# Basic R Skills

This series is provides tutorials and references on key skills needed to complete more complex tasks in R. It is not intended as a complete introduction to learning R. There are many wonderful online tutorials and R packages, including Swirl, for learning R.

**R Skill Level:** Beginner - you're learning, or refreshing on, the basics!

# Series Goals/Objectives

After completing the series, you will be able to:

**Getting Started with the R Programming Language**- Use basic R syntax
- Explain the concepts of objects and assignment
- Explain the concepts of vector and data types
- Describe why you would or would not use
*factors* - Use basic few functions

**Installing & Updating Packages in R**- Describe the basics of an R package
- Install a package in R
- Call (use) an installed R package
- Update a package in R
- View the packages installed on your computer

**Build & Work With Functions in R**- Explain why we should divide programs into small, single-purpose functions
- Use a function that takes parameters (input values)
- Return a value from a function
- Set default values for function parameters
- Write, or define, a function

## Things You’ll Need To Complete This Series

### Setup RStudio

To complete the tutorial series you will need an updated version of R and, preferably, RStudio installed on your computer.

# Getting Started with the R Programming Language

R is a versatile, open source programming language that was specifically designed for data analysis. R is extremely useful for data management, statistics and analyzing data.

This tutorial should be seem more as a reference on the basics of R and not a tutorial for learning to use R. Here we define many of the basics, however, this can get overwhelming if you are brand new to R.

## Learning Objectives

After completing this tutorial, you will be able to:

- Use basic R syntax
- Explain the concepts of objects and assignment
- Explain the concepts of vector and data types
- Describe why you would or would not use
*factors* - Use basic few functions

## Things You’ll Need To Complete This Tutorial

You will need the most current version of R and, preferably, `RStudio`

loaded
on your computer to complete this tutorial.

**Set Working Directory:** This lesson assumes that you have set your working
directory to the location of the downloaded and unzipped data subsets.

An overview of setting the working directory in R can be found here.

**R Script & Challenge Code:** NEON data lessons often contain challenges that reinforce
learned skills. If available, the code for challenge solutions is found in the
downloadable R script of the entire lesson, available in the footer of each lesson page.

## The Very Basics of R

R is a versatile, open source programming language that was specifically designed for data analysis. R is extremely useful for data management, statistics and analyzing data.

**Cool Fact:** R was inspired by the programming language S.

R is:

- Open source software under a GNU General Public License (GPL).
- A good alternative to commercial analysis tools. R has over 5,000 user contributed packages (as of 2014) and is widely used both in academia and industry.
- Available on all platforms.
- Not just for statistics, but also general purpose programming.
- Supported by a large and growing community of peers.

## Introduction to R

You can use R alone or with a user interace like RStudio to write your code. Some people prefer RStudio as it provides a graphic interface where you can see what objects have been created and you can also set variables like your working directory, using menu options.

Learn more about RStudio with thier online learning materials.

We want to use R to create code and a workflow is more reproducible. 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 -- this includes ourselves in 3 months when the paper reviews come back!

## Code & Comments in R

Everything you type into an R script is code, unless you demark it otherwise.

Anything to the right of a `#`

is ignored by R. Use these comments within the
code to describe what it is that you code is doing. Comment liberally in your R
scripts. This will help you when you return to it and will also help others
understand your scripts and analyses.

```
# this is a comment. It allows text that is ignored by the program.
# for clean, easy to read comments, use a space between the # and text.
# there is a line of code below this comment
a <- 1+2
```

## Basic Operations in R

Let's take a few moments to play with R. You can get output from R simply by typing in math

```
# basic math
3 + 5
## [1] 8
12/7
## [1] 1.714286
```

or by typing words, with the command `writeLines()`

. Words that you want to be
recognized as text (as opposed to a field name or other text that signifies an
object) must be enclosed within quotes.

```
# have R write words
writeLines("hello world")
## hello world
```

We can assign our results to an `object`

and name the object. Objects names cannot
contain spaces.

```
# assigning values to objects
b <- 60 * 60
hours <- 365 * 24
# object names can't contain spaces. Use a period, underscore, or camelCase to
# create longer names
temp_HARV <- 90
```

The *result* of the operation on the right hand side of `<-`

is *assigned* to
an object with the name specified on the left hand side of `<-`

. The *result*
could be any type of R object, including your own functions (see the
*Build & Work With Functions in R* tutorial).

