Believe it or not, reading in data is often the hardest part of working with R. If you collect and store your data in Excel or Google Docs, you will need to carefully format your spreadsheet. It should obey the following rules:
The spreadsheet should contain a single sheet.
Row 1 should contain variable names in consecutive cells, starting with Cell A1. For convenience, the names should be comprised of lowercase words and contain no symbols or punctuation.
Subsequent rows (starting with Row 2) should contain your observations (data).
If the value of a variable is missing for a particular observation, the coressponding cell in the spreadsheet should be empty.
All other cells in the spreadsheet should be empty.
This sounds straightforward, but many spreadsheets that you find “in the wild” do not obey these rules. You will have to reformat these spreadsheets, usually by deleting empty rows and columns and by deleting notes and other annotations.
Even if your spreadsheet is formatted as above, R cannot open Excel files. To save your data to an R-compatible file format, exportyour data as a “Column-Separated Value” (CSV) file. You can do this from the File menu in Excel.
If you have a property-formatted CSV file, you can read it into R
using the read.csv function. There are two ways to specify the
file. To use your system's file chooser, run the command.
data <- read.csv(file.choose())
Alternatively, if you know the name of the file, you can pass it
directly to the read.csv function. Note that if you pass the
file name directly, you must either specify the full path to the
file, or you must set the “working directory” to be the directory
thatcontains the file. To set the working directory, either use
the setwd function or run the Set Working Directory command
from RStudio's Session menu.
Suppose that I want to open a file named “bikedata.csv”, which is stored in the “~/Datasets” directory on my system. Ifirst set the working directory to “~/Datasets” by Choosing Session > Set Working Directory > Choose Directory …. This will execute the command
setwd("~/Datasets")
(In fact, if I do not want to use the menu system, then I can just
type this command directly to achieve the same effect.) Once the
working directory is set, I can read in the data to a variable
named data by executing the command
bikedata <- read.csv("bikedata.csv")
In R, we use the term “variable” to refer to a name-value pair. You should not confuse this concept with the types of variables you have seen in your math classes (they are similar in some ways, but different in others).
In the last section, when we ran the command
data <- read.csv(file.choose()) we created a variable with name
data and value equal to the contents of the chosen file.
To create a variable or to assign a new value to an existing
variable, use the assignment command (<-), which is meant to
look like an arrow pointing from the value to the variable name.
For example, the command
a <- 2.7
means “assign the value 2.7 to the variable named a”.
Another way to read this is “variable a gets the value 2.7”.
When you have a variable, you can use the name in place of the value:
a + 10
## [1] 12.7
5 * a
## [1] 13.5
You can see the value of a variable, by typing its name and pressing enter:
a
## [1] 2.7
An alternative way to read in a file to the variable named data
is to run the following sequence of commands:
filename <- file.choose()
data <- read.csv(filename)
The first command asks the user to choose a file, and stores the
resulting name in the filename variable. This variable contains
the name of the file, but not the actual contents. The second
command takes the name of the file, opens it, reads the contents
into memory, and stores the result in the data variable.
Besides variables, the other main concept you need to learn in R is that of a function. You are probably familiar with the concept of a function from your mathematics courses, and a function in R is very similar: a function is something that takes zero or more values, then performs a sequence of actions and returns a result.
We have already seen three functions: file.choose, read.csv,
and setwd. We call a function by putting a pair of parenteses
() after the function name. Many functions, including
read.csv and setwd require one or more values as input. We
refer to these values as arguments, and we specify them by
putting the values inside the parentheses. When we do so, we
say that we are passing the value of the argument to the
function.
Sometimes a function will have optional arguments. These are
arguments that, if left unspecified, will be given reasonable
default values. For example, by default, the file.choose
function forces the user to choose an existing file. To allow
the user to choose a name for new file, pass the argument
new=TRUE to file file.choose function:
file.choose(new = TRUE)
Before, we did not specify the new argument, and it defaulted
to the value FALSE.
The read.csv command opens the file and reads the data into a
type of object called a “dataframe''. Conceptually, a data frame
is just like a spreadsheet: it has columns, corresponding to
variables, and rows, corresponding to observations. Each row and
column has a name. Usually, the row names are the character
strings "1”, “2”, etc., but this is not always the case.
To see the first 6 rows in the bikedata data frame, run the
command
head(bikedata)
## vehicle colour passing.distance street helmet kerb datetime
## 1 Car Blue 2.114 Urban N 0.5 2006-05-11 16:30:00
## 2 HGV Red 0.998 Urban N 0.5 2006-05-11 16:30:00
## 3 LGV Blue 1.817 Urban N 0.5 2006-05-11 16:30:00
## 4 Car <NA> 1.640 Urban N 0.5 2006-05-11 16:30:00
## 5 Bus Other 1.544 Urban N 0.5 2006-05-11 16:30:00
## 6 Car Grey 1.509 Urban N 0.5 2006-05-11 16:30:00
## bikelane city
## 1 N Salisbury
## 2 N Salisbury
## 3 N Salisbury
## 4 N Salisbury
## 5 N Salisbury
## 6 N Salisbury
We can see that there are nine columns, named vehicle,
colour, passing.distance, street, helmet, kerb,
datetime, bikelane, and city.
