---
title: "Introduction to R"
author: "[Statistical Genetics Lab](http://statgen.esalq.usp.br) <br/> Department of Genetics <br/> Luiz de Queiroz College of Agriculture <br/> University of São Paulo"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to R}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r knitr_init, echo=FALSE, cache=FALSE}
library(knitr)
library(rmarkdown)

knitr::opts_chunk$set(collapse = TRUE,
                      comment = "#>",
                      fig.width = 6,
                      fig.height = 6,
                      fig.align = "center",
                      dev = "png",
                      dpi = 36,
                      cache = TRUE)

```

R is a language and environment for statistical computing and
graphics. To download R, please visit the [Comprehensive R Archive
Network](https://cran.r-project.org). You do not need to be an expert
on it to be able to build your linkage map using _OneMap_.

Although we prefer and recommend the Linux version, in this tutorial
it is assumed that the user is running Windows. Users of R under Linux
or Mac OS should have no difficulty following this tutorial.

We would like to recommend those new users, instead of using plain R,
use it through the fantastic software
RStudio. With this package, there is no noticeable difference between operating systems.

As advertised on the website, _RStudio is an integrated development
environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for
plotting, history, debugging, and workspace management_. In other
words, it offers a number of facilities for your convenience that will
make your life easier, especially if you have never used R before.

So, go ahead and download and install R and RStudio. The window on the
left is where you type the R commands you want.

# Getting started

In the left window, you can see a _greater than_ sign (``>''), which
means that R is waiting for a command. We call this a _prompt_. 

Let us start with a simple example of adding two numbers. Type `2 + 3` at the
prompt then type the _Enter_ key. You will see the result directly on
the screen.

```{r }
2 + 3
```

You can store this result into a variable for future use, applying the
assignment operator _ <- _ (_less than_ sign and _ minus_ altogether):

```{r }
x <- 2 + 3
```

The result of the calculation was stored into the variable _x_. You
can access this result by typing _x_ at the prompt:

```{r }
x
```

You can also use the variable _x_ in other calculations. For example:

```{r } 
x + 4
```

So, play a little just to start understanding what is going on.

# Functions

Another fundamental aspect in R is the usage of _functions_. A
function is a predefined routine used to do specific calculations. For
example, to calculate the natural logarithm of $6.7$, we can use the
function _log_:

```{r }
log(6.7)
```
 
The function _log_ contains a group of internal procedures to
calculate the natural logarithm of a positive real number. The input
values of a function are called _arguments_. 

In the previous example, we provided only one argument ($6.7$) to the
function. Sometimes a function has more than one argument. For
example, to obtain the logarithm of $6.7$ to base $4$, you can use:

```{r }
log(6.7, base = 4)
```

It is possible to calculate the natural logarithm of a set of numbers
by defining a vector and using it as the first argument of the
function _log_. To do so we use the function _c()_, that _combines_ a
set of values into a vector. Thus, to calculate the logarithm of the
numbers 6.7, 3.2, 5.4, 8.1, 4.9, 9.7, and 2.5, one can use:

```{r }
y <- c(6.7, 3.2, 5.4, 8.1, 4.9, 9.7, 2.5)
log(y)
```

Notice that _y_ is a vector, that is the argument to the function
_log()_.

# Getting help

Every R function has a help page that can be accessed using a
question mark before the name of the function. For example, to get
help on function _log_, you would type:

```{r, eval=FALSE}
?log
``` 

This command will open a help page in the default web browser of your
system. The help page contains some important information about the
function such as its syntax, its arguments, and some usage examples.

There are many other ways of getting help, of course. For example, from RStudio,
click _Help_ on the menu. For doing searches on the internet, it is
better to first go to [https://rseek.org/](https://rseek.org/), since R
is a very common letter to include in searches.  

# Packages

Although R has a huge amount of internal functions, for doing very
specific computations (like constructing genetic linkage maps), it is
necessary to add extra functionalities. These can be done by
installing a _package_ (that, loosely speaking, will include a number
of new functions for helping you to achieve what you are trying to
do). A package is a collection of related functions, help files and
example data files that have been bundled together (Adler, 2010).

For example, let us assume that you need to convert a set of
recombination fractions into centimorgan distance using the Kosambi
mapping function. One possible way to do this is by using basic R
to write a function to calculate the distances. Another way is to use the _OneMap_ package. To install it you can type:

```{r, eval=FALSE}
setRepositories(ind = 1:2)
install.packages("onemap")
``` 

You also can use the console menus on RStudio. On the bottom window to
the right, select **Packages**, then **Install**, and finally select
_OneMap_ (select CRAN as your repository). Yes, it is that easy!

Returning to the console, you need to load _OneMap_ by typing:

```{r }
library(onemap)
``` 

Some Linux users reported the error message below:

```{r, eval=FALSE}
ERROR: dependency ‘tkrplot’ is not available for package ‘onemap’
```

To fix it, in a terminal (outside R), install `r-cran-tkrplot`:

```{r, eval=FALSE}
sudo apt-get install r-cran-tkrplot
```

To finish our example, let us enter some recombination fractions, for
example, 0.01, 0.12, 0.05, 0.11, 0.21, 0.07, and save it into a
variable named _rf_:

```{r }
rf <- c(0.01, 0.12, 0.05, 0.11, 0.21, 0.07)
``` 

Now, let us use _OneMap_'s function _kosambi_ to do the calculation:

```{r }
kosambi(rf)
```

You can also obtain help on the function _kosambi_ using the
question mark in the same way as done before:

