. . . . . .

LATEX Basics

Kristen Sauby, Rosana Zenil-Lopez, Gabriela Blohm

Department of BiologyUniversity of Florida

April 1, 2011

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 1 / 29

. . . . . .

What is LATEX?

a programming language used to create attractive andconsistently formatted documents

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 2 / 29

. . . . . .

Why would you want to use LATEX?

consistent formatting

fancy fonts

make posters, presentations, and other types ofdocuments

automatic numbering of sections, figures, tables, andformulas

creation of a bibliography and index

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 3 / 29

. . . . . .

Why would you want to use LATEX?

consistent formatting

fancy fonts

make posters, presentations, and other types ofdocuments

automatic numbering of sections, figures, tables, andformulas

creation of a bibliography and index

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 3 / 29

. . . . . .

Why would you want to use LATEX?

consistent formatting

fancy fonts

make posters, presentations, and other types ofdocuments

automatic numbering of sections, figures, tables, andformulas

creation of a bibliography and index

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 3 / 29

. . . . . .

Why would you want to use LATEX?

consistent formatting

fancy fonts

make posters, presentations, and other types ofdocuments

automatic numbering of sections, figures, tables, andformulas

creation of a bibliography and index

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 3 / 29

. . . . . .

Why would you want to use LATEX?

consistent formatting

fancy fonts

make posters, presentations, and other types ofdocuments

automatic numbering of sections, figures, tables, andformulas

creation of a bibliography and index

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 3 / 29

. . . . . .

Why would you want to use LATEX?

!"##$ %"##& '"##( )"##g

*"##+ ,"##- ."##g /"##g

D. Taraborelli !2008", The Beauty of LATEX

Some rights reserved. ##$%&$'(

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 4 / 29

. . . . . .

Why would you want to use LATEX?

include, align, and number attractive mathematicalformulas

n!

k !(n − k)!=

(n

k

)(1)

limx→∞

exp(−x) = 0 (2)

Am,n =

a1,1 a1,2 · · · a1,na2,1 a2,2 · · · a2,n...

... . . . ...am,1 am,2 · · · am,n

(3)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 5 / 29

. . . . . .

Why would you want to use LATEX?

Embed R code and objects

> sample(100, 5)

[1] 85 79 82 62 73

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 6 / 29

. . . . . .

Why would you want to use LATEX?

Embed R code and objects

> library(xtable)

> counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)

> outcome <- gl(3, 1, 9)

> treatment <- gl(3, 3)

> print(xtable(data.frame(treatment, outcome, counts)))

treatment outcome counts1 1 1 18.002 1 2 17.003 1 3 15.004 2 1 20.005 2 2 10.006 2 3 20.007 3 1 25.008 3 2 13.009 3 3 12.00

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 7 / 29

. . . . . .

We’ll Work Through an Example Together

Go to latexlab.org or open the example .tex file on yourcomputer.

We’ll use this example document to understand better thestructure of LATEX documents.

In LATEX lab, select“split” (near the bottom left of thepage)

this lets us see the .tex document and the ouputdocument (the compiled document) in the samewindow.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 8 / 29

. . . . . .

We’ll Work Through an Example Together

Go to latexlab.org or open the example .tex file on yourcomputer.

We’ll use this example document to understand better thestructure of LATEX documents.

In LATEX lab, select“split” (near the bottom left of thepage)

this lets us see the .tex document and the ouputdocument (the compiled document) in the samewindow.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 8 / 29

. . . . . .

We’ll Work Through an Example Together

Go to latexlab.org or open the example .tex file on yourcomputer.

We’ll use this example document to understand better thestructure of LATEX documents.

In LATEX lab, select“split” (near the bottom left of thepage)

this lets us see the .tex document and the ouputdocument (the compiled document) in the samewindow.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 8 / 29

. . . . . .

What types of documents can you make in LATEX?

Classes of LATEX documents include:

article

book

beamer (for presentations)

and more

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 9 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

preamble (commands that affect the entire document)

top matter (title, date, authors, etc.)

the written document (abstract, sections, etc.)

appendices

table of contents

bibliography

comments (i.e., text that does not show up in thefinal document)

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 10 / 29

. . . . . .

LATEX Document Structure

Begin your document using the following command:\documentstyle[options]{class}

where options include such specifications as

font size

number of columns

paper size

and the class is the type of document that you want tomake

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 11 / 29

. . . . . .

LATEX Document Structure

Next list the packages to be used:\usepackage[options]{package}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 12 / 29

. . . . . .

LATEX Document Structure

The preamble can also include:

title and author information

date

font specification

and more

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 13 / 29

. . . . . .

LATEX Document Structure

After completing the preamble begin the document:

\begin{document}

At the end of the document you must include thecommand:

\end{document}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 14 / 29

. . . . . .

Compiling Your LATEX

Once you have the document set up, you can then addtext, figures, formulas, tables, etc. to the document.

When you are ready to create a PDF, you“compile” thedocument.

In LATEX lab, go to the“Compiler”drop-down menu andselect“Compile”.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 15 / 29

. . . . . .