To see a summary of the entire data frame, use the summary function:
summary(bikedata)
## vehicle colour passing.distance street helmet
## Bus : 46 Blue :636 Min. :0.394 Main :1637 N:1206
## Car :1708 Grey :531 1st Qu.:1.303 OneWay1 : 9 Y:1149
## HGV : 82 Red :378 Median :1.529 OneWay2 : 13
## LGV : 293 White :333 Mean :1.564 Residential: 39
## PTW : 34 Black :262 3rd Qu.:1.790 Rural : 2
## SUV : 143 (Other):201 Max. :3.787 Urban : 655
## Taxi: 49 NA's : 14
## kerb datetime bikelane city
## Min. :0.25 2006-05-20 16:21:00: 93 N:2305 Bristol : 450
## 1st Qu.:0.25 2006-05-20 15:48:00: 75 Y: 50 Salisbury:1905
## Median :0.50 2006-05-31 09:04:00: 70
## Mean :0.67 2006-05-20 15:34:00: 65
## 3rd Qu.:1.00 2006-05-27 10:01:00: 64
## Max. :1.25 2006-05-27 09:25:00: 63
## (Other) :1925
Let's say we want to investigate the passing.distance variable.
To do this, we must first extract that column from the
bikedata dataframe. There are three ways to do this:
x <- bikedata$passing.distance
x <- bikedata[["passing.distance"]]
x <- bikedata[, "passing.distance"]
All three commands are equivalent ways to extract the
passing.distance column and store it in a variable named x.
The $ form is the most common, but you will sometimes see the
other two forms, as well.
Data frame columns are stored in a data type called a “vector”.
Conceptually, a vector is a one-dimensional array of values,
indexed by integers starting at 1. Most functions in R operate
on vectors.
You can access individual values by using double square-brackets.
For example, to see the first element of the vector, type the
command
x[[1]]
## [1] 2.114
To see the fifth value, type the command
x[[5]]
## [1] 1.544
To see how many elements are contained in the vector, use the
length function:
length(x)
## [1] 2355
To see the last element, type
x[[length(x)]]
## [1] 1.031
To extract a subvector, use single square brackets. For example, the subvector consisting of the first 25 elements is
x[1:25]
## [1] 2.114 0.998 1.817 1.640 1.544 1.509 1.290 1.512 1.049 1.932 1.145
## [12] 1.410 1.428 1.494 1.570 2.103 0.896 1.160 1.290 1.963 2.436 2.304
## [23] 1.482 1.492 1.432
Here, 1:25 is shorthand for “integers 1 to 25”. Since not all
25 values fit onto a single line, R wraps the values. At the
start of each line, R prints the index of the first value on the
line in square brackets. Looking at the output above, we can
see that 1.410 is the 12th element and 1.492 is the 24th
element of the result.
You may have asked yourself earlier why the output of x[[1]]
and other similar commands was prefixed by [1]. The reason for
this is that R doesn't have the concept of a “single value” or
“scalar”. The only way to represent the value of x[[1]] is
as a length-one vector. The output
[1] 2.114
denotes a vector with a single value (2.114), stored at
index 1.
Since there is no concept of a “scalar” in R, the command
x[[1]] is equivalent to x[1:1], which is also the same as
x[1]. In other programming languages, x[[1]],
“the first element of x”, and x[1], “the subvector of x
starting and ending at index 1” would be different; in R, these
are identical. Because of this, most people use single brackets instead of double brackets when indexing vectors, writing
x[1] and x[5] instead of x[[1]] and x[[5]]].
There are a variety of functions for computing descriptive statistics for the values stored in a vector.
Sum of values:
sum(x)
## [1] 3683
Measures of central tendency (sample mean and median):
mean(x)
## [1] 1.564
median(x)
## [1] 1.529
Measures of variability (sample standard deviation and sample variance):
sd(x)
## [1] 0.3835
var(x)
## [1] 0.147
Extreme values (minimum and maximum):
min(x)
## [1] 0.394
max(x)
## [1] 3.787
Quantiles:
quantile(x, 0.25) # first quartile
## 25%
## 1.303
quantile(x, 0.75) # third quartile
## 75%
## 1.79
quantile(x, 0.99) # 99th percentile
## 99%
## 2.58
We can use the hist command to make a histogram of the values
stored in a vector:
hist(x)
By default, the output looks fine when printed in black and white,
but it isn't very pretty. We can specify the bin color, change the axis lables, and omit the main title by passing additional arguments to this hist function
hist(x, col="steelblue", xlab="Passing Distance", ylab="Count",
main="")
Use the boxplot and qqnorm commands to make boxplots and
normal probability plots, as in the following examples:
boxplot(x, border="darkred", ylab="Passing Distance")
qqnorm(x, col="darkgreen", xlab="Normal Quantiles",
ylab="Passing Distance Quantiles",
main="")
So far, we have seen how to use R to summarize and plot a numeric (quantitative) variable. R also has very good support for categorical (qualitative) variables, referred to as factors.
