Data frame Manipulation with dplyr

Estimated time: 40 minutes

Overview

Questions

• 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() and summarize() 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:

R

gapminder <- read.csv("data/gapminder_data.csv", header = TRUE)

mean(gapminder[gapminder$continent == "Africa", "gdpPercap"])

OUTPUT

[1] 2193.755

R

mean(gapminder[gapminder$continent == "Americas", "gdpPercap"])

OUTPUT

[1] 7136.11

R

mean(gapminder[gapminder$continent == "Asia", "gdpPercap"])

OUTPUT

[1] 7902.15

But this isn’t very efficient, and can become tedious quickly 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

---

Instructor Note

• Introduce the dplyr package as a simpler, more intuitive way of doing subsetting.
• Unlike other SWC and DC R lessons, this lesson does not include data reshaping with tidyr as it isn’t used in the rest of the workshop.

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.

1. select()
2. filter()
3. group_by()
4. summarize()
5. count() and n()
6. mutate()

If you have have not installed this package earlier, please do so:

R

install.packages('dplyr')

Now let’s load the package:

R

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.

R

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.

R

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 data frame 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: You may 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

R

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, country and year, but not for other Continents. How many rows does your dataframe have and why?

Show me the solution

R

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 data frame 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.

R

str(gapminder)

OUTPUT

'data.frame':	1704 obs. of  6 variables:
 $ country  : chr  "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
 $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
 $ pop      : num  8425333 9240934 10267083 11537966 13079460 ...
 $ continent: chr  "Asia" "Asia" "Asia" "Asia" ...
 $ lifeExp  : num  28.8 30.3 32 34 36.1 ...
 $ gdpPercap: num  779 821 853 836 740 ...

R

gapminder %>% group_by(continent) %>% str()

OUTPUT

gropd_df [1,704 × 6] (S3: grouped_df/tbl_df/tbl/data.frame)
 $ country  : chr [1:1704] "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
 $ year     : int [1:1704] 1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
 $ pop      : num [1:1704] 8425333 9240934 10267083 11537966 13079460 ...
 $ continent: chr [1:1704] "Asia" "Asia" "Asia" "Asia" ...
 $ lifeExp  : num [1:1704] 28.8 30.3 32 34 36.1 ...
 $ gdpPercap: num [1:1704] 779 821 853 836 740 ...
 - attr(*, "groups")= tibble [5 × 2] (S3: tbl_df/tbl/data.frame)
  ..$ continent: chr [1:5] "Africa" "Americas" "Asia" "Europe" ...
  ..$ .rows    : list<int> [1:5] 
  .. ..$ : int [1:624] 25 26 27 28 29 30 31 32 33 34 ...
  .. ..$ : int [1:300] 49 50 51 52 53 54 55 56 57 58 ...
  .. ..$ : int [1:396] 1 2 3 4 5 6 7 8 9 10 ...
  .. ..$ : int [1:360] 13 14 15 16 17 18 19 20 21 22 ...
  .. ..$ : int [1:24] 61 62 63 64 65 66 67 68 69 70 ...
  .. ..@ ptype: int(0) 
  ..- 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(). To end our group_by(), we need to close off the pipe by using ungroup().

R

gdp_bycontinents <- gapminder %>%
  group_by(continent) %>%
  summarize(mean_gdpPercap = mean(gdpPercap)) %>% 
  ungroup()

gdp_bycontinents

OUTPUT

# A tibble: 5 × 2
  continent mean_gdpPercap
  <chr>              <dbl>
1 Africa             2194.
2 Americas           7136.
3 Asia               7902.
4 Europe            14469.
5 Oceania           18622.

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?

Show me the solution

R

lifeExp_bycountry <- gapminder %>%
   group_by(country) %>%
   summarize(mean_lifeExp=mean(lifeExp)) %>% 
   ungroup()

lifeExp_bycountry %>%
   filter(mean_lifeExp == min(mean_lifeExp) | mean_lifeExp == max(mean_lifeExp))

OUTPUT

# A tibble: 2 × 2
  country      mean_lifeExp
  <chr>               <dbl>
1 Iceland              76.5
2 Sierra Leone         36.8

Another way to do this is to use the dplyr function arrange(), 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 the dplyr package. You can use desc() inside arrange() to sort in descending order.