### Assignment Operator: Drop the Equals Sign

The assignment operator is `<-`

. It assigns values on the right to `objects`

on
the left. It is similar to `=`

but there are some subtle differences. Learn to
use `<-`

as it is good programming practice. Using `=`

in place of `<-`

can lead
to issues down the line.

```
# this is preferred syntax
a <- 1+2
# this is NOT preferred syntax
a = 1+2
```

**Typing Tip:** If you are using RStudio, you can use
a keyboard shortcut for the assignment operator: **Windows/Linux: "Alt" + "-"**
or **Mac: "Option" + "-"**.

### List All Objects in the Environment

Some functions are the same as in other languages. These might be familiar from command line.

`ls()`

: to list objects in your current environment.`rm()`

: remove objects from your current environment.

Now try them in the console.

```
# assign value "5" to object "x"
x <- 5
ls()
## [1] "a" "b" "base.url" "codeDir" "dat"
## [6] "dir" "dirs" "f" "fig.path" "files"
## [11] "gitRepoPath" "hours" "imagePath" "input" "m"
## [16] "m2" "m2_row" "m3" "mdFile" "n"
## [21] "o" "p" "postsDir" "rmd.files" "subDir"
## [26] "temp_HARV" "wd" "x" "x1" "x2"
## [31] "y" "z"
# remove x
rm(x)
# what is left?
ls()
## [1] "a" "b" "base.url" "codeDir" "dat"
## [6] "dir" "dirs" "f" "fig.path" "files"
## [11] "gitRepoPath" "hours" "imagePath" "input" "m"
## [16] "m2" "m2_row" "m3" "mdFile" "n"
## [21] "o" "p" "postsDir" "rmd.files" "subDir"
## [26] "temp_HARV" "wd" "x1" "x2" "y"
## [31] "z"
# remove all objects
rm(list = ls())
ls()
## character(0)
```

Using `rm(list=ls())`

, you combine several functions to remove all objects.
If you typed `x`

on the console now you will get `Error: object 'x' not found'`

.

## Data Types and Structures

To make the best of the R language, you'll need a strong understanding of the basic data types and data structures and how to operate on those. These are the objects you will manipulate on a day-to-day basis in R. Dealing with object conversions is one of the most common sources of frustration for beginners.

First, **everything** in R is an object. But there are different types of
objects. One of the basic differences in in the *data structures* which are
different ways data are stored.

R has many different **data structures**. These include

- atomic vector
- list
- matrix
- data frame
- array

These data structures vary by the dimensionality of the data and if they can handle data of differnt types (homogenous vs heterogeneous).

Dimensions | Homogenous | Heterogeneous |
---|---|---|

1-D | atomic vector | list |

2-D | matrix | data frame |

none | array |

### Vectors

A vector is the most common and basic data structure in R and is the workhorse of R. Technically, vectors can be one of two types:

- atomic vectors
- lists

although the term "vector" most commonly refers to the atomic types not to lists.

#### Atomic Vectors

R has 6 atomic vector types.

- character
- numeric (real or decimal)
- integer
- logical
- complex
- raw (not discussed in this tutorial)

By *atomic*, we mean the vector only holds data of a single type.

**character**:`"a"`

,`"swc"`

**numeric**:`2`

,`15.5`

**integer**:`2L`

(the`L`

tells R to store this as an integer)**logical**:`TRUE`

,`FALSE`

**complex**:`1+4i`

(complex numbers with real and imaginary parts)

R provides many functions to examine features of vectors and other objects, for example

`typeof()`

- what is it?`length()`

- how long is it? What about two dimensional objects?`attributes()`

- does it have any metadata?

