Content from Before we start

Last updated on 2025-10-03 | Edit this page

Overview

Questions

  • Why should you use R and RStudio?
  • How do you get started working in R and RStudio?

Objectives

  • Understand the difference between R and RStudio
  • Describe the purpose of the different RStudio panes
  • Organize files and directories into R Projects
  • Use the RStudio help interface to get help with R functions
  • Be able to format questions to get help in the broader R community

What is R? What is RStudio?

The term “R” is used to refer to both the programming language and the software that interprets the scripts written using it.

RStudio is a popular way to write R scripts and interact with the R software. To function correctly, RStudio needs R and therefore both need to be installed on your computer.

Why learn R?

R does not involve lots of pointing and clicking, and that’s a good thing

In R, the results of your analysis rely on a series of written commands, and not on remembering a succession of pointing and clicking. That is a good thing! So, if you want to redo your analysis because you collected more data, you don’t have to remember which button you clicked in which order to obtain your results. With a stored series of commands in an R script, you can repeat running them and R will process the new dataset exactly the same way as before.

Working with scripts makes the steps you used in your analysis clear, and the code you write can be inspected by someone else who can give you feedback and spot mistakes.

Working with scripts forces you to have a deeper understanding of what you are doing, and facilitates your learning and comprehension of the methods you use.

R code is great for reproducibility

Reproducibility is when someone else, including your future self, can obtain the same results from the same dataset when using the same analysis.

R integrates with other tools to generate manuscripts from your code. If you collect more data, or fix a mistake in your dataset, the figures and the statistical tests in your manuscript are updated automatically.

R is widely used in academia and in industries such as pharma and biotech. These organisations expect analyses to be reproducible, so knowing R will give you an edge with these requirements.

R is interdisciplinary and extensible

With 10,000+ packages that can be installed to extend its capabilities, R provides a framework that allows you to combine statistical approaches from many scientific disciplines to best suit the analytical framework you need to analyze your data. For instance, R has packages for image analysis, GIS, time series, population genetics, and a lot more.

R works on data of all shapes and sizes

The skills you learn with R scale easily with the size of your dataset. Whether your dataset has hundreds or millions of lines, it won’t make much difference to you.

R is designed for data analysis. It comes with special data structures and data types that make handling of missing data and statistical factors convenient.

R can connect to spreadsheets, databases, and many other data formats, on your computer or on the web.

R produces high-quality graphics

The plotting functionalities in R are endless, and allow you to adjust any aspect of your graph to visualize your data more effectively.

R has a large and welcoming community

Thousands of people use R daily. Many of them are willing to help you through mailing lists and websites such as Stack Overflow, RStudio community, and Slack channels such as
the R for Data Science online community (https://www.rfordatasci.com/). In addition, there are numerous online and in person meetups organised globally through organisations such as R Ladies Global (https://rladies.org/).

Not only is R free, but it is also open-source and cross-platform

Anyone can inspect the source code to see how R works. Because of this transparency, there is less chance for mistakes, and if you (or someone else) find some, you can report and fix bugs.

Knowing your way around RStudio

Let’s start by learning about RStudio, which is an Integrated Development Environment (IDE) for working with R.

The RStudio IDE open-source product is free under the Affero General Public License (AGPL) v3. The RStudio IDE is also available with a commercial license and priority email support from RStudio, PBC.

We will use RStudio IDE to write code, navigate the files on our computer, inspect the variables we are going to create, and visualize the plots we will generate. RStudio can also be used for other things (e.g., version control, developing packages, writing Shiny apps) that we will not cover during the workshop.

RStudio interface screenshot. Clockwise from top left: Source,Environment/History, Files/Plots/Packages/Help/Viewer,Console.

RStudio is divided into 4 “panes”:

  • The Source for your scripts and documents (top-left, in the default layout)
  • Your Environment/History (top-right) which shows all the objects in your working space (Environment) and your command history (History)
  • Your Files/Plots/Packages/Help/Viewer (bottom-right)
  • The R Console (bottom-left)

The placement of these panes and their content can be customized (see menu, Tools --> Global Options --> Pane Layout). For ease of use, settings such as background color, font color, font size, and zoom level can also be adjusted in this menu (Global Options --> Appearance).

One of the advantages of using RStudio is that all the information you need to write code is available in a single window. Additionally, with many shortcuts, autocompletion, and highlighting for the major file types you use while developing in R, RStudio will make typing easier and less error-prone.

Getting set up

It is good practice to keep a set of related data, analyses, and text self-contained in a single folder, called the working directory. All of the scripts within this folder can then use relative paths to files that indicate where inside the project a file is located (as opposed to absolute paths, which point to where a file is on a specific computer). Working this way allows you to move your project around on your computer and share it with others without worrying about whether or not the underlying scripts will still work.

RStudio provides a helpful set of tools to do this through its “Projects” interface, which not only creates a working directory for you, but also remembers its location (allowing you to quickly navigate to it) and optionally preserves custom settings and (re-)open files to assist resume work after a break. Go through the steps for creating an “R Project” for this tutorial below.

  1. Start RStudio.
  2. Under the File menu, click on New Project. Choose New Directory, then New Project.
  3. Enter a name for this new folder (or “directory”), and choose a convenient location for it. This will be your working directory for the rest of the day (e.g., ~/r-ecology).
  4. Click on Create Project.

A workspace is your current working environment in R which includes any user-defined object. By default, all of these objects will be saved, and automatically loaded, when you reopen your project. Saving a workspace to .RData can be cumbersome, especially if you are working with larger datasets, and it can lead to hard to debug errors by having objects in memory you forgot you had. Therefore, it is often a good idea to turn this off. To do so, go to Tools --> Global Options and uncheck Restore .RData into workspace at startup and select the ‘Never’ option for Save workspace to .RData' on exit.

Set 'Save workspace to .RData on exit' to'Never'

Organizing your working directory

Using a consistent folder structure across your projects will help keep things organized, and will help you to find/file things in the future. This can be especially helpful when you have multiple projects. In general, you may create directories (folders) for scripts, data, plots, and documents.

  • data_raw/ & data/
    • Use these folders to store raw data and intermediate datasets you may create for the need of a particular analysis. For the sake of transparency and provenance, you should always keep a copy of your raw data accessible and do as much of your data cleanup and preprocessing programmatically (i.e., with scripts, rather than manually) as possible.
    • Separating raw data from processed data is also a good idea. For example, you could have files data_raw/tree_survey.plot1.txt and ...plot2.txt kept separate from a data/tree.survey.csv file generated by the scripts/01.preprocess.tree_survey.R script.
  • scripts/ This would be the location to keep your R scripts for different analyses or plotting, and potentially a separate folder for functions that you might create.
  • fig/ This is a location for the plots that you make with your scripts.
  • documents/ This would be a place to keep outlines, drafts, and other text.
  • Additional (sub)directories depending on your project needs.

For this workshop, we will need a data_raw/ folder to store our raw data, and we will use data/ for when we learn how to export data as CSV files, and a fig/ folder for the figures that we will save.

  • Under the Files tab on the right of the screen, click on New Folder and create a folder named data_raw within your newly created working directory (e.g., ~/data-carpentry/). (Alternatively, type dir.create("data_raw") at your R console.) Repeat these operations to create a data and a fig folder.

We are going to keep the script in the root of our working directory because we are only going to use one file. Later, when you start create more complex projects, it might make sense to organize scripts in sub-directories.

Your working directory should now look like this:

How it should look like at the beginning of this lesson
How it should look like at the beginning of this lesson

Interacting with R

The basis of programming is that we write down instructions for the computer to follow, and then we tell the computer to follow those instructions. We write these instructions in the form of code, which is a common language that is understood by the computer and humans (after some practice). We call these instructions commands, and we tell the computer to follow the instructions by running (also called executing) the commands.

Console vs. script

You can run commands directly in the R console, or you can write them into an R script. It may help to think of working in the console vs. working in a script as something like cooking. The console is like making up a new recipe, but not writing anything down. You can carry out a series of steps and produce a nice, tasty dish at the end. However, because you didn’t write anythingdown, it’s harder to figure out exactly what you did, and in what order.

