lifeExp, color = continent)) +
geom_line() +
facet_wrap( ~ country)
Using dplyr functions also helps us simplify things, for example we could
combine the first two steps:
gapminder %>%
# Filter countries that start with "A" or "Z"
filter(substr(country, start = 1, stop = 1) %in% c("A", "Z")) %>%
# Make the plot
ggplot(aes(x = year, y = lifeExp, color = continent)) +
geom_line() +
facet_wrap( ~ country)
Other great resources
- R for Data Science
- Data Wrangling Cheat sheet
- Introduction to dplyr
- Data wrangling with R and RStudio
Key Points
Use the
dplyrpackage to manipulate dataframes.Use
select()to choose variables from a dataframe.Use
filter()to choose data based on values.Use
group_by()andsummarize()to work with subsets of data.Use
mutate()to create new variables.