Introduction to R and RStudio http://htmlpreview.github.io/?https://github.com/andrewpbray/o...

Introduction to R and RStudio

The goal of this lab is to introduce you to R and RStudio, which you’ll be using throughout the course
both to learn the statistical concepts discussed in the texbook and also to analyze real data and come
to informed conclusions. To straighten out which is which: R is the name of the programming language
itself and RStudio is a convenient interface.

As the labs progress, you are encouraged to explore beyond what the labs dictate; a willingness to
experiment will make you a much better programmer. Before we get to that stage, however, you need
to build some basic fluency in R. Today we begin with the fundamental building blocks of R and
RStudio: the interface, reading in data, and basic commands.

The panel in the upper right contains your workspace as well as a history of the commands that you’ve
previously entered. Any plots that you generate will show up in the panel in the lower right corner.

The panel on the left is where the action happens. It’s called the console. Everytime you launch
RStudio, it will have the same text at the top of the console telling you the version of R that you’re
running. Below that information is the prompt. As its name suggests, this prompt is really a request, a
request for a command. Initially, interacting with R is all about typing commands and interpreting the
output. These commands and their syntax have evolved over decades (literally) and now provide what
many users feel is a fairly natural way to access data and organize, describe, and invoke statistical
computations.

To get you started, enter the following command at the R prompt (i.e. right after > on the console).
You can either type it in manually or copy and paste it from this document.

source("http://www.openintro.org/stat/data/arbuthnot.R")

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This command instructs R to access the OpenIntro website and fetch some data: the Arbuthnot
baptism counts for boys and girls. You should see that the workspace area in the upper righthand
corner of the RStudio window now lists a data set called arbuthnot that has 82 observations on 3
variables. As you interact with R, you will create a series of objects. Sometimes you load them as we
have done here, and sometimes you create them yourself as the byproduct of a computation or some
analysis you have performed. Note that because you are accessing data from the web, this command
(and the entire assignment) will work in a computer lab, in the library, or in your dorm room; anywhere
you have access to the Internet.

The Data: Dr. Arbuthnot’s Baptism Records

The Arbuthnot data set refers to Dr. John Arbuthnot, an 18th century physician, writer, and
mathematician. He was interested in the ratio of newborn boys to newborn girls, so he gathered the
baptism records for children born in London for every year from 1629 to 1710. We can take a look at
the data by typing its name into the console.

arbuthnot

What you should see are four columns of numbers, each row representing a different year: the first
entry in each row is simply the row number (an index we can use to access the data from individual
years if we want), the second is the year, and the third and fourth are the numbers of boys and girls
baptized that year, respectively. Use the scrollbar on the right side of the console window to examine
the complete data set.

Note that the row numbers in the first column are not part of Arbuthnot’s data. R adds them as part of
its printout to help you make visual comparisons. You can think of them as the index that you see on
the left side of a spreadsheet. In fact, the comparison to a spreadsheet will generally be helpful. R has
stored Arbuthnot’s data in a kind of spreadsheet or table called a data frame.

You can see the dimensions of this data frame by typing:

dim(arbuthnot)

## [1] 82 3

This command should output [1] 82 3 , indicating that there are 82 rows and 3 columns (we’ll get to
what the [1] means in a bit), just as it says next to the object in your workspace. You can see the
names of these columns (or variables) by typing:

names(arbuthnot)

## [1] "year" "boys" "girls"

You should see that the data frame contains the columns year , boys , and girls . At this point, you
might notice that many of the commands in R look a lot like functions from math class; that is,

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invoking R commands means supplying a function with some number of arguments. The dim and
names commands, for example, each took a single argument, the name of a data frame.

One advantage of RStudio is that it comes with a built-in data viewer. Click on the name arbuthnot
in the Environment pane (upper right window) that lists the objects in your workspace. This will bring
up an alternative display of the data set in the Data Viewer (upper left window). You can close the data
viewer by clicking on the x in the upper lefthand corner.

Some Exploration
Let’s start to examine the data a little more closely. We can access the data in a single column of a
data frame separately using a command like

arbuthnot$boys

This command will only show the number of boys baptized each year.

Exercise 1 What command would you use to extract just the counts of girls
baptized? Try it!

Notice that the way R has printed these data is different. When we looked at the complete data frame,
we saw 82 rows, one on each line of the display. These data are no longer structured in a table with
other variables, so they are displayed one right after another. Objects that print out in this way are
called vectors; they represent a set of numbers. R has added numbers in [brackets] along the left side
of the printout to indicate locations within the vector. For example, 5218 follows [1] , indicating that
5218 is the first entry in the vector. And if [43] starts a line, then that would mean the first number
on that line would represent the 43rd entry in the vector.

R has some powerful functions for making graphics. We can create a simple plot of the number of girls
baptized per year with the command

plot(x = arbuthnot$year, y = arbuthnot$girls)

By default, R creates a scatterplot with each x,y pair indicated by an open circle. The plot itself should
appear under the Plots tab of the lower right panel of RStudio. Notice that the command above again
looks like a function, this time with two arguments separated by a comma. The first argument in the
plot function specifies the variable for the x-axis and the second for the y-axis. If we wanted to
connect the data points with lines, we could add a third argument, the letter l for line.

plot(x = arbuthnot$year, y = arbuthnot$girls, type = "l")

You might wonder how you are supposed to know that it was possible to add that third argument.
Thankfully, R documents all of its functions extensively. To read what a function does and learn the
arguments that are available to you, just type in a question mark followed by the name of the function
that you’re interested in. Try the following.