Writing a script is like taking nice notes while cooking- you can tweak and edit the recipe all you want, you can come back in 6 months and try it again, and you don’t have to try to remember what went well and what didn’t. It’s actually even easier than cooking, since you can hit one button and the computer “cooks” the whole recipe for you!

An additional benefit of scripts is that you can leave comments for yourself or others to read. Lines that start with # are considered comments and will not be interpreted as R code.

Console

  • The R console is where code is run/executed
  • The prompt, which is the > symbol, is where you can type commands
  • By pressing Enter, R will execute those commands and print the result.
  • You can work here, and your history is saved in the History pane, but you can’t access it in the future

Script

  • A script is a record of commands to send to R, preserved in a plain text file with a .R extension
  • You can make a new R script by clicking File → New File → R Script, clicking the green + button in the top left corner of RStudio, or pressing Shift+Cmd+N (Mac) or Shift+Ctrl+N (Windows). It will be unsaved, and called “Untitled1”
  • If you type out lines of R code in a script, you can send them to the R console to be evaluated
    • Cmd+Enter (Mac) or Ctrl+Enter (Windows) will run the line of code that your cursor is on
    • If you highlight multiple lines of code, you can run all of them by pressing Cmd+Enter (Mac) or Ctrl+Enter (Windows)
    • By preserving commands in a script, you can edit and rerun them quickly, save them for later, and share them with others
    • You can leave comments for yourself by starting a line with a # or placing # after a line of code.

Example

Let’s try running some code in the console and in a script. First, click down in the Console pane, and type out 1+1. Hit Enter to run the code. You should see your code echoed, and then the value of 2 returned.

Now click into your blank script, and type out 1+1. With your cursor on that line, hit Cmd+Enter (Mac) or Ctrl+Enter (Windows) to run the code. You will see that your code was sent from the script to the console, where it returned a value of 2, just like when you ran your code directly in the console.

Now save and name the script that we will be working on for the rest of the workshop. You might name it intro.R. Try to choose simple, memorable names for your scripts and avoid using spaces.

Seeking help

Searching function documentation with ? and ??

If you need help with a specific function, let’s say mean(), you can type ?mean or press F1 while your cursor is on the function name. If you are looking for a function to do a particular task, but don’t know the function name, you can use the double question mark ??, for example ??kruskall. Both commands will open matching help files in RStudio’s help panel in the lower right corner. You can also use the help panel to search help directly, as seen in the screenshot.

RStudio help panel. When typing a word in the search field, it will showrelated suggestions.

Automatic code completion

When you write code in RStudio, you can use its automatic code completion to remind yourself of a function’s name or arguments. Start typing the function name and pay attention to the suggestions that pop up. Use the up and down arrow to select a suggested code completion and Tab to apply it. You can also use code completion to complete function’s argument names, object, names and file names. It even works if you don’t get the spelling 100% correct.

Package vignettes and cheat sheets

In addition to the documentation for individual functions, many packages have vignettes – instructions for how to use the package to do certain tasks. Vignettes are great for learning by example. Vignettes are accessible via the package help and by using the function browseVignettes().

There is also a Help menu at the top of the RStudio window, that has cheat sheets for popular packages, RStudio keyboard shortcuts, and more.

Finding more functions and packages

RStudio’s help only searches the packages that you have installed on your machine, but there are many more available on CRAN and GitHub. To search across all available R packages, you can use the website rdocumentation.org. Often, a generic Google or internet search “R <task>” will send you to the appropriate package documentation or a forum where someone else has already asked your question. Many packages also have websites with additional help, tutorials, news and more (for example tidyverse.org).

Dealing with error messages

Don’t get discouraged if your code doesn’t run immediately! Error messages are common when programming, and fixing errors is part of any programmer’s daily work. Often, the problem is a small typo in a variable name or a missing parenthesis. Watch for the red x’s next to your code in RStudio. These may provide helpful hints about the source of the problem.

RStudio shows a red x next to a line of code that R doesn't understand.

If you can’t fix an error yourself, start by googling it. Some error messages are too generic to diagnose a problem (e.g. “subscript out of bounds”). In that case it might help to include the name of the function or package you’re using in your query.

Asking for help

If your Google search is unsuccessful, you may want to ask other R users for help. There are different places where you can ask for help. During this workshop, don’t hesitate to talk to your neighbor, compare your answers, and ask for help. You might also be interested in organizing regular meetings following the workshop to keep learning from each other. If you have a friend or colleague with more experience than you, they might also be able and willing to help you.

Learning to search for help is probably the most useful skill for any R user. The key skill is figuring out what you should actually search for. It’s often a good idea to start your search with R or R programming. If you have the name of a package you want to use, start with R package_name.

Many of the answers you find will be from a website called Stack Overflow, where people ask programming questions and others provide answers.

Generative AI Help

In addition to the resources we’ve already mentioned for getting help with R, it’s becoming increasingly common to turn to generative AI chatbots such as ChatGPT to get help while coding. You will probably receive some useful guidance by presenting your error message to the chatbot and asking it what went wrong.

However, the way this help is provided by the chatbot is different. Answers on Stack Overflow have (probably) been given by a human as a direct response to the question asked. But generative AI chatbots, which are based on an advanced statistical model, respond by generating the most likely sequence of text that would follow the prompt they are given.

While responses from generative AI tools can often be helpful, they are not always reliable. These tools sometimes generate plausible but incorrect or misleading information, so (just as with an answer found on the internet) it is essential to verify their accuracy. You need the knowledge and skills to be able to understand these responses, to judge whether or not they are accurate, and to fix any errors in the code it offers you.

In addition to asking for help, programmers can use generative AI tools to generate code from scratch; extend, improve and reorganise existing code; translate code between programming languages; figure out what terms to use in a search of the internet; and more. However, there are drawbacks that you should be aware of.

The models used by these tools have been “trained” on very large volumes of data, much of it taken from the internet, and the responses they produce reflect that training data, and may recapitulate its inaccuracies or biases. The environmental costs (energy and water use) of LLMs are a lot higher than other technologies, both during development (known as training) and when an individual user uses one (also called inference). For more information see the AI Environmental Impact Primer developed by researchers at HuggingFace, an AI hosting platform. Concerns also exist about the way the data for this training was obtained, with questions raised about whether the people developing the LLMs had permission to use it. Other ethical concerns have also been raised, such as reports that workers were exploited during the training process.

We recommend that you avoid getting help from generative AI during the workshop for several reasons:

  1. For most problems you will encounter at this stage, help and answers can be found among the first results returned by searching the internet.
  2. The foundational knowledge and skills you will learn in this lesson by writing and fixing your own programs are essential to be able to evaluate the correctness and safety of any code you receive from online help or a generative AI chatbot. If you choose to use these tools in the future, the expertise you gain from learning and practising these fundamentals on your own will help you use them more effectively.
  3. As you start out with programming, the mistakes you make will be the kinds that have also been made – and overcome! – by everybody else who learned to program before you. Since these mistakes and the questions you are likely to have at this stage are common, they are also better represented than other, more specialised problems and tasks in the data that was used to train generative AI tools. This means that a generative AI chatbot is more likely to produce accurate responses to questions that novices ask, which could give you a false impression of how reliable they will be when you are ready to do things that are more advanced.

How to learn more after the workshop?

The material we cover during this workshop will give you a taste of how you can use R to analyze data for your own research. However, to do advanced operations such as cleaning your dataset, using statistical methods, or creating beautiful graphics you will need to learn more.

The best way to become proficient and efficient at R, as with any other tool, is to use it to address your actual research questions. As a beginner, it can feel daunting to have to write a script from scratch, and given that many people make their code available online, modifying existing code to suit your purpose might get first hands-on experience using R for your own work and help you become comfortable eventually creating your own scripts.

More resources

More about R

How to ask good programming questions?

Content from Introduction to R

Last updated on 2025-10-02 | Edit this page

Overview

Questions

  • How do you create variables in R?
  • What are the main types of vectors in R?