Types of Functions in LATEX

Ways to organize or include data:

verbatim

itemize

enumerate

figure

table

tabular

Try adding a bulleted list to the example .tex file.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 16 / 29

. . . . . .

Types of Functions in LATEX

Ways to organize or include data:

verbatim

itemize

enumerate

figure

table

tabular

Try adding a bulleted list to the example .tex file.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 16 / 29

. . . . . .

Types of Functions

You can also include comments (that don’t appear in thefinal, compiled document) by using the % symbol.

Anything after the % symbol will not be evaluated byLATEX when compiling the document.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 17 / 29

. . . . . .

Including Math in LATEX

Note that our example .tex file includes\usepackage{amsmath} in the preamble.

This package lets us include mathematical formulas in ourLATEX document.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 18 / 29

. . . . . .

Including Math in LATEX

The example .tex file includes this formula:\begin{align}E &= mcˆ2 \\m &= \frac{m 0}{\sqrt{1-\frac{vˆ2}{cˆ2}}}\end{align}The“align”command is specific to mathematical formulasand allows you to align the“=”symbol of multipleformulas.

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 19 / 29

. . . . . .

Using R and LATEX

Unfortunately, LATEX lab doesn’t support Sweave...

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 20 / 29

. . . . . .

Using R and LATEX

To include R objects/code in a LATEX document:

In the preamble include:

\usepackage{Sweave}

After \begin{document} include:

<<include Sweave options here>>=include R data here@

Save your file with the“.Rnw”extension instead of“.tex”

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 21 / 29

. . . . . .

Using R and LATEX

To include R objects/code in a LATEX document:

In the preamble include:

\usepackage{Sweave}

After \begin{document} include:

<<include Sweave options here>>=include R data here@

Save your file with the“.Rnw”extension instead of“.tex”

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 21 / 29

. . . . . .

Using R and LATEX

To include R objects/code in a LATEX document:

In the preamble include:

\usepackage{Sweave}

After \begin{document} include:

<<include Sweave options here>>=include R data here@

Save your file with the“.Rnw”extension instead of“.tex”

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 21 / 29

. . . . . .

Using R and LATEX

To include R objects/code in a LATEX document:

Execute the“.Rnw”fileI using your text editorI using R

This produces a“.tex”file which you can then compile

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 22 / 29

. . . . . .

Using R and LATEX

Example:

<<>>=sample(100,5)@

Will produce:

> sample(100, 5)

[1] 72 67 41 24 83

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 23 / 29

. . . . . .

Using R and LATEX

Use the function xtable from library xtable to includetables:<<Results=TEX>>=library(xtable)counts <- c(18,17,15,20,10,20,25,13,12)outcome <- gl(3,1,9)treatment <- gl(3,3)print(xtable(data.frame(treatment, outcome, counts)))@

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 24 / 29

. . . . . .

Using R and LATEX

Use the function xtable from library xtable to includetables

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 25 / 29

. . . . . .

Using R and LATEX

print(xtable(data.frame(treatment, outcome, counts)))produces this table:

treatment outcome counts

1 1 1 18.002 1 2 17.003 1 3 15.004 2 1 20.005 2 2 10.006 2 3 20.007 3 1 25.008 3 2 13.009 3 3 12.00

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 26 / 29

. . . . . .

Use as a Reference Manager

make a“.bib”file containing reference information

include \usepackage{cite} in your preamble

use commands such as \citep{your-ref-name} in thebody of your document where you want to include acitationinclude the following commands at the end of thedocument to compile the reference list:

I \bibliography{name-of-your-bib-file}I \bibliographystyle{name-of-ref-style}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 27 / 29

. . . . . .

Use as a Reference Manager

make a“.bib”file containing reference information

include \usepackage{cite} in your preamble

use commands such as \citep{your-ref-name} in thebody of your document where you want to include acitationinclude the following commands at the end of thedocument to compile the reference list:

I \bibliography{name-of-your-bib-file}I \bibliographystyle{name-of-ref-style}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 27 / 29

. . . . . .

Use as a Reference Manager

make a“.bib”file containing reference information

include \usepackage{cite} in your preamble

use commands such as \citep{your-ref-name} in thebody of your document where you want to include acitation

include the following commands at the end of thedocument to compile the reference list:

I \bibliography{name-of-your-bib-file}I \bibliographystyle{name-of-ref-style}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 27 / 29

. . . . . .

Use as a Reference Manager

make a“.bib”file containing reference information

include \usepackage{cite} in your preamble

use commands such as \citep{your-ref-name} in thebody of your document where you want to include acitationinclude the following commands at the end of thedocument to compile the reference list:

I \bibliography{name-of-your-bib-file}I \bibliographystyle{name-of-ref-style}

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 27 / 29

. . . . . .

Good Resources for LATEX

LATEX Wikibook

Online LATEX Equation Editor

Sweave User Manual

A Beamer Quickstart

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 28 / 29

. . . . . .

This is a very brief overview of LATEX but we hope that youhave learned something useful!

Questions?

Sauby, Zenil, Blohm (U of Fl) LATEXBasics April 1, 2011 29 / 29