Let's look at some examples:

```
# assign word "april" to x"
x <- "april"
# return the type of the object
typeof(x)
## [1] "character"
#
attributes(x)
## NULL
# assign all values 1 to 10 to the object y
y <- 1:10
y
## [1] 1 2 3 4 5 6 7 8 9 10
typeof(y)
## [1] "integer"
# how many
length(y)
## [1] 10
#
z <- as.numeric(y)
z
## [1] 1 2 3 4 5 6 7 8 9 10
typeof(z)
## [1] "double"
```

A vector is a collection of elements that are most commonly `character`

,
`logical`

, `integer`

or `numeric`

.

You can create an empty vector with `vector()`

. (By default the mode is
`logical`

. You can be more explicit as shown in the examples below.) It is more
common to use direct constructors such as `character()`

, `numeric()`

, etc.

```
x <- vector()
# Create vector with a length and type
vector("character", length = 10)
## [1] "" "" "" "" "" "" "" "" "" ""
# create character vector with length of 5
character(5)
## [1] "" "" "" "" ""
# numeric vector length=5
numeric(5)
## [1] 0 0 0 0 0
# logical vector length=5
logical(5)
## [1] FALSE FALSE FALSE FALSE FALSE
# create a list with combine `c()`
x <- c(1, 2, 3)
x
## [1] 1 2 3
length(x)
## [1] 3
typeof(x)
## [1] "double"
```

`x`

is a numeric vector. These are the most common kind. They are numeric
objects and are treated as double precision real numbers (they can store
decimal points). To explicitly create integers (no decimal points), add an
`L`

to each (or *coerce* to the integer type using `as.integer()`

.

```
# a numeric vector with integers (L)
x1 <- c(1L, 2L, 3L)
x1
## [1] 1 2 3
typeof(x1)
## [1] "integer"
# or using as.integer()
x2 <- as.integer(x)
typeof(x2)
## [1] "integer"
```

You can also have logical vectors.

```
# logical vector
y <- c(TRUE, TRUE, FALSE, FALSE)
y
## [1] TRUE TRUE FALSE FALSE
typeof(y)
## [1] "logical"
```

Finally, you can have character vectors.

```
# character vector
z <- c("Sarah", "Tracy", "Jon")
z
## [1] "Sarah" "Tracy" "Jon"
typeof(z)
## [1] "character"
length(z)
## [1] 3
# what class is it
class(z)
## [1] "character"
# what is the structure
str(z)
## chr [1:3] "Sarah" "Tracy" "Jon"
```

You can also add to a list

```
z <- c(z, "Annette")
z
## [1] "Sarah" "Tracy" "Jon" "Annette"
```

More examples of how to create vectors

- x <- c(0.5, 0.7)
- x <- c(TRUE, FALSE)
- x <- c("a", "b", "c", "d", "e")
- x <- 9:100
- x <- c(1 + (0+0i), 2 + (0+4i))

You can also create vectors as a sequence of numbers.

```
# simple series
1:10
## [1] 1 2 3 4 5 6 7 8 9 10
# use seq() 'sequence'
seq(10)
## [1] 1 2 3 4 5 6 7 8 9 10
# specify values for seq()
seq(from = 1, to = 10, by = 0.1)
## [1] 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3
## [15] 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7
## [29] 3.8 3.9 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5.0 5.1
## [43] 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5
## [57] 6.6 6.7 6.8 6.9 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9
## [71] 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 9.0 9.1 9.2 9.3
## [85] 9.4 9.5 9.6 9.7 9.8 9.9 10.0
```

You can also get non-numeric outputs.

`Inf`

is infinity. You can have either positive or negative infinity.`NaN`

means Not a Number. It's an undefined value.