Objectives

  • Define the following terms as they relate to R: object, assign, call, function, arguments, options.
  • Create objects and assign values to them in R.
  • Learn how to name objects.
  • Save a script file for later use.
  • Use comments to inform script.
  • Solve simple arithmetic operations in R.
  • Call functions and use arguments to change their default options.
  • Inspect the content of vectors and manipulate their content.
  • Subset and extract values from vectors.
  • Analyze vectors with missing data.

Note: This lesson is a shortened and modified version of the Data Carpentry Ecology R Lesson. Please refer to the original for additional functions and examples, as well as regular updates.

Creating objects in R

You can get output from R simply by typing math in the console:

R 

3 + 5
12 / 7

However, to do useful and interesting things, we need to assign values to objects. To create an object, we need to give it a name followed by the assignment operator <-, and the value we want to give it:

R 

weight_kg <- 55

<- is the assignment operator. It assigns values on the right to objects on the left. So, after executing x <- 3, the value of x is 3. For historical reasons, you can also use = for assignments, but not in every context. Because of the slight differences in syntax, it is good practice to always use <- for assignments.

Objects can be given almost any name such as x, current_temperature, or subject_id. Here are some further guidelines on naming objects:

  • You want your object names to be explicit and not too long.
  • They cannot start with a number (2x is not valid, but x2 is).
  • R is case sensitive, so for example, weight_kg is different from Weight_kg.
  • Don’t use function names of fundamental functions in R (e.g., if, else, for, c, T, mean, data, df, weights, etc.). If in doubt, check the help to see if the name is already in use.
  • Avoid dots (.) within names.
  • Be consistent in the styling of your code, such as where you put spaces, how you name objects, etc. Styles can include “lower_snake”, “UPPER_SNAKE”, “lowerCamelCase”, “UpperCamelCase”, etc.
Callout

Objects vs. variables

What are known as objects in R are known as variables in many other programming languages. Depending on the context, object and variable can have drastically different meanings. However, in this lesson, the two words are used synonymously. For more information see: https://cran.r-project.org/doc/manuals/r-release/R-lang.html#Objects

When assigning a value to an object, R does not print anything. You can force R to print the value by typing the object name:

R 

weight_kg <- 55    # doesn't print anything
weight_kg          # but typing the name of the object does (once it's created)

Now that R has weight_kg in memory, we can do arithmetic with it. For instance, we may want to convert this weight into pounds (weight in pounds is 2.2 times the weight in kg):

R 

2.2 * weight_kg

We can also change an object’s value by assigning it a new one:

R 

weight_kg <- 57.5
2.2 * weight_kg

Assigning a value to one object does not change the values of other objects. For example, let’s store the animal’s weight in pounds in a new object, weight_lb:

R 

weight_lb <- 2.2 * weight_kg

and then change weight_kg to 100.

R 

weight_kg <- 100

What do you think is the current content of the object weight_lb? 126.5 or 220?

Functions and their arguments

Functions are “canned scripts” that automate more complicated sets of commands including operations assignments, etc. Many functions are predefined, or can be made available by importing R packages (more on that later). A function usually takes one or more inputs called arguments. Functions often (but not always) return a value. A typical example would be the function round(). The input (the argument) must be a number, and the return value (in fact, the output) is the input rounded to the nearest whole number. Executing a function (‘running it’) is called calling the function. An example of a function call is:

R 

round(3.14159)

OUTPUT 

#> [1] 3

Here, we’ve called round() with just one argument, 3.14159, and it has returned the value 3. That’s because the default is to round to the nearest whole number.

The return ‘value’ of a function need not be numerical, and it also does not need to be a single item: it can be a set of things, or even a dataset. We’ll see that when we read data files into R.

Arguments can be anything, not only numbers or filenames, but also other objects. Exactly what each argument means differs per function, and must be looked up in the documentation (see below). Some functions take arguments which may either be specified by the user, or, if left out, take on a default value: these are called options. Options are typically used to alter the way the function operates, such as whether it ignores ‘bad values’, or what symbol to use in a plot. However, if you want something specific, you can specify a value of your choice which will be used instead of the default.

If we want more digits we can see how to do that by getting information about the round function. We can use args(round) to find what arguments it takes, or look at the help for this function using ?round.

R 

args(round)

OUTPUT 

#> function (x, digits = 0, ...)
#> NULL

R 

?round

We see that if we want a different number of digits, we can type digits = 2 or however many we want.

R 

round(3.14159, digits = 2)

OUTPUT 

#> [1] 3.14

If you provide the arguments in the exact same order as they are defined you don’t have to name them:

R 

round(3.14159, 2)

OUTPUT 

#> [1] 3.14

And if you do name the arguments, you can switch their order:

R 

round(digits = 2, x = 3.14159)

OUTPUT 

#> [1] 3.14

It’s good practice to put the non-optional arguments (like the number you’re rounding) first in your function call, and to then specify the names of all optional arguments. If you don’t, someone reading your code might have to look up the definition of a function with unfamiliar arguments to understand what you’re doing.

Vectors and data types

A vector is the most common and basic data type in R, and is pretty much the workhorse of R. A vector is composed by a series of values, which can be either numbers or characters. We can assign a series of values to a vector using the c() function. For example we can create a vector of animal weights and assign it to a new object weight_g:

R 

weight_g <- c(50, 60, 65, 82)
weight_g

A vector can also contain characters:

R 

animals <- c("mouse", "rat", "dog")
animals

The quotes around “mouse”, “rat”, etc. are essential here. Without the quotes R will assume objects have been created called mouse, rat and dog. As these objects don’t exist in R’s memory, there will be an error message.

There are many functions that allow you to inspect the content of a vector. length() tells you how many elements are in a particular vector:

R 

length(weight_g)
length(animals) #notice this doesn't return the number of characters

An important feature of a vector, is that all of the elements are the same type of data. The function class() indicates what kind of object you are working with:

R 

class(weight_g)
class(animals)

The function str() provides an overview of the structure of an object and its elements. It is a useful function when working with large and complex objects:

R 

str(weight_g)
str(animals)

You can use the c() function to add other elements to your vector:

R 

weight_g <- c(weight_g, 90) # add to the end of the vector
weight_g <- c(30, weight_g) # add to the beginning of the vector
weight_g

In the first line, we take the original vector weight_g, add the value 90 to the end of it, and save the result back into weight_g. Then we add the value 30 to the beginning, again saving the result back into weight_g.

We can do this over and over again to grow a vector, or assemble a dataset. As we program, this may be useful to add results that we are collecting or calculating.

An atomic vector is the simplest R data type and is a linear vector of a single type. Above, we saw 2 of the 6 main atomic vector types that R uses: "character" and "numeric" (or "double"). These are the basic building blocks that all R objects are built from. The other 4 atomic vector types are:

  • "logical" for TRUE and FALSE (the boolean data type)
  • "integer" for integer numbers (e.g., 2L, the L indicates to R that it’s an integer)
  • "complex" to represent complex numbers with real and imaginary parts (e.g., 1 + 4i) and that’s all we’re going to say about them
  • "raw" for bitstreams that we won’t discuss further

You can check the type of your vector using the typeof() function and inputting your vector as the argument.

Vectors are one of the many data structures that R uses. Other important types you may encounter are lists (list), matrices (matrix), data frames (data.frame), factors (factor) and arrays (array).

Challenge

Challenge

  • We’ve seen that atomic vectors can be of type character, numeric (or double), integer, and logical. But what happens if we try to mix these types in a single vector?

R implicitly converts them to all be the same type

Challenge

Challenge (continued)

  • What will happen in each of these examples? (hint: use class() to check the data type of your objects):

    R 

    num_char <- c(1, 2, 3, "a")
num_logical <- c(1, 2, 3, TRUE)
char_logical <- c("a", "b", "c", TRUE)
tricky <- c(1, 2, 3, "4")

  • Why do you think it happens?

Vectors can be of only one data type. R tries to convert (coerce) the content of this vector to find a “common denominator” that doesn’t lose any information.

