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Before we start
15
knitr::opts_chunk$set(results='hide', fig.path='img/r-lesson-')

Learning Objectives

  • Articulating motivations for this lesson
  • Introduce participants to the RStudio interface
  • Set up participants to have a working directory with a data/ folder inside
  • Introduce R syntax
  • Point to relevant information on how to get help, and understand how to ask well formulated questions

Demonstration of what we will learn to do

Before we get started

  • Start RStudio (presentation of RStudio -below- should happen here)
  • Under the File menu, click on New project, choose New directory, then Empty project
  • Enter a name for this new folder, and choose a convenient location for it. This will be your working directory for the rest of the day (e.g., ~/data-carpentry)
  • Click on "Create project"
  • Under the Files tab on the right of the screen, click on New Folder and create a folder named data within your newly created working directory. (e.g., ~/data-carpentry/data)
  • Create a new R script (File > New File > R script) and save it in your working directory (e.g. data-carpentry-script.R)

Your working directory should now look like this:

How it should look like at the beginning of this lesson

Presentation of RStudio

Let's start by learning about our tool.

  • Console, Scripts, Environments, Plots
  • Code and workflow are more reproducible if we can document everything that we do.
  • Our end goal is not just to "do stuff" but to do it in a way that anyone can easily and exactly replicate our workflow and results.

Interacting with R

There are two main ways of interacting with R: using the console or by using script files (plain text files that contain your code).

The console window (in RStudio, the bottom left panel) is the place where R is waiting for you to tell it what to do, and where it will show the results of a command. You can type commands directly into the console, but they will be forgotten when you close the session. It is better to enter the commands in the script editor, and save the script. This way, you have a complete record of what you did, you can easily show others how you did it and you can do it again later on if needed. You can copy-paste into the R console, but the Rstudio script editor allows you to 'send' the current line or the currently selected text to the R console using the Ctrl-Enter shortcut.

At some point in your analysis you may want to check the content of variable or the structure of an object, without necessarily keep a record of it in your script. You can type these commands directly in the console. RStudio provides the Ctrl-1 and Ctrl-2 shortcuts allow you to jump between the script and the console windows.

If R is ready to accept commands, the R console shows a > prompt. If it receives a command (by typing, copy-pasting or sent from the script editor using Ctrl-Enter), R will try to execute it, and when ready, show the results and come back with a new >-prompt to wait for new commands.

If R is still waiting for you to enter more data because it isn't complete yet, the console will show a + prompt. It means that you haven't finished entering a complete command. This is because you have not 'closed' a parenthesis or quotation. If you're in Rstudio and this happens, click inside the console window and press Esc; this should help you out of trouble.

Basics of R

R is a versatile, open source programming/scripting language that's useful both for statistics but also data science. Inspired by the programming language S.

  • Open source software under GPL.
  • Superior (if not just comparable) to commercial alternatives. R has over 7,000 user contributed packages at this time. It's widely used both in academia and industry.
  • Available on all platforms.
  • Not just for statistics, but also general purpose programming.
  • For people who have experience in programmming: R is both an object-oriented and a so-called functional language
  • Large and growing community of peers.

Commenting

Use # signs to comment. Comment liberally in your R scripts. Anything to the right of a # is ignored by R.

Assignment operator

<- 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. The arrow can be read as 3 goes into x. You can also use = for assignments but not in all contexts so it is good practice to use <- for assignments. = should only be used to specify the values of arguments in functions, see below.

In RStudio, typing Alt + - (push Alt, the key next to your space bar at the same time as the - key) will write <- in a single keystroke.

Functions and their arguments

Functions are "canned scripts" that automate something complicated or convenient or both. Many functions are predefined, or become available when using the function library() (more on that later). A function usually gets one or more inputs called arguments. Functions often (but not always) return a value. A typical example would be the function sqrt(). The input (the argument) must be a number, and the return value (in fact, the output) is the square root of that number. Executing a function ('running it') is called calling the function. An example of a function call is:

b <- sqrt(a)

Here, the value of a is given to the sqrt() function, the sqrt() function calculates the square root, and returns the value which is then assigned to variable b. This function is very simple, because it takes just one argument. It is useful to specify the arguments by their name, especially if the function can takes several arguments. An example (using just one argument) is shown here:

surveys <- read.csv(file="data/surveys.csv")

The return 'value' of a function need not be numerical (like that of sqrt()), and it also does not need to be a single item: it can be a set of things, or even a data set, like read.csv() does. More on this later.

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). If an argument alters the way the function operates, such as whether to ignore 'bad values', such an argument is sometimes called an option.

