Introduction to tidyverse 2019

Motivation: Global Health and Economic Data

Throughout this section we will be analyzing global health and economic data. We will be exploring one question:

  1. Is there a relationship between life expectancy and GDP per capita?

We will use the data that has been organized and delivered in the gapminder package available in an R package from Jenny Bryan.

To install the gapminder data set

library(devtools)
install_github("jennybc/gapminder")

Loading data into R

library(gapminder)

Meet the gapminder data frame or “tibble”

By loading the gapminder package, we now have access to a data frame by the same name. Get an overview of this with str(), which displays the structure of an object.

str(gapminder)
## Classes '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 ...
##  $ continent: Factor w/ 5 levels "Africa","Americas",..: 3 3 3 3 3 3 3 3 3 3 ...
##  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
##  $ lifeExp  : num  28.8 30.3 32 34 36.1 ...
##  $ pop      : int  8425333 9240934 10267083 11537966 13079460 14880372 12881816 13867957 16317921 22227415 ...
##  $ gdpPercap: num  779 821 853 836 740 ...

str() will provide a sensible description of almost anything and, worst case, nothing bad can actually happen. When in doubt, just str() some of the recently created objects to get some ideas a bout what to do next.

We could print the gapminder object itself to screen. However, if you’ve used R before, you might be reluctant to do this, because large datasets just fill up your console and provide very little insight.

This is the first big win for tibbles. The tidyverse offers a special case of R’s default data frame: the “tibble”, which is a nod to the actual class of these objects, tbl_df.

Now we can boldly print gapminder to screen! It is a tibble (and also a regular data frame) and the tidyverse provides a nice print method that shows the most important stuff and doesn’t fill up your Console.

## see? it's still a regular data frame, but also a tibble
class(gapminder)
## [1] "tbl_df"     "tbl"        "data.frame"
gapminder
## # A tibble: 1,704 x 6
##    country     continent  year lifeExp      pop gdpPercap
##    <fct>       <fct>     <int>   <dbl>    <int>     <dbl>
##  1 Afghanistan Asia       1952    28.8  8425333      779.
##  2 Afghanistan Asia       1957    30.3  9240934      821.
##  3 Afghanistan Asia       1962    32.0 10267083      853.
##  4 Afghanistan Asia       1967    34.0 11537966      836.
##  5 Afghanistan Asia       1972    36.1 13079460      740.
##  6 Afghanistan Asia       1977    38.4 14880372      786.
##  7 Afghanistan Asia       1982    39.9 12881816      978.
##  8 Afghanistan Asia       1987    40.8 13867957      852.
##  9 Afghanistan Asia       1992    41.7 16317921      649.
## 10 Afghanistan Asia       1997    41.8 22227415      635.
## # … with 1,694 more rows

This package provides a subset of the data provided by Gapminder. The data comes as a data frame (or tbl_df if you’re using dplyr). We can visit Gapminder.org documentation page to obtain information about the columns:

variable meaning
country
continent
year
lifeExp life expectancy at birth
pop total population
gdpPercap per-capita GDP

If you are dealing with plain vanilla data frames, you can rein in data frame printing explicitly with head() and tail(). Or turn it into a tibble with as_tibble()!

head(gapminder)
## # A tibble: 6 x 6
##   country     continent  year lifeExp      pop gdpPercap
##   <fct>       <fct>     <int>   <dbl>    <int>     <dbl>
## 1 Afghanistan Asia       1952    28.8  8425333      779.
## 2 Afghanistan Asia       1957    30.3  9240934      821.
## 3 Afghanistan Asia       1962    32.0 10267083      853.
## 4 Afghanistan Asia       1967    34.0 11537966      836.
## 5 Afghanistan Asia       1972    36.1 13079460      740.
## 6 Afghanistan Asia       1977    38.4 14880372      786.
tail(gapminder)
## # A tibble: 6 x 6
##   country  continent  year lifeExp      pop gdpPercap
##   <fct>    <fct>     <int>   <dbl>    <int>     <dbl>
## 1 Zimbabwe Africa     1982    60.4  7636524      789.
## 2 Zimbabwe Africa     1987    62.4  9216418      706.
## 3 Zimbabwe Africa     1992    60.4 10704340      693.
## 4 Zimbabwe Africa     1997    46.8 11404948      792.
## 5 Zimbabwe Africa     2002    40.0 11926563      672.
## 6 Zimbabwe Africa     2007    43.5 12311143      470.