Challenge

Challenge (continued)

  • How many values in combined_logical are "TRUE" (as a character) in the following example (reusing the 2 ..._logicals from above):

    R 

    combined_logical <- c(num_logical, char_logical)

Only one. There is no memory of past data types, and the coercion happens the first time the vector is evaluated. Therefore, the TRUE in num_logical gets converted into a 1 before it gets converted into "1" in combined_logical.

Challenge

Challenge (continued)

  • You’ve probably noticed that objects of different types get converted into a single, shared type within a vector. In R, we call converting objects from one class into another class coercion. These conversions happen according to a hierarchy, whereby some types get preferentially coerced into other types. Can you draw a diagram that represents the hierarchy of how these data types are coerced?

logical → numeric → character ← logical

Subsetting vectors

If we want to extract one or several values from a vector, we must provide one or several indices in square brackets. For instance:

R 

animals <- c("mouse", "rat", "dog", "cat")
animals[2]

OUTPUT 

#> [1] "rat"

R 

animals[c(3, 2)]

OUTPUT 

#> [1] "dog" "rat"
Callout

Program in other languages?

R indices start at 1. Some other languages (like C++, Java, Perl, and Python) count from 0 because that’s simpler for computers to do.

Conditional subsetting

Another common way of subsetting is by selecting only values where a condition is TRUE. To do so, we use the [] notation with a logical test:

R 

## we can use this to select only the values above 50
weight_g[weight_g > 50]

OUTPUT 

#> [1] 60 65 82 90

You can combine multiple tests using & (both conditions are true, AND) or | (at least one of the conditions is true, OR):

R 

weight_g[weight_g > 30 & weight_g < 50]

OUTPUT 

#> numeric(0)

R 

weight_g[weight_g <= 30 | weight_g == 55]

OUTPUT 

#> [1] 30

R 

weight_g[weight_g >= 30 & weight_g == 21]

OUTPUT 

#> numeric(0)

Here, > for “greater than”, < stands for “less than”, <= for “less than or equal to”, and == for “equal to”. The double equal sign == is a test for numerical equality between the left and right hand sides, and should not be confused with the single = sign, which performs variable assignment (similar to <-).

A common task is to search for certain strings in a vector. One could use the “or” operator | to test for equality to multiple values, but this can quickly become tedious. The function %in% allows you to test if any of the elements of a search vector are found:

R 

animals <- c("mouse", "rat", "dog", "cat", "cat")

# use the logical vector created by %in% to return elements from animals
# that are found in the character vector
animals[animals %in% c("rat", "cat", "dog")]

OUTPUT 

#> [1] "rat" "dog" "cat" "cat"

Missing data

As R was designed to analyze datasets, it includes the concept of missing data (which is uncommon in other programming languages). Missing data are represented in vectors as NA.

When doing operations on numbers, most functions will return NA if the data you are working with include missing values. This feature makes it harder to overlook the cases where you are dealing with missing data. You can add the argument na.rm = TRUE to calculate the result as if the missing values were removed (rm stands for ReMoved) first.

R 

heights <- c(2, 4, 4, NA, 6)
mean(heights)
max(heights)
mean(heights, na.rm = TRUE)
max(heights, na.rm = TRUE)

If your data include missing values, you may want to become familiar with the functions is.na(), na.omit(), and complete.cases(). See below for examples.

R 

## Extract those elements which are not missing values.
heights[!is.na(heights)]

## Returns the object with incomplete cases removed.
#The returned object is an atomic vector of type `"numeric"` (or #`"double"`).
na.omit(heights)

## Extract those elements which are complete cases.
#The returned object is an atomic vector of type `"numeric"` (or #`"double"`).
heights[complete.cases(heights)]

Recall that you can use the typeof() function to find the type of your atomic vector.

Challenge

Challenge

  1. Using this vector of heights in inches, create a new vector, heights_no_na, with the NAs removed.

R 

heights <- c(63, 69, 60, 65, NA, 68, 61, 70, 61, 59, 64, 69, 63, 63, NA, 72, 65, 64, 70, 63, 65)

  1. Use the function median() to calculate the median of the heights vector.

  2. Use R to figure out how many people in the set are taller than 67 inches.

R 

heights <- c(63, 69, 60, 65, NA, 68, 61, 70, 61, 59, 64, 69, 63, 63, NA, 72, 65, 64, 70, 63, 65)

# 1.
heights_no_na <- heights[!is.na(heights)]
# or
heights_no_na <- na.omit(heights)
# or
heights_no_na <- heights[complete.cases(heights)]

# 2.
median(heights, na.rm = TRUE)

# 3.
heights_above_67 <- heights_no_na[heights_no_na > 67]
length(heights_above_67)

Now that we have learned how to write scripts, and the basics of R’s data structures, we are ready to start working with a real dataset and learn about data frames.

Content from Working with data in the tidyverse

Last updated on 2025-10-02 | Edit this page

Overview

Questions

  • How do you work with tabular data in R
  • Why use the tidyverse to wrangle data?

Objectives

  • Load external data from a .csv file into a data frame.
  • Install and load packages.
  • Describe what a data frame is.
  • Summarize the contents of a data frame.
  • Wrangle data with dplyr.
  • Export a data frame to a .csv file.

Loading the survey data

We are investigating the animal species diversity and weights found within plots at our study site. The dataset is stored as a comma separated value (CSV) file. Each row holds information for a single animal, and the columns represent:

Column Description
record_id Unique id for the observation
month month of observation
day day of observation
year year of observation
plot_id ID of a particular experimental plot of land
species_id 2-letter code
sex sex of animal (“M”, “F”)
hindfoot_length length of the hindfoot in mm
weight weight of the animal in grams
genus genus of animal
species species of animal
taxon e.g. Rodent, Reptile, Bird, Rabbit
plot_type type of plot

Downloading the data

We created the folder that will store the downloaded data (data_raw) in the chapter “Before we start”. If you skipped that part, it may be a good idea to have a look now, to make sure your working directory is set up properly.

We are going to use the R function download.file() to download the CSV file that contains the survey data from Figshare, and we will use read_csv() to load the content of the CSV file into R.

Inside the download.file command, the first entry is a character string with the source URL (“https://ndownloader.figshare.com/files/2292169”). This source URL downloads a CSV file from figshare. The text after the comma (“data_raw/portal_data_joined.csv”) is the destination of the file on your local machine. You’ll need to have a folder on your machine called “data_raw” where you’ll download the file. So this command downloads a file from Figshare, names it “portal_data_joined.csv” and adds it to a preexisting folder named “data_raw”.

R 

download.file(url = "https://ndownloader.figshare.com/files/2292169",
              destfile = "data_raw/portal_data_joined.csv")

Reading the data into R

The file has now been downloaded to the destination you specified, but R has not yet loaded the data from the file into memory. To do this, we can use the read_csv() function from the `readr`` package.

Packages in R are basically sets of additional functions that let you do more stuff. The functions we’ve been using so far, like round(), sqrt(), or c() come built into R. Packages give you access to additional functions beyond base R. A similar function to read_csv() from the tidyverse package is read.csv() from base R. We don’t have time to cover their differences but notice that the exact spelling determines which function is used. Before you use a package for the first time you need to install it on your machine, and then you should import it in every subsequent R session when you need it.

The tidyverse package contains readr and other packages we’ll use. To install it, we can type install.packages("tidyverse") straight into the console. In fact, it’s better to write this in the console than in our script for any package, as there’s no need to re-install packages every time we run the script. Then, to load the package type:

R 

## load the tidyverse packages, incl. dplyr
library(tidyverse)

Now we can use the functions from any tidyverse package. Let’s use read_csv() to read the data into a data frame (we will learn more about data frames later):

R 

surveys <- read_csv("data_raw/portal_data_joined.csv")

OUTPUT 

#> Rows: 34786 Columns: 13
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (6): species_id, sex, genus, species, taxa, plot_type
#> dbl (7): record_id, month, day, year, plot_id, hindfoot_length, weight
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

When you execute read_csv on a data file, it looks through the first 1000 rows of each column and guesses its data type. For example, in this dataset, read_csv() reads weight as col_double (a numeric data type), and species as col_character. You have the option to specify the data type for a column manually by using the col_types argument in read_csv.