Try it out in the console.

```
# infinity return
1/0
## [1] Inf
# non numeric return
0/0
## [1] NaN
```

Objects can have **attributes**. Attribues are part of the object. These include:

**names**: the field or variable name within the object**dimnames**:**dim**:**class**:**attributes**: this contain metadata

You can also glean other attribute-like information such as `length()`

(works on vectors and lists) or number of characters `nchar()`

(for
character strings).

```
# length of an object
length(1:10)
## [1] 10
length(x)
## [1] 3
# number of characters in a text string
nchar("NEON Data Skills")
## [1] 16
```

#### Heterogeneous Data - Mixing Types?

When you mix types, R will create a resulting vector that is the least common
denominator. The coercion will move towards the one that's easiest to **coerce**
to.

Guess what the following do:

- m <- c(1.7, "a")
- n <- c(TRUE, 2)
- o <- c("a", TRUE)

Were you correct?

```
n <- c(1.7, "a")
n
## [1] "1.7" "a"
o <- c(TRUE, 2)
o
## [1] 1 2
p <- c("a", TRUE)
p
## [1] "a" "TRUE"
```

This is called implicit coercion. You can also coerce vectors explicitly using
the `as.<class_name>`

.

```
# making values numeric
as.numeric(c("1")
# make values charactor
as.character(1:2)
# make values
as.factor("male","female")
## Error: <text>:5:1: unexpected symbol
## 4: # make values charactor
## 5: as.character
## ^
```

### Matrix

In R, matrices are an extension of the numeric or character vectors. They are not a separate type of object but simply an atomic vector with dimensions; the number of rows and columns.

```
# create an empty matrix that is 2x2
m <- matrix(nrow = 2, ncol = 2)
m
## [,1] [,2]
## [1,] NA NA
## [2,] NA NA
# what are the dimensions of m
dim(m)
## [1] 2 2
```

Matrices in R are by default filled column-wise. You can also use the `byrow`

argument to specify how the matrix is filled.

```
# create a matrix. Notice R fills them by columns
m2 <- matrix(1:6, nrow = 2, ncol = 3)
m2
## [,1] [,2] [,3]
## [1,] 1 3 5
## [2,] 2 4 6
m2_row <- matrix(c(1:6), nrow = 2, ncol = 3, byrow = TRUE)
m2_row
## [,1] [,2] [,3]
## [1,] 1 2 3
## [2,] 4 5 6
```

`dim()`

takes a vector and transform into a matrix with 2 rows and 5 columns.
Another way to shape your matrix is to bind columns `cbind()`

or rows `rbind()`

.

```
# create vector with 1:10
m3 <- 1:10
m3
## [1] 1 2 3 4 5 6 7 8 9 10
class(m3)
## [1] "integer"
# set the dimensions so it becomes a matrix
dim(m3) <- c(2, 5)
m3
## [,1] [,2] [,3] [,4] [,5]
## [1,] 1 3 5 7 9
## [2,] 2 4 6 8 10
class(m3)
## [1] "matrix"
# create matrix from two vectors
x <- 1:3
y <- 10:12
# cbind will bind the two by column
cbind(x, y)
## x y
## [1,] 1 10
## [2,] 2 11
## [3,] 3 12
# rbind will bind the two by row
rbind(x, y)
## [,1] [,2] [,3]
## x 1 2 3
## y 10 11 12
```

### List

In R, lists act as containers. Unlike atomic vectors, the contents of a list are not restricted to a single mode and can encompass any mixture of data types. Lists are sometimes called generic vectors, because the elements of a list can by of any type of R object, even lists containing further lists. This property makes them fundamentally different from atomic vectors.

A list is different from an atomic vector because each element can be a different type -- it can contain heterogeneous data types.