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?plot

Notice that the help file replaces the plot in the lower right panel. You can toggle between plots and
help files using the tabs at the top of that panel.

Exercise 2 Is there an apparent trend in the number of girls baptized over the
years?
How would you describe it?

Now, suppose we want to plot the total number of baptisms. To compute this, we could use the fact
that R is really just a big calculator. We can type in mathematical expressions like

5218 + 4683

to see the total number of baptisms in 1629. We could repeat this once for each year, but there is a
faster way. If we add the vector for baptisms for boys and girls, R will compute all sums
simultaneously.

arbuthnot$boys + arbuthnot$girls

What you will see are 82 numbers (in that packed display, because we aren’t looking at a data frame
here), each one representing the sum we’re after. Take a look at a few of them and verify that they are
right. Therefore, we can make a plot of the total number of baptisms per year with the command

plot(arbuthnot$year, arbuthnot$boys + arbuthnot$girls, type = "l")

This time, note that we left out the names of the first two arguments. We can do this because the help
file shows that the default for plot is for the first argument to be the x-variable and the second
argument to be the y-variable.

Similarly to how we computed the proportion of boys, we can compute the ratio of the number of boys
to the number of girls baptized in 1629 with

5218 / 4683

or we can act on the complete vectors with the expression

arbuthnot$boys / arbuthnot$girls

The proportion of newborns that are boys

5218 / (5218 + 4683)

or this may also be computed for all years simultaneously:

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arbuthnot$boys / (arbuthnot$boys + arbuthnot$girls)

Note that with R as with your calculator, you need to be conscious of the order of operations. Here, we
want to divide the number of boys by the total number of newborns, so we have to use parentheses.
Without them, R will first do the division, then the addition, giving you something that is not a
proportion.

Exercise 3 Now, make a plot of the proportion of boys over time. What do you see?
Tip: If you use the up and down arrow keys, you can scroll through your
previous commands, your so-called command history. You can also
access it by clicking on the history tab in the upper right panel. This will
save you a lot of typing in the future.

Finally, in addition to simple mathematical operators like subtraction and division, you can ask R to
make comparisons like greater than, > , less than, < , and equality, == . For example, we can ask if
boys outnumber girls in each year with the expression

arbuthnot$boys > arbuthnot$girls

This command returns 82 values of either TRUE if that year had more boys than girls, or FALSE if that
year did not (the answer may surprise you). This output shows a different kind of data than we have
considered so far. In the arbuthnot data frame our values are numerical (the year, the number of
boys and girls). Here, we’ve asked R to create logical data, data where the values are either TRUE or
FALSE . In general, data analysis will involve many different kinds of data types, and one reason for
using R is that it is able to represent and compute with many of them.

This seems like a fair bit for your first lab, so let’s stop here. To exit RStudio you can click the x in the
upper right corner of the whole window.
You will be prompted to save your workspace. If you click save, RStudio will save the history of your
commands and all the objects in your workspace so that the next time you launch RStudio, you will
see arbuthnot and you will have access to the commands you typed in your previous session. For
now, click save, then start up RStudio again.

On Your Own
In the previous few pages, you recreated some of the displays and preliminary analysis of Arbuthnot’s
baptism data. Your assignment involves repeating these steps, but for present day birth records in the
United States. Load up the present day data with the following command.

source("http://www.openintro.org/stat/data/present.R")

The data are stored in a data frame called present .

1. What years are included in this data set? What are the dimensions of the data frame and what
are the variable or column names?

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2. How do these counts compare to Arbuthnot’s? Are they on a similar scale?

3. Make a plot that displays the boy-to-girl ratio for every year in the data set. What do you see?
Does Arbuthnot’s observation about boys being born in greater proportion than girls hold up in
the U.S.? Include the plot in your response.

4. In what year did we see the most total number of births in the U.S.? You can refer to the help
files or the R reference card (http://cran.r-project.org/doc/contrib/Short-refcard.pdf)http://cran.r-
project.org/doc/contrib/Short-refcard.pdf (http://cran.r-project.org/doc/contrib/Short-
refcard.pdf) to find helpful commands.

These data come from a report by the Centers for Disease Control (http://www.cdc.gov/nchs/data
/nvsr/nvsr53/nvsr53_20.pdf)http://www.cdc.gov/nchs/data/nvsr/nvsr53/nvsr53_20.pdf
(http://www.cdc.gov/nchs/data/nvsr/nvsr53/nvsr53_20.pdf). Check it out if you would like to read more
about an analysis of sex ratios at birth in the United States.

That was a short introduction to R and RStudio, but we will provide you with more functions and a
more complete sense of the language as the course progresses. Feel free to browse around the
websites for R (http://www.r-project.org) and RStudio (http://rstudio.org) if you’re interested in learning
more, or find more labs for practice at http://openintro.org (http://openintro.org).

This is a product of OpenIntro that is released under a Creative Commons Attribution-ShareAlike

3.0 Unported (http://creativecommons.org/licenses/by-sa/3.0). This lab was adapted for OpenIntro
by Andrew Bray and Mine Çetinkaya-Rundel from a lab written by Mark Hansen of UCLA Statistics.

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