Callout

Note

read_csv() is actually a special case of read_delim() that assumes fields are delineated by commas. Check out the help by typing ?read_csv to learn more.

You may sometimes see a similar function called read.csv() with a dot instead of an underscore. This is an older function that doesn’t require tidyverse with different arguments and slightly different output.

We can see the contents of the first few lines of the data by typing its name: surveys. By default, this will show you as many rows and columns of the data as fit on your screen. If you wanted the first 50 rows, you could type print(surveys, n = 50)

We can also extract the first few lines of this data using the function head():

R 

head(surveys)

OUTPUT 

#> # A tibble: 6 × 13
#>   record_id month   day  year plot_id species_id sex   hindfoot_length weight
#>       <dbl> <dbl> <dbl> <dbl>   <dbl> <chr>      <chr>           <dbl>  <dbl>
#> 1         1     7    16  1977       2 NL         M                  32     NA
#> 2        72     8    19  1977       2 NL         M                  31     NA
#> 3       224     9    13  1977       2 NL         <NA>               NA     NA
#> 4       266    10    16  1977       2 NL         <NA>               NA     NA
#> 5       349    11    12  1977       2 NL         <NA>               NA     NA
#> 6       363    11    12  1977       2 NL         <NA>               NA     NA
#> # ℹ 4 more variables: genus <chr>, species <chr>, taxa <chr>, plot_type <chr>

Unlike the print() function, head() returns the extracted data. You could use it to assign the first 100 rows of surveys to an object using surveys_sample <- head(surveys, 100). This can be useful if you want to try out complex computations on a subset of your data before you apply them to the whole data set. There is a similar function that lets you extract the last few lines of the data set. It is called (you might have guessed it) tail().

To open the dataset in RStudio’s Data Viewer, use the view() function:

R 

view(surveys)
Callout

Note

There are two functions for viewing which are case-sensitive. Using view() with a lowercase ‘v’ is part of tidyverse, whereas using View() with an uppercase ‘V’ is loaded through base R in the utils package.

What are data frames?

When we loaded the data into R, it got stored as an object of class tibble, which is a special kind of data frame (the difference is not important for our purposes, but you can learn more about tibbles here). Data frames are the de facto data structure for most tabular data, and what we use for statistics and plotting. Data frames can be created by hand, but most commonly they are generated by functions like read_csv(); in other words, when importing spreadsheets from your hard drive or the web.

A data frame is the representation of data in the format of a table where the columns are vectors that all have the same length. Because columns are vectors, each column must contain a single type of data (e.g., characters, integers, factors). For example, here is a figure depicting a data frame comprising a numeric, a character, and a logical vector.

We can see this also when inspecting the structure of a data frame with the function str():

R 

str(surveys)

Inspecting data frames

We already saw how the functions head() and str() can be useful to check the content and the structure of a data frame. Here is a non-exhaustive list of functions to get a sense of the content/structure of the data. Let’s try them out!

  • Size:

    • dim(surveys) - returns a vector with the number of rows in the first element, and the number of columns as the second element (the dimensions of the object)
    • nrow(surveys) - returns the number of rows
    • ncol(surveys) - returns the number of columns

  • Content:

    • head(surveys) - shows the first 6 rows
    • tail(surveys) - shows the last 6 rows
    • glimpse(surveys) - turns a data frame on its side to focus on the columns. Similar to str() but with nicer printing.

  • Names:

    • names(surveys) - returns the column names (synonym of colnames() for data.frame objects)
    • rownames(surveys) - returns the row names

  • Summary:

    • str(surveys) - structure of the object and information about the class, length and content of each column
    • summary(surveys) - summary statistics for each column

Note: most of these functions are “generic”; they can be used on other types of objects besides data.frame.

Callout

tidyverse vs. base R The tidyverse package is an “umbrella-package” that installs dplyr and several other useful packages for data analysis, such as ggplot2, tibble, etc.

As we begin to delve more deeply into the tidyverse, we should briefly pause to mention some of the reasons for focusing on the tidyverse set of tools. In R, there are often many ways to get a job done, and there are other approaches that can accomplish tasks similar to the tidyverse.

The phrase base R is used to refer to approaches that utilize functions contained in R’s default packages. We have already used some base R functions, such as str(), head(), and mean(), and we will be using more scattered throughout this lesson. However, there are some key base R approaches we will not be teaching. These include square bracket subsetting and base plotting. You may come across code written by other people that looks like surveys[1:10, 2] or plot(surveys$weight, surveys$hindfoot_length), which are base R commands. If you’re interested in learning more about these approaches, you can check out other Carpentries lessons like the Software Carpentry Programming with R lesson.

We choose to teach the tidyverse set of packages because they share a similar syntax and philosophy, making them consistent and producing highly readable code. They are also very flexible and powerful, with a growing number of packages designed according to similar principles and to work well with the rest of the packages. The tidyverse packages tend to have very clear documentation and wide array of learning materials that tend to be written with novice users in mind. Finally, the tidyverse has only continued to grow, and has strong support from RStudio, which implies that these approaches will be relevant into the future.

Data wrangling with dplyr

Next, we’re going to learn some of the most common dplyr functions:

  • select(): subset columns
  • filter(): subset rows on conditions
  • mutate(): create new columns by using information from other columns
  • group_by() and summarize(): create summary statistics on grouped data
  • arrange(): sort results
  • count(): count discrete values

Selecting columns and filtering rows

To select columns of a data frame, use select(). The first argument to this function is the data frame (surveys), and the subsequent arguments are the columns to keep.

R 

select(surveys, plot_id, species_id, weight)

To select all columns except certain ones, put a “-” in front of the variable to exclude it.

R 

select(surveys, -record_id, -species_id)

This will select all the variables in surveys except record_id and species_id.

To choose rows based on a specific criterion, use filter():

R 

filter(surveys, year == 1995)

Pipes

What if you want to select and filter at the same time? There are three ways to do this: use intermediate steps, nested functions, or pipes.

With intermediate steps, you create a temporary data frame and use that as input to the next function, like this:

R 

surveys2 <- filter(surveys, weight < 5)
surveys_sml <- select(surveys2, species_id, sex, weight)

This is readable, but can clutter up your workspace with lots of objects that you have to name individually. With multiple steps, that can be hard to keep track of.

You can also nest functions (i.e. one function inside of another), like this:

R 

surveys_sml <- select(filter(surveys, weight < 5), species_id, sex, weight)

This is handy, but can be difficult to read if too many functions are nested, as R evaluates the expression from the inside out (in this case, filtering, then selecting).

The last option, pipes, are a recent addition to R. Pipes let you take the output of one function and send it directly to the next, which is useful when you need to do many things to the same dataset. There are two Pipes in R: 1) %>% (called magrittr pipe; made available via the magrittr package, installed automatically with dplyr) or 2) |> (called native R pipe and it comes preinstalled with R v4.1.0 onwards). Both the pipes are, by and large, function similarly with a few differences (For more information, check: https://www.tidyverse.org/blog/2023/04/base-vs-magrittr-pipe/). The choice of which pipe to be used can be changed in the Global settings in R studio and once that is done, you can type the pipe with:

  • Ctrl + Shift + M if you have a PC or Cmd + Shift + M if you have a Mac.

R 

surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

In the above code, we use the pipe to send the surveys dataset first through filter() to keep rows where weight is less than 5, then through select() to keep only the species_id, sex, and weight columns. Since %>% takes the object on its left and passes it as the first argument to the function on its right, we don’t need to explicitly include the data frame as an argument to the filter() and select() functions any more.

Some may find it helpful to read the pipe like the word “then.” For instance, in the example above, we took the data frame surveys, then we filtered for rows with weight < 5, then we selected columns species_id, sex, and weight. The dplyr functions by themselves are somewhat simple, but by combining them into linear workflows with the pipe we can accomplish more complex manipulations of data frames.