Create lists using `list()`

or coerce other objects using `as.list()`

. An empty
list of the required length can be created using `vector()`

```
x <- list(1, "a", TRUE, 1 + (0+4i))
x
## [[1]]
## [1] 1
##
## [[2]]
## [1] "a"
##
## [[3]]
## [1] TRUE
##
## [[4]]
## [1] 1+4i
class(x)
## [1] "list"
x <- vector("list", length = 5) ## empty list
length(x)
## [1] 5
x[[1]]
## NULL
x <- 1:10
x <- as.list(x)
```

Questions:

- What is the class of
`x[1]`

? - What about
`x[[1]]`

?

Try it out.

```
xlist <- list(a = "Karthik Ram", b = 1:10, data = head(iris))
xlist
$a
$b
$data
## Error: <text>:5:1: unexpected '$'
## 4:
## 5: $
## ^
```

- What is the length of this object? What about its structure?

- Lists can be extremely useful inside functions. You can “staple” together lots of different kinds of results into a single object that a function can return.
- A list does not print to the console like a vector. Instead, each element of the list starts on a new line.
- Elements are indexed by double brackets. Single brackets will still return a(nother) list.

### Factors

Factors are special vectors that represent categorical data. Factors can be
ordered or unordered and are important for modelling functions such as `lm()`

and `glm()`

and also in `plot()`

methods. Once created, factors can only contain
a pre-defined set values, known as *levels*.

Factors are stored as integers that have labels associated the unique integers. While factors look (and often behave) like character vectors, they are actually integers under the hood. You need to be careful when treating them like strings. Some string methods will coerce factors to strings, while others will throw an error.

- Sometimes factors can be left unordered. Example: male, female.
- Other times you might want factors to be ordered (or ranked). Example: low, medium, high.
- Underlying it's represented by numbers 1, 2, 3.
- They are better than using simple integer labels because factors are what are called self describing. male and female is more descriptive than 1s and 2s. Helpful when there is no additional metadata.

Which is male? 1 or 2? You wouldn't be able to tell with just integer data. Factors have this information built in.

Factors can be created with `factor()`

. Input is often a character vector.

```
x <- factor(c("yes", "no", "no", "yes", "yes"))
x
## [1] yes no no yes yes
## Levels: no yes
```

`table(x)`

will return a frequency table counting the number of elements in
each level.

If you need to convert a factor to a character vector, simply use

```
as.character(x)
## [1] "yes" "no" "no" "yes" "yes"
```

To convert a factor to a numeric vector, go via a character. Compare

```
f <- factor(c(1, 5, 10, 2))
as.numeric(f) ## wrong!
## [1] 1 3 4 2
as.numeric(as.character(f))
## [1] 1 5 10 2
```

In modeling functions, it is important to know what the baseline level is. This
is the first factor but by default the ordering is determined by alphanumerical
order of elements. You can change this by speciying the `levels`

(another option
is to use the function `relevel()`

).

```
x <- factor(c("yes", "no", "yes"), levels = c("yes", "no"))
x
## [1] yes no yes
## Levels: yes no
```

### Data Frame

A data frame is a very important data type in R. It's pretty much the *de facto*
data structure for most tabular data and what we use for statistics.

- A data frame is a special type of list where every element of the list has same length.
- Data frames can have additional attributes such as
`rownames()`

, which can be useful for annotating data, like`subject_id`

or`sample_id`

. But most of the time they are not used.

Some additional information on data frames:

- Usually created by
`read.csv()`

and`read.table()`

. - Can convert to matrix with
`data.matrix()`

(preferred) or`as.matrix()`

- Coercion will be forced and not always what you expect.
- Can also create with
`data.frame()`

function. - Find the number of rows and columns with
`nrow(dat)`

and`ncol(dat)`

, respectively. - Rownames are usually 1, 2, ..., n.