More ways to query basic info on a data frame:

names(gapminder)
## [1] "country"   "continent" "year"      "lifeExp"   "pop"       "gdpPercap"
ncol(gapminder)
## [1] 6
length(gapminder)
## [1] 6
dim(gapminder)
## [1] 1704    6
nrow(gapminder)
## [1] 1704

A statistical overview can be obtained with summary()

summary(gapminder)
##         country        continent        year         lifeExp     
##  Afghanistan:  12   Africa  :624   Min.   :1952   Min.   :23.60  
##  Albania    :  12   Americas:300   1st Qu.:1966   1st Qu.:48.20  
##  Algeria    :  12   Asia    :396   Median :1980   Median :60.71  
##  Angola     :  12   Europe  :360   Mean   :1980   Mean   :59.47  
##  Argentina  :  12   Oceania : 24   3rd Qu.:1993   3rd Qu.:70.85  
##  Australia  :  12                  Max.   :2007   Max.   :82.60  
##  (Other)    :1632                                                
##       pop              gdpPercap       
##  Min.   :6.001e+04   Min.   :   241.2  
##  1st Qu.:2.794e+06   1st Qu.:  1202.1  
##  Median :7.024e+06   Median :  3531.8  
##  Mean   :2.960e+07   Mean   :  7215.3  
##  3rd Qu.:1.959e+07   3rd Qu.:  9325.5  
##  Max.   :1.319e+09   Max.   :113523.1  
## 

Although we haven’t begun our formal coverage of visualization yet, it’s so important for smell-testing dataset that we will make a few figures anyway. Here we use only base R graphics, which are very basic.

plot(lifeExp ~ year, gapminder)

plot(lifeExp ~ gdpPercap, gapminder)

plot(lifeExp ~ log(gdpPercap), gapminder)

Welcome to the “Tidyverse”

The tidyverse is “an opinionated collection of R packages designed for data science. All packages share an underlying philosophy and common APIs.”

Another way of putting it is that it’s a set of packages that are useful specifically for data manipulation, exploration and visualization with a common philosphy.

What is this common philosphy?

The common philosphy is called “tidy” data. It is a standard way of mapping the meaning of a dataset to its structure.

In tidy data:

  • Each variable forms a column.
  • Each observation forms a row.
  • Each type of observational unit forms a table.

Below, we are interested in transformating the table on the right to the the table on the left, which is considered “tidy”.

Working with tidy data is useful because it creates a structured way of organizing data values within a data set. This makes the data analysis process more efficient and simplifies the development of data analysis tools that work together. In this way, you can focus on the problem you are investigating, rather than the uninteresting logistics of data.

What is in the tidyverse?

We can install and load the set of R packages using install.packages("tidyverse") function.

When we load the tidyverse package using library(tidyverse), there are six core R packages that load:

  • readr, for data import.
  • tidyr, for data tidying.
  • dplyr, for data wrangling.
  • ggplot2, for data visualisation.
  • purrr, for functional programming.
  • tibble, for tibbles, a modern re-imagining of data frames.

Here, we load in the tidyverse.

library(tidyverse)

Because these packages all share the “tidy” philosphy, the data analysis workflow is easier as you move from package to package.

Today we will focus on dplyr and ggplot2, for data wrangling and visualiation, but definitely check out the other packages such as readr, tidyr, R packages to import data, to transform data to the “tidy” format.

Data wrangling

In the real world, analyzing data rarely involves data that can be easily imported and ready for analysis. According to Wikipedia:

Data munging or data wrangling is loosely the process of manually converting or mapping data from one “raw” form into another format that allows for more convenient consumption of the data with the help of semi-automated tools.

As you will see in class, one of the most time-consuming aspects of the data analysis process is “data wrangling”. This is also is a trendy term for cleaning up a messy data set.

R provides incredibly powerful and flexible language for data wrangling. However, the syntax is somewhat hard to get used to. We will therefore introducing a package that makes the syntax much more like the English language. This package is dplyr.

The dplyr R package

dplyr is a powerful R-package to transform and summarize tabular data with rows and columns.

The package contains a set of functions (or “verbs”) to perform common data manipulation operations such as filtering for rows, selecting specific columns, re-ordering rows, adding new columns and summarizing data.

In addition, dplyr contains a useful function to perform another common task which is the is the “split-apply-combine” concept. We will discuss that in a little bit.

How does it compare to using base functions R?

If you are familiar with R, you are probably familiar with base R functions such as split(), subset(), apply(), sapply(), lapply(), tapply() and aggregate(). Compared to base functions in R, the functions in dplyr are easier to work with, are more consistent in the syntax and are targeted for data analysis around data frames instead of just vectors.