If we want to create a new object with this smaller version of the data, we can assign it a new name:

R 

surveys_sml <- surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

surveys_sml

Note that the final data frame is the leftmost part of this expression.

Challenge

Challenge

Using pipes, subset the surveys data to include animals collected before 1995 and retain only the columns year, sex, and weight.

R 

surveys %>%
    filter(year < 1995) %>%
    select(year, sex, weight)

Mutate

Frequently you’ll want to create new columns based on the values in existing columns, for example to do unit conversions, or to find the ratio of values in two columns. For this we’ll use mutate().

To create a new column of weight in kg:

R 

surveys %>%
  mutate(weight_kg = weight / 1000)

You can also create a second new column based on the first new column within the same call of mutate():

R 

surveys %>%
  mutate(weight_kg = weight / 1000,
         weight_lb = weight_kg * 2.2)

If this runs off your screen and you just want to see the first few rows, you can use a pipe to view the head() of the data. (Pipes work with non-dplyr functions, too, as long as the dplyr or magrittr package is loaded).

R 

surveys %>%
  mutate(weight_kg = weight / 1000)

The first few rows of the output are full of NAs, so if we wanted to remove those we could insert a filter() in the chain:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  mutate(weight_kg = weight / 1000)

is.na() is a function that determines whether something is an NA. The ! symbol negates the result, so we’re asking for every row where weight is not an NA.

Challenge

Challenge

Create a new data frame from the surveys data that meets the following criteria: contains only the species_id column and a new column called hindfoot_cm containing the hindfoot_length values (currently in mm) converted to centimeters. In this hindfoot_cm column, there are no NAs and all values are less than 3.

Hint: think about how the commands should be ordered to produce this data frame!

R 

surveys_hindfoot_cm <- surveys %>%
    filter(!is.na(hindfoot_length)) %>%
    mutate(hindfoot_cm = hindfoot_length / 10) %>%
    filter(hindfoot_cm < 3) %>%
    select(species_id, hindfoot_cm)

Split-apply-combine data analysis and the summarize() function

Many data analysis tasks can be approached using the split-apply-combine paradigm: split the data into groups, apply some analysis to each group, and then combine the results. Key functions of dplyr for this workflow are group_by() and summarize().

The group_by() and summarize() functions

group_by() is often used together with summarize(), which collapses each group into a single-row summary of that group. group_by() takes as arguments the column names that contain the categorical variables for which you want to calculate the summary statistics. So to compute the mean weight by sex:

R 

surveys %>%
  group_by(sex) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE))

You may also have noticed that the output from these calls doesn’t run off the screen anymore. It’s one of the advantages of tbl_df over data frame.

You can also group by multiple columns:

R 

surveys %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE))

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Here, we used tail() to look at the last six rows of our summary. Before, we had used head() to look at the first six rows. We can see that the sex column contains NA values because some animals had escaped before their sex and body weights could be determined. The resulting mean_weight column does not contain NA but NaN (which refers to “Not a Number”) because mean() was called on a vector of NA values while at the same time setting na.rm = TRUE. To avoid this, we can remove the missing values for weight before we attempt to calculate the summary statistics on weight. Because the missing values are removed first, we can omit na.rm = TRUE when computing the mean:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight))

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Here, again, the output from these calls doesn’t run off the screen anymore. If you want to display more data, you can use the print() function at the end of your chain with the argument n specifying the number of rows to display:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight))

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Once the data are grouped, you can also summarize multiple variables at the same time (and not necessarily on the same variable). For instance, we could add a column indicating the minimum weight for each species for each sex:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight))

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

It is sometimes useful to rearrange the result of a query to inspect the values. For instance, we can sort on min_weight to put the lighter species first:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight)) %>%
  arrange(min_weight)

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

To sort in descending order, we need to add the desc() function. If we want to sort the results by decreasing order of mean weight:

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight)) %>%
  arrange(desc(mean_weight))

OUTPUT 

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Counting

When working with data, we often want to know the number of observations found for each factor or combination of factors. For this task, dplyr provides count(). For example, if we wanted to count the number of rows of data for each sex, we would do:

R 

surveys %>%
  count(sex)

The count() function is shorthand for something we’ve already seen: grouping by a variable, and summarizing it by counting the number of observations in that group. In other words, surveys %>% count() is equivalent to:

R 

surveys %>%
  group_by(sex) %>%
  summarize(count = n())

For convenience, count() provides the sort argument:

R 

surveys %>%
  count(sex, sort = TRUE)

Previous example shows the use of count() to count the number of rows/observations for one factor (i.e., sex). If we wanted to count combination of factors, such as sex and species, we would specify the first and the second factor as the arguments of count():

R 

surveys %>%
  count(sex, species)

With the above code, we can proceed with arrange() to sort the table according to a number of criteria so that we have a better comparison. For instance, we might want to arrange the table above in (i) an alphabetical order of the levels of the species and (ii) in descending order of the count:

R 

surveys %>%
  count(sex, species) %>%
  arrange(species, desc(n))

From the table above, we may learn that, for instance, there are 75 observations of the albigula species that are not specified for its sex (i.e. NA).

Challenge

Challenge

  1. How many animals were caught in each plot_type surveyed?

R 

surveys %>%
  count(plot_type)
Challenge

Challenge (continued)

  1. Use group_by() and summarize() to find the mean, min, and max hindfoot length for each species (using species_id). Also add the number of observations (hint: see ?n).

R 

surveys %>%
  filter(!is.na(hindfoot_length)) %>%
  group_by(species_id) %>%
  summarize(
      mean_hindfoot_length = mean(hindfoot_length),
      min_hindfoot_length = min(hindfoot_length),
      max_hindfoot_length = max(hindfoot_length),
      n = n()
    )
Challenge

Challenge (continued)

  1. What was the heaviest animal measured in each year? Return the columns year, genus, species_id, and weight.

R 

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(year) %>%
  filter(weight == max(weight)) %>%
  select(year, genus, species, weight) %>%
  arrange(year)

Exporting data

Now that you have learned how to use dplyr to extract information from or summarize your raw data, you may want to export these new data sets to share them with your collaborators or for archival.

Similar to the read_csv() function used for reading CSV files into R, there is a write_csv() function that generates CSV files from data frames.

Before using write_csv(), we are going to create a new folder, data, in our working directory that will store this generated dataset. We don’t want to write generated datasets in the same directory as our raw data. It’s good practice to keep them separate. The data_raw folder should only contain the raw, unaltered data, and should be left alone to make sure we don’t delete or modify it. In contrast, our script will generate the contents of the data directory, so even if the files it contains are deleted, we can always re-generate them.

In preparation for our next lesson on plotting, we are going to prepare a cleaned up version of the data set that doesn’t include any missing data.

Let’s start by removing observations of animals for which weight and hindfoot_length are missing, or the sex has not been determined:

R 

surveys_complete <- surveys %>%
  filter(!is.na(weight),           # remove missing weight
         !is.na(hindfoot_length),  # remove missing hindfoot_length
         !is.na(sex))                # remove missing sex

Because we are interested in plotting how species abundances have changed through time, we are also going to remove observations for rare species (i.e., that have been observed less than 50 times). We will do this in two steps: first we are going to create a data set that counts how often each species has been observed, and filter out the rare species; then, we will extract only the observations for these more common species:

R 

## Extract the most common species_id
species_counts <- surveys_complete %>%
    count(species_id) %>%
    filter(n >= 50)

## Only keep the most common species
surveys_complete <- surveys_complete %>%
  filter(species_id %in% species_counts$species_id)

To make sure that everyone has the same data set, check that surveys_complete has 30463 rows and 13 columns by typing dim(surveys_complete).

Now that our data set is ready, we can save it as a CSV file in our data folder.

R 

write_csv(surveys_complete, file = "data/surveys_complete.csv")

Content from Data visualization with ggplot2

Last updated on 2025-10-03 | Edit this page

Overview

Questions

  • How do you make plots using R?
  • How do you customize and modify plots?