#### Manually Create Data Frames

You can manually create a data frame using `data.frame`

.

```
# create a dataframe
dat <- data.frame(id = letters[1:10], x = 1:10, y = 11:20)
dat
## id x y
## 1 a 1 11
## 2 b 2 12
## 3 c 3 13
## 4 d 4 14
## 5 e 5 15
## 6 f 6 16
## 7 g 7 17
## 8 h 8 18
## 9 i 9 19
## 10 j 10 20
```

#### Useful Data Frame Functions

`head()`

- shown first 6 rows`tail()`

- show last 6 rows`dim()`

- returns the dimensions`nrow()`

- number of rows`ncol()`

- number of columns`str()`

- structure of each column`names()`

- shows the`names`

attribute for a data frame, which gives the column names.

See that it is actually a special list:

```
list()
## list()
is.list(iris)
## [1] TRUE
class(iris)
## [1] "data.frame"
```

A recap of the different data types

Dimensions | Homogenous | Heterogeneous |
---|---|---|

1-D | atomic vector | list |

2-D | matrix | data frame |

none | array |

### Indexing

Vectors have positions, these positions are ordered and can be called using
`object[index]`

```
# index
letters[2]
## [1] "b"
```

### Functions

A function is an R object that takes inputs to perform a task. Functions take in information and may return desired outputs.

`output <- name_of_function(inputs)`

```
# create a list of 1 to 10
x <- 1:10
# the sum of all x
y <- sum(x)
y
## [1] 55
```

### Help

All functions come with a help screen. It is critical that you learn to read the
help screens since they provide important information on what the function does,
how it works, and usually sample examples at the very bottom. You can use `help()`

or more simply `??()`

```
# call up a help search
help.start()
# help (documentation) for a package
?? ggplot2
# help for a function
?? sum()
```

You can't ever learn all of R as it is ever changing with new packages and new tools, but once you have the basics and know how to find help to do the things that you want to do, you'll be able to use R in your science.

### Sample Data

R comes with sample datasets. You will often find these as the date sets in
documentation files or responses to inquires on public forums like *StackOverflow*.
To see all available sample datasets you can type in `data()`

to the console.

### Packages in R

R comes with a set of functions or commands that perform particular sets of
calculations. For example, in the equation `1+2`

, R knows that the "+" means to
add the two numbers, 1 and 2 together. However, you can expand the capability of
R by installing packages that contain suites of functions and compiled code that
you can also use in your code.

### Get Lesson Code:

R-Basics-Getting-Started.R# Build & Work With Functions in R

Sometimes we want to perform a calculation, or a set of calculations, multiple times in our code. We could write out the equation over and over in our code -- OR -- we could chose to build a function that allows us to repeat several operations with a single command. This tutorial will focus on creating functions in R.

## Learning Objectives

After completing this tutorial, you will be able to:

- Explain why we should divide programs into small, single-purpose functions.
- Use a function that takes parameters (input values).
- Return a value from a function.
- Set default values for function parameters.
- Write, or define, a function.
- Test and debug a function. (This section in construction).

## Things You’ll Need To Complete This Tutorial

You will need the most current version of R and, preferably, `RStudio`

loaded
on your computer to complete this tutorial.

**Set Working Directory:** This lesson assumes that you have set your working
directory to the location of the downloaded and unzipped data subsets.

An overview of setting the working directory in R can be found here.

**R Script & Challenge Code:** NEON data lessons often contain challenges that reinforce
learned skills. If available, the code for challenge solutions is found in the
downloadable R script of the entire lesson, available in the footer of each lesson page.

## Creating Functions

Sometimes we want to perform a calculation, or a set of calculations, multiple times in our code. For example, we might need to convert units from Celsius to Kelvin, across multiple datasets and save if for future use.

We could write out the equation over and over in our code -- OR -- we could chose to build a function that allows us to repeat several operations with a single command. This tutorial will focus on creating functions in R.

