Appendix B: Latex survival guide

Transcription

1 Appendix B: Latex survival guide The philosophy in this course is that we would like to be good citizens of the scientific community. An important part of being a good citizen is being able to communicate results, papers, and ideas. Since many of our colleagues live in different parts of the world and hence have different resources available to them we cannot always assume that our friends have the same software for preparing manuscripts that we do. Moreover, since we use mathematics as our laboratory tool, how can equations be exchanged easily by . The solution we are choosing in this course is to make use of the open source computing network. In other words, the only requirement that we require is that our colleagues have access to the Internet. There are all sorts of computer software packages available on the Internet; many of them are exactly the same softwares that are presently used at the cutting edges of scientific research. A big advantage is that once we become familiar with these products we have access to them anywhere in the world. Study abroad students from The Claremont Colleges have already been able to use their experience with the open source computing network to help students, workers and scientists in the countries they have visited. In this lab we address the problem as to how to manuscripts and figures to each other. The software package we will use is called LaTeX. This is the same software package that is used by the publishers of most of the scientific articles that you read. LaTeX has a completely different concept than, for example, WORD. Packages such as WORD are actually programs that produce the document the way that the programmers who designed this package wanted it to be produced. In contrast, when we use LaTex we write the program ourselves that will be used to generate the document. Since we are writing the program ourselves we can get an article that looks exactly like we want it to look like. More importantly, the program is written using a text editor (the same editor we will also use to write computer programs that integrate equations) and has the form of an ASCII file. This means that we can easily send it to our friends by and they can then use it locally on their own computer to generate the document. 1

2 1 LaTeX manuals There are several manuals for LaTeX that are available for free on the Internet. Moreover you can also buy a variety of manuals at a bookstore. These notes give a minimum background and set of commands that will be useful for this course. However, as you get more and more experienced using LaTeX I suspect that you will learn more commands. 2 LaTeX There are three components to a LaTeX environment 1. An editor to edit and prepare tex files (named xxxxx.tex) 2. The TeX program itself (latex xxxxx.tex or pdflatex xxxxx.tex) 3. A way to view the result There are many different combinations of the above components. In the past we heavily used MiTeK which is a Latex package designed to work with Windows. In this package all of these components are assembled into a single operating environment. This year we are switching to LINUX so that both PC and Mac users will essentially be working in the same environment. In LINUX there are a number of options available. However, they all work about the same; you will likely have your favorite. Here are some guidelines. 2.1 Text Editor A LaTeX file can be thought of as the instructions that the LaTeX computer program uses to produce your article the way you told it to be produced. Like all computer program files the code is produced using a Text Editor. Note that the important point of a text editor is that the editor adds no editing commands itself. In other words you are completely in control of exactly the way the article will appear in print. You no longer have to worry about the WORD program doing lists the way you do not want. This is why LaTeX is the program used by publishing companies, etc. This year we are switching to a LINUX environment. At the beginning of the course we will work in an opensuse LINUX environment. Here, the text editor is called emacs. When we switch to a Ubuntu LINUX environment, the text editor 2

3 is called gedit. It should be noted that in both environments you can install whatever text editor you want (anything is likely better than Notepad/Wordpad); so you might as well learn one and stick to it. All LaTeX files have the form myfile name.tex, where the extension.tex is the important part. Using the text editors on LINUX we can created a new file with the command emacs xxx.tex or gedit xxx.tex or whatever. If the file already exists we can open it the same way. A nice thing about LINUX is that you can easily find out which text editor your system has by knowing some of the names of existing text editors and using Help or man. It has become extremely easy to download these editors from the Internet and install them on your system. 2.2 Latex versus pdflatex When you use the command latex xxx.tex you generate a file with the extension xxx.dvi. When you use the command pdflatex xxx.tex you will produce a xxx.pdf file. The important difference between these files occurs when we try to incorporate a figure into the document. When we use the command latex xxx.tex all of the figures in the document must be xxx.eps type files. When we use the command pdflatex xxx.tex all of the figures in the document must be xxx.png type files. Why are there two different ways to generate a LaTeX file? The advantage of xxx.pdf files is that they do not require a postscript type printer in order to print. All we need is Adobe Reader which can be freely downloaded from the Internet. A second advantage of the use of pdflatex is that *.png, *.jpg, and *.pdf figures can be incorporated into the document using the \includegraphics. Why worry about xxx.eps files at all? Journals require that final figures be in the xxx.eps format. Thus when most people prepare figures for their documents they will prepare both a xxx.eps and a xxx.png version of the figure (as we will see this is really easy to do). 2.3 Viewing the LaTeX file In opensuse the tool that is used to view a xxx.dvi file is xdvi xxx.dvi. The tool that is used to view a xxx.pdf file is acroread xxx.pdf. 3