The important dplyr verbs to remember are:

dplyr verbs Description
select() select columns
filter() filter rows
arrange() re-order or arrange rows
mutate() create new columns
summarize() summarize values
group_by() allows for group operations in the “split-apply-combine” concept

Pipe operator: %>%

Before we go any futher, let’s introduce the pipe operator: %>%. In our stocks example, we briefly saw this symbol. It is called the pipe operator. dplyr imports this operator from another package (magrittr) see help file here. This operator allows you to pipe the output from one function to the input of another function. Instead of nesting functions (reading from the inside to the outside), the idea of of piping is to read the functions from left to right.

dplyr verbs in action

The two most basic functions are select() and filter() which selects columns and filters rows, respectively.

Selecting columns using select()

To select all the columns except a specific column, use the “-” (subtraction) operator (also known as negative indexing).

gapminder %>% 
    select(-lifeExp)
## # A tibble: 1,704 x 5
##    country     continent  year      pop gdpPercap
##    <fct>       <fct>     <int>    <int>     <dbl>
##  1 Afghanistan Asia       1952  8425333      779.
##  2 Afghanistan Asia       1957  9240934      821.
##  3 Afghanistan Asia       1962 10267083      853.
##  4 Afghanistan Asia       1967 11537966      836.
##  5 Afghanistan Asia       1972 13079460      740.
##  6 Afghanistan Asia       1977 14880372      786.
##  7 Afghanistan Asia       1982 12881816      978.
##  8 Afghanistan Asia       1987 13867957      852.
##  9 Afghanistan Asia       1992 16317921      649.
## 10 Afghanistan Asia       1997 22227415      635.
## # … with 1,694 more rows

The function select() is much more powerful though. To select a range of columns by name, use the “:” (colon) operator

gapminder %>% 
  select(lifeExp:gdpPercap)
## # A tibble: 1,704 x 3
##    lifeExp      pop gdpPercap
##      <dbl>    <int>     <dbl>
##  1    28.8  8425333      779.
##  2    30.3  9240934      821.
##  3    32.0 10267083      853.
##  4    34.0 11537966      836.
##  5    36.1 13079460      740.
##  6    38.4 14880372      786.
##  7    39.9 12881816      978.
##  8    40.8 13867957      852.
##  9    41.7 16317921      649.
## 10    41.8 22227415      635.
## # … with 1,694 more rows

To select all columns that start with the character string “c”, use the function starts_with()

gapminder %>% 
  select(starts_with("c"))
## # A tibble: 1,704 x 2
##    country     continent
##    <fct>       <fct>    
##  1 Afghanistan Asia     
##  2 Afghanistan Asia     
##  3 Afghanistan Asia     
##  4 Afghanistan Asia     
##  5 Afghanistan Asia     
##  6 Afghanistan Asia     
##  7 Afghanistan Asia     
##  8 Afghanistan Asia     
##  9 Afghanistan Asia     
## 10 Afghanistan Asia     
## # … with 1,694 more rows

Some additional options to select columns based on a specific criteria include

  1. ends_with() = Select columns that end with a character string
  2. contains() = Select columns that contain a character string
  3. matches() = Select columns that match a regular expression
  4. one_of() = Select columns names that are from a group of names

Selecting rows using filter()

Let’s say we only want the data from 2007.

To do this, we can use the filter() function to filter the rows for years in 2007.

gapminder %>% 
  filter(year == "2007")
## # A tibble: 142 x 6
##    country     continent  year lifeExp       pop gdpPercap
##    <fct>       <fct>     <int>   <dbl>     <int>     <dbl>
##  1 Afghanistan Asia       2007    43.8  31889923      975.
##  2 Albania     Europe     2007    76.4   3600523     5937.
##  3 Algeria     Africa     2007    72.3  33333216     6223.
##  4 Angola      Africa     2007    42.7  12420476     4797.
##  5 Argentina   Americas   2007    75.3  40301927    12779.
##  6 Australia   Oceania    2007    81.2  20434176    34435.
##  7 Austria     Europe     2007    79.8   8199783    36126.
##  8 Bahrain     Asia       2007    75.6    708573    29796.
##  9 Bangladesh  Asia       2007    64.1 150448339     1391.
## 10 Belgium     Europe     2007    79.4  10392226    33693.
## # … with 132 more rows

Note: you can use the boolean operators (e.g. >, <, >=, <=, !=, %in%) to create logical tests.