## Getting Started

Let's start by defining a function `fahr_to_kelvin`

that converts temperature
values from Fahrenheit to Kelvin:

```
fahr_to_kelvin <- function(temp) {
kelvin <- ((temp - 32) * (5/9)) + 273.15
kelvin
}
```

Notice the syntax used to define this function:

```
FunctionNameHere <- function(Input-variable-here){
what-to-do-here
what-to-return-here
}
```

The definition begins with the name of your new function. Use a good descriptor of the function you are doing and make sure it isn't the same as a a commonly used R function!

This is followed by the call to make it a `function`

and a parenthesized list of parameter names.
The parameters are the input values that the function will use to perform any
calculations. In the case of `fahr_to_kelvin`

, the input will be the temperature value that we
wish to convert from fahrenheit to kelvin. You can have as many input parameters
as you would like (but too many are poor style).

The body, or implementation, is surrounded by curly braces `{ }`

. Leaving the
initial curly bracket at the end of the first line and the final one on its own
line makes functions easier to read (for the human, the machine doesn't care).
In many languages, the body of the function - the statements that are executed
when it runs - must be indented, typically using 4 spaces.

**Data Tip:** While it is not mandatory in R to indent
your code 4 spaces within a function, it is strongly recommended as good
practice!

When we call the function, the values we pass to it are assigned to those variables so that we can use them inside the function.

The last line within the function is what R will evaluate as a returning value.
Remember that the last line has to be a command that will print to the screen,
and not an object definition, otherwise the function will return nothing - it
will work, but will provide no output. In our example we print the value of
the object `Kelvin`

.

Calling our own function is no different from calling any other built in R function that you are familiar with. Let's try running our function.

```
# call function for F=32 degrees
fahr_to_kelvin(32)
## [1] 273.15
# We could use `paste()` to create a sentence with the answer
paste('The boiling point of water (212 Farenheit) is', fahr_to_kelvin(212),'degrees Kelvin.')
## [1] "The boiling point of water (212 Farenheit) is 373.15 degrees Kelvin."
```

We've successfully called the function that we defined, and we have access to the value that we returned.

**Question**: What would happen if we instead wrote our function as:

```
fahr_to_kelvin_test <- function(temp) {
kelvin <- ((temp - 32) * (5/9)) + 273.15
}
```

Try it:

```
fahr_to_kelvin_test(32)
```

Nothing is returned! This is because we didn't specify what the output was in the final line of the function.

However, we can see that the fuction still worked by assigning the function to object "a" and calling "a".

```
# assign to a
a <- fahr_to_kelvin_test(32)
# value of a
a
## [1] 273.15
```

We can see that even though there was no output from the function, the function was still operational.

### Challenge: Writing Functions

Now that we've seen how to turn Fahrenheit into Kelvin, try your hand at converting Kelvin to Celsius. Remember, for the same temperature Kelvin is 273.15 degrees less than Celsius.

## Compound Functions

What about converting Fahrenheit to Celsius? We could write out the formula as a new function or we can combine the two functions we have already created. It might seem a bit silly to do this just for converting from Fahrenheit to Celcius but think about the other applciations where you will use fuctions!

```
# use two functions (F->K & K->C) to create a new one (F->C)
fahr_to_celsius <- function(temp) {
temp_k <- fahr_to_kelvin(temp)
temp_c <- kelvin_to_celsius(temp_k)
temp_c
}
paste('freezing point of water (32 Fahrenheit) in Celsius:', fahr_to_celsius(32.0))
## [1] "freezing point of water (32 Fahrenheit) in Celsius: 0"
```

This is our first taste of how larger programs are built: we define basic operations, then combine them in ever-large chunks to get the effect we want. Real-life functions will usually be larger than the ones shown here—typically half a dozen to a few dozen lines—but they shouldn't ever be much longer than that, or the next person who reads it won't be able to understand what's going on.

### Get Lesson Code:

R-Basics-Of-Functions.R# Installing & Updating Packages in R

This tutorial provides the basics of installing and working with packages in R.