R

lifeExp_bycountry %>%
   arrange(mean_lifeExp) %>%
   head(1)

OUTPUT

# A tibble: 1 × 2
  country      mean_lifeExp
  <chr>               <dbl>
1 Sierra Leone         36.8

R

lifeExp_bycountry %>%
   arrange(desc(mean_lifeExp)) %>%
   head(1)

OUTPUT

# A tibble: 1 × 2
  country mean_lifeExp
  <chr>          <dbl>
1 Iceland         76.5

The function group_by() allows us to group by multiple variables. Let’s group by year and continent.

R

gdp_bycontinents_byyear <- gapminder %>%
  group_by(continent, year) %>%
  summarize(mean_gdpPercap = mean(gdpPercap)) %>% 
  ungroup()

That is already quite powerful, but it gets even better! You’re not limited to defining 1 new variable in summarize().

R

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)) %>% 
  ungroup()

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:

R

gapminder %>%
    filter(year == 2002) %>%
    count(continent, sort = TRUE)

OUTPUT

  continent  n
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 expectancy per continent:

R

gapminder %>%
  group_by(continent) %>%
  summarize(sd_le = sd(lifeExp), # standard deviation
            n_le = n(), # number of observations
            se_le = sd_le/sqrt(n_le)) %>% # standard error
  ungroup()

OUTPUT

# A tibble: 5 × 4
  continent sd_le  n_le se_le
  <chr>     <dbl> <int> <dbl>
1 Africa     9.15   624 0.366
2 Americas   9.35   300 0.540
3 Asia      11.9    396 0.596
4 Europe     5.43   360 0.286
5 Oceania    3.80    24 0.775

In the above example, we chained together several summary operations to simplify our calculation of standard error. We can also chain operations to calculate the minimum, maximum, mean and se of each continent’s per-country life-expectancy. This time, we will calculate the se in just one line:

R

gapminder %>%
    group_by(continent) %>%
    summarize(
      mean_le = mean(lifeExp),
      min_le = min(lifeExp),
      max_le = max(lifeExp), 
      se_le = sd(lifeExp)/sqrt(n())) %>% 
  ungroup()

OUTPUT

# A tibble: 5 × 5
  continent mean_le min_le max_le se_le
  <chr>       <dbl>  <dbl>  <dbl> <dbl>
1 Africa       48.9   23.6   76.4 0.366
2 Americas     64.7   37.6   80.7 0.540
3 Asia         60.1   28.8   82.6 0.596
4 Europe       71.9   43.6   81.8 0.286
5 Oceania      74.3   69.1   81.2 0.775

Using mutate()

---

We can also create new variables prior to (or even after) summarizing information using mutate().

R

gdp_pop_billion <- gapminder %>%
  mutate(gdp_billion = gdpPercap*pop/10^9)

head(gdp_pop_billion)

OUTPUT

      country year      pop continent lifeExp gdpPercap gdp_billion
1 Afghanistan 1952  8425333      Asia  28.801  779.4453    6.567086
2 Afghanistan 1957  9240934      Asia  30.332  820.8530    7.585449
3 Afghanistan 1962 10267083      Asia  31.997  853.1007    8.758856
4 Afghanistan 1967 11537966      Asia  34.020  836.1971    9.648014
5 Afghanistan 1972 13079460      Asia  36.088  739.9811    9.678553
6 Afghanistan 1977 14880372      Asia  38.438  786.1134   11.697659

Other great resources

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• R for Data Science
• Data Wrangling Cheat sheet
• Introduction to dplyr
• Data wrangling with R and RStudio

Key Points

• Use the dplyr package to manipulate dataframes.
• Use select() to choose variables from a dataframe.
• Use filter() to choose data based on values.
• Use group_by() and summarize() to work with subsets of data.
• Use count() and n() to obtain the number of observations in columns.
• Use mutate() to create new variables.