In this short notebook, I will go through a few basic
examples in `R`

that you may find useful for the course.

These are just some of the things I find useful. Feel free to search around for others.

For those of you who have done some programming before, you will notice
that `R`

is a functional programming language.

In [1]:

```
%%R
useful_function = function(dataname) {
return(paste("http://stats191.stanford.edu/data/", dataname, sep=''))
}
useful_function("groundhog.table")
```

Let's load the heights data with less code

In [2]:

```
%%R
h.table = read.table(useful_function("groundhog.table"), header=TRUE, sep=',')
head(h.table)
```

Or, for all data sets in the course directory, we might try

In [3]:

```
%%R
course_dataset = function(dataname, sep='', header=TRUE) {
read.table(useful_function(dataname), header=header, sep=sep)
}
head(course_dataset('groundhog.table', sep=','))
```

`return`

in the function above. By default, `R`

will return the
object in the last line of the function code.

In [4]:

```
%%R
test_func = function(x) {
x^2
3
}
test_func(4)
```

*source* is an easy way to do this, and it takes either
the name of a file or a URL as argument.
Suppose we have a
webpage http://stats191.stanford.edu/R/helper_code.R

In [5]:

```
import urllib
print urllib.urlopen('http://stats191.stanford.edu/R/helper_code.R').read()
```

Then, we can execute this as follows

In [6]:

```
%%R
source("http://stats191.stanford.edu/R/helper_code.R")
head(course_dataset("groundhog.table", sep=','))
```

As you go through the course, you might copy this file to a your computer and add some other useful functions to this file.

For larger collections of functions, `R`

allows the creation of packages that can be
installed and loaded with a call to the `library`

function. Documentation on packages can be found here.

Many tasks involving sequences of numbers. Here are some basic examples on how to manipulate and create sequences.

The function `c`

, concatenation, is used often in R, as are
`rep`

and `seq`

In [7]:

```
%%R
X = 3
Y = 4
c(X,Y)
```

The function `rep`

denotes *repeat*.

In [8]:

```
%%R
print(rep(1,4))
print(rep(2,3))
c(rep(1,4), rep(2,3))
```

The function `seq`

denotes sequence. There are various ways of specifying the sequence.

In [9]:

```
%%R
seq(0,10,length=11)
```

In [10]:

```
%%R
seq(0,10,by=2)
```

You can sort and order sequences

In [11]:

```
%%R
X = c(4,6,2,9)
sort(X)
```

Use an ordering of X to sort a list of Y in the same order

In [12]:

```
%%R
Y = c(1,2,3,4)
o = order(X)
X[o]
Y[o]
```

A word of caution. In `R`

you can overwrite builtin functions so try not to call variables `c`

:

In [13]:

```
%%R
c = 3
c
```

However, this has not overwritten the function `c`

.

In [14]:

```
%%R
c(3,4,5)
```

`T`

for `TRUE`

and `F`

for `FALSE`

. Since we compute $t$ and $F$ statistics it is natural to also have variables named `T`

so when you are expecting `T`

to be `TRUE`

you might get a surprise.

In [15]:

```
%%R
c(T,F)
```

`R`

supports using logical vectors as index objects.

In [16]:

```
%%R
X = c(4,5,3,6,7,9)
Y = c(4,2,65,3,5,9)
X[Y>=5]
```

`data.frame`

and want to extract from rows or columns. Rows are the first of two indexing objects while columns correspond to the second indexing object. Suppose we want to find take the mother and daughter heights where the daughter's height is less than or equal to 62 inches. Note the "," in the square brackets below: this tells `R`

that it is looking for a subset of *rows* of the `data.frame`

.

In [17]:

```
%%R
library(alr3)
data(heights)
head(heights)
subset_heights = heights[heights$Dheight <= 62,]
print(c(nrow(heights), nrow(subset_heights)))
```

`R`

has a very rich plotting library. Most of our plots will be
fairly straightforward, "scatter plots".

In [18]:

```
%%R
X = c(1:40)
Y = 2 + 3 * X + rnorm(40) * 10
plot(X, Y)
```

*par*.

In [19]:

```
%%R
plot(X, Y, pch=21, bg='red')
```

You can add titles, as well as change the axis labels.

In [20]:

```
%%R
plot(X, Y, pch=23, bg='red', main='A simulated data set', xlab='Predictor', ylab='Outcome')
```

*abline*. We'll add some lines to our previous plot: a yellow line with
intercept 2, slope 3, width 3, type 2, as well as a vertical line at x=20 and horizontal line at y=60.

In [21]:

```
%%R
plot(X, Y, pch=23, bg='red', main='A simulated data set', xlab='Predictor', ylab='Outcome')
abline(2, 3, lwd=3, lty=2, col='yellow')
abline(h=60, col='green')
abline(v=20, col='red')
```

`plot`

, then add the rest in blue with
an orange line connecting them.

In [22]:

```
%%R
plot(X[1:20], Y[1:20], pch=21, bg='red', xlim=c(min(X),max(X)), ylim=c(min(Y),max(Y)))
points(X[21:40], Y[21:40], pch=21, bg='blue')
lines(X[21:40], Y[21:40], lwd=2, lty=3, col='orange')
```

You can put more than one plot on each device. Here we create a 2-by-1 grid of plots

In [23]:

```
%%R
par(mfrow=c(2,1))
plot(X, Y, pch=21, bg='red')
plot(Y, X, pch=23, bg='blue')
par(mfrow=c(1,1))
```

*pdf*, *png*, *jpg* among other formats.
Let's save a plot in a file called "myplot.jpg"

In [24]:

```
%%R
jpeg("myplot.jpg")
plot(X, Y, pch=21, bg='red')
dev.off()
```

In [25]:

```
from IPython.display import Image
Image('myplot.jpg')
```

Out[25]:

Several plots can be saved using *pdf* files. This example has
two plots in it.

In [26]:

```
%%R
pdf("myplots.pdf")
# make whatever plot you want
# first page
plot(X, Y, pch=21, bg='red')
# a new call to plot will make a new page
plot(Y, X, pch=23, bg='blue')
# close the current "device" which is this pdf file
dev.off()
```

It is easy to use *for* loops in R

In [27]:

```
%%R
for (i in 1:10) {
print(i^2)
}
```

In [28]:

```
%%R
for (w in c('red', 'blue', 'green')) {
print(w)
}
```

Note that big loops can get really slow, a drawback of many high-level languages.

R has a builtin help system, which can be accessed and searched as follows

```
> help(t.test)
> help.search('t.test')
```

Many objects also have examples that show you their usage

`> example(lm)`

In [29]:

```
%%R
help(t.test)
```

In [30]:

```
%%R
example(lm)
```

In practice, we will often be using the distribution (CDF), quantile (inverse
CDF) of standard random variables like the *T*, *F*, chi-squared and normal.

The standard 1.96 (about 2) standard deviation rule for $\alpha=0.05$: (note that 1-0.05/2=0.975)

In [31]:

```
%%R
qnorm(0.975)
```

We might want the $\alpha=0.05$ upper quantile for an F with 2,40 degrees of freedom:

In [32]:

```
%%R
qf(0.95, 2, 40)
```

In [33]:

```
%%R
1 - pf(5, 2, 40)
```

In [34]:

```
%%R
c(1 - pchisq(5*2, 2), 1 - pf(5, 2, 4000))
```

Other common distributions used in applied statistics are `norm`

and `t`

.

In [35]:

```
```