Most functions can take several arguments, but many have so-called defaults. If you don't specify such an argument when calling the function, the function itself will fall back on using the default. This is a standard value that the author of the function specified as being "good enough in standard cases". An example would be what symbol to use in a plot. However, if you want something specific, simply change the argument yourself with a value of your choice.

To see these default values, you can either type args(read.csv) or look at the help for this function (e.g., ?read.csv).

args(read.csv)

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

read.csv(file="data/surveys.csv", header=TRUE) # is identical to:
read.csv("data/surveys.csv", TRUE)

However, it's usually not recommended practice because it's a lot of remembering to do, and if you share your code with others that includes less known functions it makes your code difficult to read. (It's however OK to not include the names of the arguments for basic functions like mean, min, etc...)

Another advantage of naming arguments, is that the order doesn't matter:

read.csv(file="data/surveys.csv", header=TRUE) # is identical to:
read.csv(header=TRUE, file="data/surveys.csv")

Organizing your working directory

You should separate the original data (raw data) from intermediate datasets that you may create for the need of a particular analysis. For instance, you may want to create a data/ directory within your working directory that stores the raw data, and have a data_output/ directory for intermediate datasets and a figure_output/ directory for the plots you will generate.

Seeking help

I know the name of the function I want to use, but I'm not sure how to use it

If you need help with a specific function, let's say barplot(), you can type:

?barplot

If you just need to remind yourself of the names of the arguments, you can use:

args(lm)

If the function is part of a package that is installed on your computer but don't remember which one, you can type:

??geom_point

I want to use a function that does X, there must be a function or it but I don't know which one...

If you are looking for a function to do a particular task, you can use help.search() (but only looks through the installed packages):

help.search("kruskal")

If you can't find what you are looking for, you can use the rdocumention.org website that search through the help files across all packages available.

I am stuck... I get an error message that I don't understand

Start by googling the error message. However, this doesn't always work very well because often, package developers rely on the error catching provided by R. You end up with general error messages that might not be very helpful to diagnose a problem (e.g. "subscript out of bounds").

However, you should check stackoverflow. Search using the [r] tag. Most questions have already been answered, but the challenge is to use the right words in the search to find the answers: http://stackoverflow.com/questions/tagged/r

The Introduction to R can also be dense for people with little programming experience but it is a good place to understand the underpinnings of the R language.

The R FAQ is dense and technical but it is full of useful information.

Asking for help

The key to get help from someone is for them to grasp your problem rapidly. You should make it as easy as possible to pinpoint where the issue might be.

Try to use the correct words to describe your problem. For instance, a package is not the same thing as a library. Most people will understand what you meant, but others have really strong feelings about the difference in meaning. The key point is that it can make things confusing for people trying to help you. Be as precise as possible when describing your problem

If possible, try to reduce what doesn't work to a simple reproducible example. If you can reproduce the problem using a very small data.frame instead of your 50,000 rows and 10,000 columns one, provide the small one with the description of your problem. When appropriate, try to generalize what you are doing so even people who are not in your field can understand the question.

To share an object with someone else, if it's relatively small, you can use the function dput(). It will output R code that can be used to recreate the exact same object as the one in memory:

dput(head(iris)) # iris is an example data.frame that comes with R

If the object is larger, provide either the raw file (i.e., your CSV file) with your script up to the point of the error (and after removing everything that is not relevant to your issue). Alternatively, in particular if your questions is not related to a data.frame, you can save any R object to a file:

saveRDS(iris, file="/tmp/iris.rds")

The content of this file is however not human readable and cannot be posted directly on stackoverflow. It can however be sent to someone by email who can read it with this command:

some_data <- readRDS(file="~/Downloads/iris.rds")

Last, but certainly not least, always include the output of sessionInfo() as it provides critical information about your platform, the versions of R and the packages that you are using, and other information that can be very helpful to understand your problem.

sessionInfo()

Where to ask for help?

  • Your friendly colleagues: if you know someone with more experience than you, they might be able and willing to help you.
  • Stackoverlow: if your question hasn't been answered before and is well crafted, chances are you will get an answer in less than 5 min.
  • The R-help: it is read by a lot of people (including most of the R core team), a lot of people post to it, but the tone can be pretty dry, and it is not always very welcoming to new users. If your question is valid, you are likely to get an answer very fast but don't expect that it will come with smiley faces. Also, here more than everywhere else, be sure to use correct vocabulary (otherwise you might get an answer pointing to the misuse of your words rather than answering your question). You will also have more success if your question is about a base function rather than a specific package.
  • If your question is about a specific package, see if there is a mailing list for it. Usually it's included in the DESCRIPTION file of the package that can be accessed using packageDescription("name-of-package"). You may also want to try to email the author of the package directly.
  • There are also some topic-specific mailing lists (GIS, phylogenetics, etc...), the complete list is here.

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