Objectives

  • Produce scatter plots and boxplots using ggplot2.
  • Represent data variables with plot components.
  • Modify the scales of plot components.
  • Iteratively build and modify ggplot2 plots by adding layers.
  • Change the appearance of existing ggplot2 plots using premade and customized themes.
  • Describe what faceting is and apply faceting in ggplot2.
  • Save plots as image files.

We start by loading the required packages. ggplot2 is included in the tidyverse package.

R 

library(tidyverse)

If not still in the workspace, load the data we saved in the previous lesson.

R 

surveys_complete <- read_csv("data/surveys_complete.csv")

Plotting with ggplot2

ggplot2 is a plotting package that provides helpful commands to create complex plots from data in a data frame. It provides a more programmatic interface for specifying what variables to plot, how they are displayed, and general visual properties. Therefore, we only need minimal changes if the underlying data change or if we decide to change from a bar plot to a scatterplot. This helps in creating publication quality plots with minimal amounts of adjustments and tweaking.

ggplot2 refers to the name of the package itself. When using the package we use the function ggplot() to generate the plots, and so references to using the function will be referred to as ggplot() and the package as a whole as ggplot2

ggplot graphics are built layer by layer by adding new elements. Adding layers in this fashion allows for extensive flexibility and customization of plots.

To build a ggplot, we will use the following basic template that can be used for different types of plots:

ggplot(data = <DATA>, mapping = aes(<MAPPINGS>)) +  <GEOM_FUNCTION>()

1: use the ggplot() function and bind the plot to a specific data frame using the data argument.

R 

ggplot(data = surveys_complete)

2: define an aesthetic mapping (using the aesthetic (aes) function), by selecting the variables to be plotted and specifying how to present them in the graph, e.g., as x/y positions or characteristics such as size, shape, color, etc.

R 

ggplot(data = surveys_complete, mapping = aes(x = weight, y = hindfoot_length))

3: add ‘geoms’ – graphical representations of the data in the plot (points, lines, bars). ggplot2 offers many different geoms; we will use some common ones today, including:

  • geom_point() for scatter plots, dot plots, etc.
  • geom_boxplot() for, well, boxplots!
  • geom_line() for trend lines, time series, etc.

To add a geom to the plot use + operator. Because we have two continuous variables, let’s use geom_point() first:

R 

ggplot(data = surveys_complete, aes(x = weight, y = hindfoot_length)) +
  geom_point()

The + in the ggplot2 package is particularly useful because it allows you to modify existing ggplot objects. This means you can easily set up plot “templates” and conveniently explore different types of plots, so the above plot can also be generated with code like this:

R 

# Assign plot to a variable
surveys_plot <- ggplot(data = surveys_complete,
                       mapping = aes(x = weight, y = hindfoot_length))

# Draw the plot
surveys_plot +
  geom_point()

Notes

  • Anything you put in the ggplot() function can be seen by any geom layers that you add (i.e., these are universal plot settings). This includes the x- and y-axis you set up in aes().
  • You can also specify aesthetics for a given geom independently of the aesthetics defined globally in the ggplot() function.
  • The + sign used to add layers must be placed at the end of each line containing a layer. If, instead, the + sign is added in the line before the other layer, ggplot2 will not add the new layer and will return an error message.
  • You may notice that we sometimes reference ‘ggplot2’ and sometimes ‘ggplot’. To clarify, ‘ggplot2’ is the name of the most recent version of the package. However, any time we call the function itself, it’s just called ‘ggplot’.
  • The previous version of the ggplot2 package, called ggplot, which also contained the ggplot() function is now unsupported and has been removed from CRAN in order to reduce accidental installations and further confusion.

R 

# This is the correct syntax for adding layers
surveys_plot +
  geom_point()

# This will not add the new layer and will return an error message
surveys_plot
  + geom_point()
Discussion

Challenge (optional)

Scatter plots can be useful exploratory tools for small datasets. For data sets with large numbers of observations, such as the surveys_complete data set, overplotting of points can be a limitation of scatter plots. One strategy for handling such settings is to use hexagonal binning of observations. The plot space is tessellated into hexagons. Each hexagon is assigned a color based on the number of observations that fall within its boundaries. To use hexagonal binning with ggplot2, first install the R package hexbin from CRAN:

R 

install.packages("hexbin")

Then use the geom_hex() function:

R 

surveys_plot +
 geom_hex()
  • What are the relative strengths and weaknesses of a hexagonal bin plot compared to a scatter plot? Examine the above scatter plot and compare it with the hexagonal bin plot that you created.

Building your plots iteratively

Building plots with ggplot2 is typically an iterative process. We start by defining the dataset we’ll use, lay out the axes, and choose a geom:

R 

ggplot(data = surveys_complete, aes(x = weight, y = hindfoot_length)) +
    geom_point()

Then, we start modifying this plot to extract more information from it. For instance, we can add transparency (alpha) to avoid overplotting:

R 

ggplot(data = surveys_complete, aes(x = weight, y = hindfoot_length)) +
    geom_point(alpha = 0.2)

We can also add colors for all the points:

R 

ggplot(data = surveys_complete, mapping = aes(x = weight, y = hindfoot_length)) +
    geom_point(alpha = 0.2, color = "blue")

Adding another variable

Let’s try coloring our points according to the sampling plot type (plot here refers to the physical area where rodents were sampled and has nothing to do with making graphs). Since we’re now mapping a variable (plot_type) to a component of the ggplot2 plot (color), we need to put the argument inside aes():

R 

ggplot(data = surveys_complete, mapping = aes(x = weight, y = hindfoot_length)) +
    geom_point(alpha = 0.2, aes(color = species_id))
Challenge

Challenge

Use what you just learned to create a scatter plot of weight over species_id with the plot types showing in different colors. Is this a good way to show this type of data?

R 

ggplot(data = surveys_complete,
       mapping = aes(x = species_id, y = weight)) +
   geom_point(aes(color = plot_type))

Changing scales

The default discrete color scale isn’t always ideal: it isn’t friendly to viewers with colorblindness and it doesn’t translate well to grayscale. However, ggplot2 comes with quite a few other color scales, including the fantastic viridis scales, which are designed to be colorblind and grayscale friendly. We can change scales by adding scale_ functions to our plots:

R 

ggplot(data = surveys_complete, mapping = aes(x = weight, y = hindfoot_length, color = plot_type)) +
  geom_point(alpha = 0.2) +
  scale_color_viridis_d()

Scales don’t just apply to colors- any plot component that you put inside aes() can be modified with scale_ functions. Just as we modified the scale used to map plot_type to color, we can modify the way that weight is mapped to the x axis by using the scale_x_log10() function:

R 

ggplot(data = surveys_complete, mapping = aes(x = weight, y = hindfoot_length, color = plot_type)) +
  geom_point(alpha = 0.2) +
  scale_x_log10()

One nice thing about ggplot and the tidyverse in general is that groups of functions that do similar things are given similar names. Any function that modifies a ggplot scale starts with scale_, making it easier to search for the right function.

Boxplot

We can use boxplots to visualize the distribution of weight within each species:

R 

ggplot(data = surveys_complete, mapping = aes(x = plot_type, y = hindfoot_length)) +
  geom_boxplot()

By adding points to the boxplot, we can have a better idea of the number of measurements and of their distribution. Because the boxplot will show the outliers by default these points will be plotted twice – by geom_boxplot and geom_jitter. To avoid this we must specify that no outliers should be added to the boxplot by specifying outlier.shape = NA.