For example, if we wanted only years after 2014, we can add a second criteria:

gapminder %>% 
  filter(year > 1977)
## # A tibble: 852 x 6
##    country     continent  year lifeExp      pop gdpPercap
##    <fct>       <fct>     <int>   <dbl>    <int>     <dbl>
##  1 Afghanistan Asia       1982    39.9 12881816      978.
##  2 Afghanistan Asia       1987    40.8 13867957      852.
##  3 Afghanistan Asia       1992    41.7 16317921      649.
##  4 Afghanistan Asia       1997    41.8 22227415      635.
##  5 Afghanistan Asia       2002    42.1 25268405      727.
##  6 Afghanistan Asia       2007    43.8 31889923      975.
##  7 Albania     Europe     1982    70.4  2780097     3631.
##  8 Albania     Europe     1987    72    3075321     3739.
##  9 Albania     Europe     1992    71.6  3326498     2497.
## 10 Albania     Europe     1997    73.0  3428038     3193.
## # … with 842 more rows

Use mutate() to add new variables

mutate() is a function that defines and inserts new variables into a tibble. You can refer to existing variables by name.

gapminder %>%
    filter(year==2007) %>% 
    select(-continent) %>%
    mutate(gdp = pop * gdpPercap)
## # A tibble: 142 x 6
##    country      year lifeExp       pop gdpPercap           gdp
##    <fct>       <int>   <dbl>     <int>     <dbl>         <dbl>
##  1 Afghanistan  2007    43.8  31889923      975.  31079291949.
##  2 Albania      2007    76.4   3600523     5937.  21376411360.
##  3 Algeria      2007    72.3  33333216     6223. 207444851958.
##  4 Angola       2007    42.7  12420476     4797.  59583895818.
##  5 Argentina    2007    75.3  40301927    12779. 515033625357.
##  6 Australia    2007    81.2  20434176    34435. 703658358894.
##  7 Austria      2007    79.8   8199783    36126. 296229400691.
##  8 Bahrain      2007    75.6    708573    29796.  21112675360.
##  9 Bangladesh   2007    64.1 150448339     1391. 209311822134.
## 10 Belgium      2007    79.4  10392226    33693. 350141166520.
## # … with 132 more rows

Arrange or re-order rows using arrange()

To arrange (or re-order) rows by a particular column such as the population, list the name of the column you want to arrange the rows by

gapminder %>%     
    filter(year==2007) %>%
    select(-continent) %>%
    mutate(gdp = pop * gdpPercap) %>% 
    arrange(gdp)
## # A tibble: 142 x 6
##    country                   year lifeExp     pop gdpPercap         gdp
##    <fct>                    <int>   <dbl>   <int>     <dbl>       <dbl>
##  1 Sao Tome and Principe     2007    65.5  199579     1598.  319014077.
##  2 Comoros                   2007    65.2  710960      986.  701111696.
##  3 Guinea-Bissau             2007    46.4 1472041      579.  852652874.
##  4 Djibouti                  2007    54.8  496374     2082. 1033689705.
##  5 Gambia                    2007    59.4 1688359      753. 1270911775.
##  6 Liberia                   2007    45.7 3193942      415. 1323912407.
##  7 Central African Republic  2007    44.7 4369038      706. 3084613079.
##  8 Eritrea                   2007    58.0 4906585      641. 3146934084.
##  9 Lesotho                   2007    42.6 2012649     1569. 3158513357.
## 10 Burundi                   2007    49.6 8390505      430. 3608510288.
## # … with 132 more rows

So if we wanted to figure out what were the top three countries with the largest gdpPercap in 2007, we could use the desc() function inside of arrange() to order rows in a descending order.

gapminder %>% 
  filter(year == 2007) %>% 
  arrange(desc(gdpPercap)) %>% 
  head(n=3)
## # A tibble: 3 x 6
##   country   continent  year lifeExp     pop gdpPercap
##   <fct>     <fct>     <int>   <dbl>   <int>     <dbl>
## 1 Norway    Europe     2007    80.2 4627926    49357.
## 2 Kuwait    Asia       2007    77.6 2505559    47307.
## 3 Singapore Asia       2007    80.0 4553009    47143.

Data visualization

ggplot2

ggplot2 is a powerful data exploration and visualization package that can create graphics in R. It was created by Hadley Wickham when he was a graduate student at Iowa State University and is based on the principals defined in the Grammar of Graphics.

Why is it useful?

The idea of the Grammar of Graphics is to break the graph into components and handle the components of a graph separately. The ggplot2 package contains a set of functions that allow us to build the features of the graph in a series of layers for versatility and control.

There are two main plotting functions in ggplot2:

  • qplot() = a quick plot, similar to the plot() function in base R
  • ggplot() = a “grammar of graphics” (gg) plot which is made up two components (a ggplot() object and at least one geom layer)

The ggplot2 is loaded whenever you load tidyverse, but you can always load it formally.

library(ggplot2)

Life expectancy and GDP per capita

To try and answer our first question we will make a scatterplot. We will do this for the latest entry in our database which is:

max( gapminder$year )
## [1] 2007

We will first make a quick plot of these two variables.

qplot

The qplot function allows us to produce simple plots, similar to plot in base R. The main input of qplot is an x and y argument, but it also accepts a data set (data) where the x and y variables are located.