```{r, eval=FALSE}
?kosambi
```

# Importing and exporting data

So far, we have entered the variables in R by typing them directly into the
console. However, in real situations, we usually **read these values
from a file** or a data bank (including files on the internet). 

To learn this procedure, copy and paste the following table into a
text editor (for example, _notepad_) and save it to a file called
_test.txt_ into any directory in your computer (such as _My
Documents_).

        x       y
     2.13    4.50
     4.48    1.98
    10.95    9.29
    10.03   16.25
    12.72   27.38
    24.63   22.60
    22.57   36.87
    29.78   31.73
    19.54   10.42
     7.86   14.68
    11.75    8.68
    23.71   37.39


To read these data set into R, first, you have to set the working
directory. Go to _Session_, then _Set Working Directory_, and _Choose
Directory_, pointing to where you saved the file _test.txt_.

Now let us read the file _test.txt_ into R and store it in a variable
named _dat_. To do this, we can use using the R function _read.table_.
The first argument is the name of the file; the second one indicates
if the file contains a header, that is, if the first line of the file
contains the names of the variables (which is true for our example):

```{r, eval=FALSE}
dat <- read.table(file = "test.txt", header = TRUE)
dat
``` 

```{r, echo=FALSE}
dat <- data.frame(x = c(2.13,4.48,10.95,10.03,12.72,24.63,22.57,29.78,19.54,7.86,11.75,23.71),
                  y= c(4.5,1.98,9.29,16.25,27.38,22.6,36.87,31.73,10.42,14.68,8.68,37.39))

``` 

The second line, with _dat_, is necessary to ask R to print the
contents of the object _dat_ (i. e., the data itself). Inspecting the
object _dat_ you can see a table with 12 rows and two columns. The
names of the columns are _x_ and _y_. We can access the
variables in columns using the dollar sign followed by the column
name:

```{r }
dat$x
dat$y 
``` 

It is also possible to use the function _summary_ to extract some
information about the object _dat_, or about each one of the columns
separately:

```{r }
summary(dat)
summary(dat$x)
summary(dat$y)
``` 

The function _summary_ provides some descriptive statistics about the
variables in the dataset. If you want to export this information to a
file you can use the function _write.table_:

```{r, eval=FALSE}
write.table(x = summary(dat), file = "test_sum.txt", quote = FALSE)
``` 

The first argument is the output of the _summary_ function. Note that
is possible to use a function as an argument of another one. The
second argument is the name of the file in which the summary will be
written. Notice that this will happen in the _working directory_,
previously set through RStudio menus. The third argument eliminates
double quotes from the output file. After running the command, you can
look for the file _test\_sum.txt_ in the working directory you defined
before.

# Classes and methods

In R, every object belongs to a **_class_**. This is a simple concept
that you must remember. For example, the _dat_ object mentioned above
belongs to class _data.frame_. We can obtain this information using
the function _class_:

```{r }
class(dat)
``` 

When we used the function _summary_, it automatically recognized the
class of the object _dat_ and applied a specific procedure developed
for class _data.frame_, which in this case involves the computation of
some descriptive statistics.

This procedure is named _method_. However, other classes of objects
can be used as arguments to function _summary_ and the result will be
different!

For example, let us adjust a linear (regression) model using column _y_ as the
response variable, and column _x_ as the independent one. This can be done
with the function _lm()_:

```{r }
ft_mod <- lm(dat$y ~ dat$x)
ft_mod
``` 

This function is used to fit linear models and, by default, prints
just a formula and the coefficients of the linear regression. Object
_ft\_mod_ is of class _lm_:

```{r }
class(ft_mod)
``` 

So, if we use function _summary_ to obtain more information about the
fitted model, the result will be:

```{r }
summary(ft_mod)
``` 

In this case, function _summary_ recognizes _ft\_mod_ as an object of
class _lm_ and applies a method that shows information about the
fitted model, such as the distribution of the residuals, regression
coefficients, t-tests, and the coefficient of determination ($R^2$),
etc.

Thus, it is possible to use the same function on different classes of
objects to obtain different results. This concept is very important in
_OneMap_ and you must remember it to use the package. For example, in
other vignettes, we will show that depending on the class of the
dataset, which can be _outcross_, _f2_, _backcross_,
_riself_ and _risib_, a certain set of procedures will
be applied. Not by coincidence, these classes correspond to all types
of populations that can be analyzed. The advantage of this approach is
that you do not need to change the function to do a specific analysis;
it will recognize the object type and will adapt accordingly.


# Saving your work

Finally, you may need to save your work to come back to it in another
working session. But before we explain how to do that, let us explain
a few other concepts.

You can save your **_R Script_**, which is the file that has all R
instructions you typed so far. You can later load them and run all
instructions again to get the same results. This is easy: just click
_File_, _Save As_, and choose a directory and a name (usually with the
extension .R, such as Example1.R, etc).

A different thing is to save your **R Session**, with all objects you
created so far (called _R Workspace_). This is not the same, because
once you load the workspace, you will have all the objects already
loaded, not requiring you to do everything again, i. e, running your
script. This will help you to save a lot of time since some of the analyses required to build linkage maps are time demanding.

To do so, click _Session_, then _Save Workspace As_ and choose a
directory and name. In your next session, open RStudio and then go to
_Session_, _Load Workspace_.

Alternatively, you can do that using the R function _save.image_, For
example, if you want to save your analysis in a file named
_myworkspace.RData_, you should use:

```{r, eval=FALSE}
save.image("myworkspace.RData")
``` 

To load:

```{r, eval=FALSE}
load("myworkspace.RData")
``` 

# References

N. Matloff, The Art of R Programming. 2011. 1st ed. San Francisco, CA:
No Starch Press, Inc., 404 pages.

Adler, J. R. 2009. R in a Nutshell. A Desktop Quick Reference.
O'Reilly Media.