R 

ggplot(data = surveys_complete, mapping = aes(x = plot_type, y = hindfoot_length)) +
  geom_boxplot(outlier.shape = NA) +
  geom_jitter(alpha = 0.3, aes(color = plot_type))

Now our points are colored according to plot_type, but the boxplots are all the same color. One thing you might notice is that even with alpha = 0.2, the points obscure parts of the boxplot. This is because the geom_point() layer comes after the geom_boxplot() layer, which means the points are plotted on top of the boxes. To put the boxplots on top, we switch the order of the layers:

R 

ggplot(data = surveys_complete, mapping = aes(x = plot_type, y = hindfoot_length)) +
  geom_jitter(aes(color = plot_type), alpha = 0.2) +
  geom_boxplot(outlier.shape = NA)

Now we have the opposite problem! The white fill of the boxplots completely obscures some of the points. To address this problem, we can remove the fill from the boxplots altogether, leaving only the black lines. To do this, we set fill to NA:

R 

ggplot(data = surveys_complete, mapping = aes(x = plot_type, y = hindfoot_length)) +
  geom_jitter(aes(color = plot_type), alpha = 0.2) +
  geom_boxplot(outlier.shape = NA, fill = NA)

Now we can see all the raw data and our boxplots on top.

Changing themes

So far we’ve been changing the appearance of parts of our plot related to our data and the geom_ functions, but we can also change many of the non-data components of our plot.

At this point, we are pretty happy with the basic layout of our plot, so we can assign it to a plot to a named object. We do this using the assignment arrow <-. What we are doing here is taking the result of the code on the right side of the arrow, and assigning it to an object whose name is on the left side of the arrow.

We will create an object called myplot. If you run the name of the ggplot2 object, it will show the plot, just like if you ran the code itself.

R 

myplot <- ggplot(data = surveys_complete, mapping = aes(x = plot_type, y = hindfoot_length)) +
  geom_jitter(aes(color = plot_type), alpha = 0.2) +
  geom_boxplot(outlier.shape = NA, fill = NA)

myplot

This process of assigning something to an object is not specific to ggplot2, but rather a general feature of R. We will be using it a lot in the rest of this lesson. We can now work with the myplot object as if it was a block of ggplot2 code, which means we can use + to add new components to it.

We can change the overall appearance using theme_ functions. Let’s try a black-and-white theme by adding theme_bw() to our plot:

R 

myplot + theme_bw()

As you can see, a number of parts of the plot have changed. theme_ functions usually control many aspects of a plot’s appearance all at once, for the sake of convenience. To individually change parts of a plot, we can use the theme() function, which can take many different arguments to change things about the text, grid lines, background color, and more. Let’s try changing the size of the text on our axis titles. We can do this by specifying that the axis.title should be an element_text() with size set to 14.

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14))

Another change we might want to make is to remove the vertical grid lines. Since our x axis is categorical, those grid lines aren’t useful. To do this, inside theme(), we will change the panel.grid.major.x to an element_blank().

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), 
        panel.grid.major.x = element_blank())

Another useful change might be to remove the color legend, since that information is already on our x axis. For this one, we will set legend.position to “none”.

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), 
        panel.grid.major.x = element_blank(), 
        legend.position = "none")
Callout

Because there are so many possible arguments to the theme() function, it can sometimes be hard to find the right one. Here are some tips for figuring out how to modify a plot element:

  • type out theme(), put your cursor between the parentheses, and hit Tab to bring up a list of arguments
    • you can scroll through the arguments, or start typing, which will shorten the list of potential matches
  • like many things in the tidyverse, similar argument start with similar names
    • there are axis, legend, panel, plot, and strip arguments
  • arguments have hierarchy
    • text controls all text in the whole plot
    • axis.title controls the text for the axis titles
    • axis.title.x controls the text for the x axis title
Callout

You may have noticed that we have used 3 different approaches to getting rid of something in ggplot:

  • outlier.shape = NA to remove the outliers from our boxplot
  • panel.grid.major.x = element_blank() to remove the x grid lines
  • legend.position = "none" to remove our legend

Why are there so many ways to do what seems like the same thing?? This is a common frustration when working with R, or with any programming language. There are a couple reasons for it:

  1. Different people contribute to different packages and functions, and they may choose to do things differently.
  2. Code may appear to be doing the same thing, when the details are actually quite different. The inner workings of ggplot2 are actually quite complex, since it turns out making plots is a very complicated process! Because of this, things that seem the same (removing parts of a plot), may actually be operating on very different components or stages of the final plot.
  3. Developing packages is a highly iterative process, and sometimes things change. However, changing too much stuff can make old code break. Let’s say removing the legend was introduced as a feature of ggplot2, and then a lot of time passed before someone added the feature letting you remove outliers from geom_boxplot(). Changing the way you remove the legend, so that it’s the same as the boxplot approach, could break all of the code written in the meantime, so developers may opt to keep the old approach in place.

Changing labels

Our plot is really shaping up now. However, we probably want to make our axis titles nicer, and perhaps add a main title to the plot. We can do this using the labs() function:

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), 
        legend.position = "none") +
  labs(title = "Rodent size by plot type",
       x = "Plot type",
       y = "Hindfoot length (mm)")

We removed our legend from this plot, but you can also change the titles of various legends using labs(). For example, labs(color = "Plot type") would change the title of a color scale legend to “Plot type”.

Challenge

Challenge 3: Customizing a plot

Modify the previous plot by adding a descriptive subtitle. Increase the font size of the plot title and make it bold.

Hint: “bold” is referred to as a font “face”

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), legend.position = "none",
        plot.title = element_text(face = "bold", size = 20)) +
  labs(title = "Rodent size by plot type",
       subtitle = "Long-term dataset from Portal, AZ",
       x = "Plot type",
       y = "Hindfoot length (mm)")

Faceting

One of the most powerful features of ggplot is the ability to quickly split a plot into multiple smaller plots based on a categorical variable, which is called faceting.

So far we’ve mapped variables to the x axis, the y axis, and color, but trying to add a 4th variable becomes difficult. Changing the shape of a point might work, but only for very few categories, and even then, it can be hard to tell the differences between the shapes of small points.

Instead of cramming one more variable into a single plot, we will use the facet_wrap() function to generate a series of smaller plots, split out by sex. We also use ncol to specify that we want them arranged in a single column:

R 

myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), 
        legend.position = "none", 
        panel.grid.major.x = element_blank()) +
  labs(title = "Rodent size by plot type",
       x = "Plot type",
       y = "Hindfoot length (mm)",
       color = "Plot type") +
  facet_wrap(vars(sex), ncol = 1)
Callout

Faceting comes in handy in many scenarios. It can be useful when:

  • a categorical variable has too many levels to differentiate by color (such as a dataset with 20 countries)
  • your data overlap heavily, obscuring categories
  • you want to show more than 3 variables at once
  • you want to see each category in isolation while allowing for general comparisons between categories

Exporting plots

Once we are happy with our final plot, we can assign the whole thing to a new object, which we can call finalplot.

R 

finalplot <- myplot +
  theme_bw() +
  theme(axis.title = element_text(size = 14), 
        legend.position = "none", 
        panel.grid.major.x = element_blank()) +
  labs(title = "Rodent size by plot type",
       x = "Plot type",
       y = "Hindfoot length (mm)",
       color = "Plot type") +
  facet_wrap(vars(sex), ncol = 1)

After this, we can run ggsave() to save our plot. The first argument we give is the path to the file we want to save, including the correct file extension. This code will make an image called rodent_size_plots.jpg in the fig/ folder of our current project. We are making a .png, but you can save .pdf, .tiff, and other file formats. Next, we tell it the name of the plot object we want to save. We can also specify things like the width and height of the plot in inches.

R 

ggsave(filename = "fig/rodent_size_plots.png", plot = finalplot,
       height = 6, width = 8)
Discussion

Challenge 4: Make your own plot

Try making your own plot! You can run glimpse(surveys_complete) to explore variables you might use in your new plot. Feel free to use variables we have already seen, or some we haven’t explored yet.

Here are a couple ideas to get you started:

  • make a histogram of one of the numeric variables
  • try using a different color scale_
  • try changing the size of points or thickness of lines in a geom
Key Points
  • the ggplot() function initiates a plot, and geom_ functions add representations of your data
  • use aes() when mapping a variable from the data to a part of the plot
  • use scale_ functions to modify the scales used to represent variables
  • use premade theme_ functions to broadly change appearance, and the theme() function to fine-tune
  • start simple and build your plots iteratively