To see levels, the set of possible values for a factor variable,
use the levels function. For example, to see the levels of
the colour variable:
levels(bikedata$colour)
## [1] "Black" "Blue" "Green" "Grey" "Other" "Red" "White"
To tabulate the values of the variable, use the table command,
as in
table(bikedata$colour)
##
## Black Blue Green Grey Other Red White
## 262 636 149 531 52 378 333
Note: be default, the table command omits missing values. To
include these values in the output, include useNA="ifany" in
the call to table:
table(bikedata$colour, useNA = "ifany")
##
## Black Blue Green Grey Other Red White <NA>
## 262 636 149 531 52 378 333 14
We can present tabulated counts in a bar plot using the following commands
tab <- table(bikedata$colour, useNA = "ifany")
barplot(tab)
Usually, it makes sense to arrange the table values in decreasing order. Here is an example with sorted counts that adds axis labels and changes the bar colors:
barplot(sort(tab, decreasing=TRUE), xlab="Colour", ylab="Count",
col="steelblue")
We can use the t.test function to test a hypothesis
about a population mean.
t.test(bikedata$passing.distance)
##
## One Sample t-test
##
## data: bikedata$passing.distance
## t = 197.9, df = 2354, p-value < 2.2e-16
## alternative hypothesis: true mean is not equal to 0
## 95 percent confidence interval:
## 1.548 1.579
## sample estimates:
## mean of x
## 1.564
This reports the t statistic, the degrees of freedom, the p-value,
and the sample mean. The command also reports a 95% confidence
interval for the population mean. To change the confidence level,
use the conf.level argument, as in
t.test(bikedata$passing.distance, conf.level = 0.99)
##
## One Sample t-test
##
## data: bikedata$passing.distance
## t = 197.9, df = 2354, p-value < 2.2e-16
## alternative hypothesis: true mean is not equal to 0
## 99 percent confidence interval:
## 1.544 1.584
## sample estimates:
## mean of x
## 1.564
By default, the null hypothesis is that the true (population)
mean is equal to 0, and the alternative hypothesis is that the
true mean is not equal to 0. To use a different null, pass the
mu argument. To use a different alternative, pass
alternative="less" or alternative="greater". For example, to
test the null hypothesis that the true mean is equal to 1.5
against the alternative that it is greater, run the command
t.test(bikedata$passing.distance, alternative = "greater", mu = 1.5)
##
## One Sample t-test
##
## data: bikedata$passing.distance
## t = 8.088, df = 2354, p-value = 4.786e-16
## alternative hypothesis: true mean is greater than 1.5
## 95 percent confidence interval:
## 1.551 Inf
## sample estimates:
## mean of x
## 1.564
Note that for a one-sided alternative, the confidence interval is one-sided, as well.
To perform a test on a population proportion, use the prop.test
function. This performs a test on a population proportion that is
slightly different than the one we cover in the core statistics
course, but it will give you a very similar answer.
In the first argument, specify x, the number of successes; in
the second argument, specify n, the number of trials. By
default, the null value of the population proportion is 0.5; to
specify a different value, use the p argument.
For example, to test the null hypothesis that the true proportion
of cars passing the rider on his route is exactly equal to 40%,
we first tabulate the colour variable,
table(bikedata$colour)
##
## Black Blue Green Grey Other Red White
## 262 636 149 531 52 378 333
In this instance, the number of “successes” is equal to the number
of blue cars, 636. Recall that some of the values for the
colour variable are missing. If the missingness is unrelated to
the actual color, then we can safely ifnore these values; in this
case, the number of “trials” is equal to the sumof the counts for
all of the non-missing values.
sum(table(bikedata$colour))
## [1] 2341
Now, to test the proportion, we run the command:
prop.test(636, 2341, p = 0.4)
##
## 1-sample proportions test with continuity correction
##
## data: 636 out of 2341, null probability 0.4
## X-squared = 160.1, df = 1, p-value < 2.2e-16
## alternative hypothesis: true p is not equal to 0.4
## 95 percent confidence interval:
## 0.2538 0.2903
## sample estimates:
## p
## 0.2717
As with the t.test function, we can use a one-sided alternative
or specify a different confidence level for the interval by
using the alternative or conf.level argument, respectively.
Here is a test of the null that the true proportion is equal to
0.5 against the alternative that it is less, along with a
one-sided 99% confidence interval:
prop.test(636, 2341, p = 0.5, alternative = "less", conf.level = 0.99)
##
## 1-sample proportions test with continuity correction
##
## data: 636 out of 2341, null probability 0.5
## X-squared = 487.2, df = 1, p-value < 2.2e-16
## alternative hypothesis: true p is less than 0.5
## 99 percent confidence interval:
## 0.0000 0.2938
## sample estimates:
## p
## 0.2717