## Learning Objectives

After completing this tutorial, you will be able to:

- Describe the basics of an R package
- Install a package in R
- Call (use) an installed R package
- Update a package in R
- View the packages installed on your computer

## Things You’ll Need To Complete This Tutorial

You will need the most current version of R and, preferably, `RStudio`

loaded
on your computer to complete this tutorial.

**Set Working Directory:** This lesson assumes that you have set your working
directory to the location of the downloaded and unzipped data subsets.

An overview of setting the working directory in R can be found here.

**R Script & Challenge Code:** NEON data lessons often contain challenges that reinforce
learned skills. If available, the code for challenge solutions is found in the
downloadable R script of the entire lesson, available in the footer of each lesson page.

## Additional Resourcs

- More on packages from Quick-R.
- Article on R-bloggers about installing packages in R.

## About Packages in R

Packages are collections of R functions, data, and compiled code in a well-defined format. When you install a package it gives you access to a set of commands that are not available in the base R set of functions. The directory where packages are stored is called the library. R comes with a standard set of packages. Others are available for download and installation. Once installed, they have to be loaded into the session to be used.

## Installing Packages in R

To install a package you have to know where to get the package. Most established packages are available from "CRAN" or the Comprehensive R Archive Network.

Packages download from specific CRAN "mirrors"" where the packages are saved
(assuming that a binary, or set of installation files, is available for your
operating system). If you have not set a preferred CRAN mirror in your
`options()`

, then a menu will pop up asking you to choose a location from which
you'd like to install your packages.

To install any package from CRAN, you use `install.packages()`

. You only need to
install packages the first time you use R (or after updating to a new version).

```
# install the ggplot2 package
install.packages("ggplot2")
```

**R Tip:** You can just type this into the command
line of R to install each package. Once a package is installed, you don't have
to install it again while using the version of R!

## Use a Package

Once a package is installed (basically the functions are downloaded to your computer), you need to "call" the package into the current session of R. This is essentially like saying, "Hey R, I will be using these functions now, please have them ready to go". You have to do this ever time you start a new R session, so this should be at the top of your script.

When you want to call a package, use `library(PackageNameHere)`

. You may also
see some people using `require()`

-- while that works in most cases, it does
function slightly differently and best practice is to use `library()`

.

```
# load the package
library(ggplot2)
```

## What Packages are Installed Now?

If you want to use a package, but aren't sure if you've installed it before,
you can check! In code you, can use `installed.packages()`

.

```
# check installed packages
installed.packages()
```

If you are using RStudio, you can also check out the Packages tab. It will list all the currently installed packages and have a check mark next to them if they are currently loaded and ready to use. You can also update and install packages from this tab. While you can "call" a package from here too by checking the box I wouldn't recommend this as calling the package isn't in your script and you if you run the script again this could trip you up!

## Updating Packages

Sometimes packages are updated by the users who created them. Updating packages can sometimes make changes to both the package and also to how your code runs. ** If you already have a lot of code using a package, be cautious about updating packages as some functionality may change or disappear.**

Otherwise, go ahead and update old packages so things are up to date.

In code you, can use `old.packages()`

to check to see what packages are out of
date.

`update.packages()`

will update all packages in the known libraries
interactively. This can take a while if you haven't done it recently! To update
everything without any user intervention, use the `ask = FALSE`

argument.

If you only want to update a single package, the best way to do it is using
`install.packages()`

again.

```
# list all packages where an update is available
old.packages()
# update all available packages
update.packages()
# update, without prompts for permission/clarification
update.packages(ask = FALSE)
# update only a specific package use install.packages()
install.packages("plotly")
```

In RStudio, you can also manage packages using Tools -> Install Packages.

### Challenge: Installing Packages

Check to see if you can install the `dplyr`

package or a package of interest to
you.

- Check to see if the
`dplyr`

package is installed on your computer. - If it is not installed, install the "dplyr" package in R.
- If installed, is it up to date?

## Leave a comment