To create a scatter-plot of life expectancy versus GDP per capita for 2007, we start by creating a subset of the data with only the 2007 year.

dat <- filter(gapminder, year==2007)

Why does this not work?

qplot(x = gdpPercap, y = lifeExp) 

We need to specify where to get these values from. Instead, we can use the vectors of dat directly

## need to specify where variables are located
qplot(x = dat$gdpPercap, y = dat$lifeExp) 

However, a cleaner way to do this does not define dat and instead uses the data argument:

## instead of having to specify name of data frame each time, just list it once
qplot(x = gdpPercap, y = lifeExp, data = filter(gapminder, year==2007))

If youw ant to add labels to the x and y axis, you can use the xlab and ylab arguments. You can read the help file to check out other arguments available in the function.

qplot(x = gdpPercap, y = lifeExp, 
      data = filter(gapminder, year==2007), 
      xlab = "GDP per Capita", 
      ylab = "Life Expectancy", 
      main = "Data from Gapminder")

From this plot, we see that there is a wide variability in life expectancy for the lower income countries and then somewhat of a positive trend. However, there are many countries with incomes below 5,000 dollars per person and it is hard to see differences between these. Next we will now learn about the grammar of graphics and create a series of visualizations.

ggplot

This function is the implementation of the “Grammar of Graphics” that allows us to build layers of graphical elements to produce plots. As explained by Hadley Wickham

the grammar tells us that a statistical graphic is a mapping from data to aesthetic attributes (colour, shape, size) of geometric objects (points, lines, bars). The plot may also contain statistical transformations of the data and is drawn on a specific coordinates system.

Terminology

  • ggplot - the main function where you specify the data set and variables to plot (this is where we define the x and y variable names)
  • geoms - geometric objects
    • e.g. geom_point(), geom_bar(), geom_line(), geom_histogram()
  • aes - aesthetics
    • shape, transparency, color, fill, linetype
  • scales - define how your data will be plotted
    • continuous, discrete, log, etc

There are three ways to initialize a ggplot() object.

An empty ggplot object

ggplot()         

A ggplot object associated with a dataset

gapminder %>% 
    filter(year==2007) %>% 
    ggplot()

or a ggplot object with a dataset and x and y defined

gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=gdpPercap, y = lifeExp))

Creating your first ggplot()

We just used the function aes() which is an aesthetic mapping function inside the ggplot() object. We use this function to specify plot attributes (e.g. x and y variable names) that will not change as we add more layers.

Anything that goes in the ggplot() object becomes a global setting. From there, we use the geom objects to add more layers to the base ggplot() object. These will define what we are interested in illustrating using the data.

Earlier we noticed that there are many countries with incomes below 5,000 dollars per person and it is hard to see differences between these. We can examine just this variable with a histogram. Here we would use a different geometry:

gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=gdpPercap)) + geom_histogram()
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

The histogram shows very large tails. We may do better by transforming the data. For data like this, the log transformation seems to work well. It also has a nice economic interpretation related to percent growth: in \(log_{10}\) a change of 1 means the country is 10 times richer.

So how do we make the x-axis in the log scale? It is convenient to have this cheat sheet around when using ggplot2. From there we see that scale_x_log10 does what we want.

gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=gdpPercap)) + 
    geom_histogram(bins=25) + 
    scale_x_log10()

We no longer see extreme tails. The scatter plot now looks much more informative:

Now we can remake the scatter plot but now make sure the x-axis is in a log-scale

gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=gdpPercap, y = lifeExp)) +
    geom_point() + scale_x_log10()

We can also do this:

gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=log10(gdpPercap), y = lifeExp)) +
    geom_point()

We can also use other really great packages, such as ggrepel:

library(ggrepel)
gapminder %>% 
    filter(year==2007) %>% 
    ggplot(aes(x=gdpPercap, y = lifeExp)) +
    geom_point(color = 'red',) + scale_x_log10() + 
    geom_text_repel(aes(label = country), size = 2) +
  theme_classic() 

Now you are ready to make presentation quality data visualizations!

Cheatsheets

Confessions and countermeasures with the tidyverse

Here are the awesome slides from Rachael Workman (PhD student in Biochemistry, Cellular and Molecular Biology (BCMB) program) where she discusses
Confessions and Countermeasures: my not ideal R habits and how the Tidyverse resolved them

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