4 In Ubuntu the tool that is used to view a xxx.dvi file and a xxx.pdf is evince xxxx.x. 3 Learning LaTeX Most people learn LaTeX by doing it, i.e. their first experience is usually the result of having to prepare their own paper because the journal publisher has asked for it. This is in fact how you will learn to use LaTeX. It s really not very hard. You do need to know the basic structure of the LaTeX file: the various commands that you need come from looking them up as you need them. This is where the Internet is so useful (that s where I found the links listed on your web page). Indeed I had to look up a number of commands that I had never used before in order to make up these notes. Here we focus on preparing the LaTeX file you will use to submit your assignments. In the next few weeks I will show you how to include a bibliography into your document and to cite references within the text. You should regard this as your first step into the scientific world! Structure of a LaTeX file There are three main parts of a LaTeX file: 1. Preamble 2. Body 3. Math modes 4. Bibliography Preamble The preamble is everything from the beginning of your file to the line \begin{document}. It tells the program what fonts and style to use, the title and author of the article, and whether additional packages of commands need to be accessed in order to produce the article. The basic structure of the preamble is 4

5 \documentclass[12pt]{article} \usepackage{graphicx,times} \title{bio--133: Assignment number xxx} \author{your Name\\ Your College} The term 12pt means twelve points. Points are the units that type setters use. This article has been printed using 12pt. If you want smaller print you could use, for example, 10pt, or bigger 14pt and so on. The term article just refers to the style that the paper will be prepared. The other style often used is book. Many other styles are possible. Under \usepackage{} you get to include user packages that are not in the basic LaTeX package. A common one is graphicx which allows you to include figures (either *.eps or *.png)into your document(see below). The user packages times means that the font will be New York Times style. Often journals, such as Nature, have there own package and require you to include it at this line. In fact you could make up your own *.sty file and include it here (minus the extension). Main Body The basic structure of the main body is \begin{document} \maketitle text here \section{your section heading here} text here \subsection{your sub-section heading here} text here \end{document} 5

6 The commands \begin{document} and \end{document} are mandatory. The line \maketitle is included only if you made use of the lines \title{} and/or \author{} in the preamble (which you will need to do for your assignments). The lines \section{} and \subsection{} generate, respectively, the appropriate section and sub section numbers, whereas the lines \section*{} and \subsection*{} generate the same headings without the numbers. Math modes Of course the whole point of LaTeX is to easily write text that includes equations and mathematical symbols. The fact that we use only a text file and the software can be downloaded from the Internet by anyone who has a connection is where the popularity and power of this program comes from. Indeed scientists and mathematicians are so familiar with the commands that many use them in their s to each other. The commands are actually pretty simple and once you get the hang of it you can guess what the command without having to look it up. However, until your brain accumulates the commands that you most frequently use it is a bit of a nuisance going back and forth between manual and your document. Inserting mathematical expressions into a text line You use $..$ to insert equations and mathematical symbols into text. For example, we have $math expression$, where $symbol$ is. What about equations? The first question to ask is whether you want the equation numbered or not. If you do not want the equation numbered, then \[ your equation, e.g. a=b \] If you want the equation numbered, but don t what to refer to it in your text, then \begin{equation} your equation here, e.g. a=b \end{equation} 6

7 Finally, if you want the equation numbered and want to be able to refer to that equation in the text, then \begin{equation} your equation here, e.g. a=b \label{your label here} \end{equation} The big difference between the last two options is the inclusion of the line \label{} in the latter. You can label anything this way, e.g. a figure, table, section heading, chapter, and so on. A useful hint is to use a label that you can remember and which in some way describes what it is that you have labeled. Here s how you refer to it in the text (\ref{label}) yields (label) Chapter \ref{label} yields Chapter label Symbols LaTeX is fun because you get to use all sorts of interesting symbols. Here are some symbols that are frequently used in latex documents α \alpha β \beta τ \tau ϑ \vartheta π \pi γ \vartheta φ \phi δ \delta κ \kappa ρ \rho ϕ \varphi ɛ \epsilon λ \lambda µ \mu σ \sigma ψ \psi ω \omage η \eta ξ \xi Γ \Gamma Λ \Lambda Ψ \Psi \Delta Ω \Omega Θ \Theta Π \Pi Φ \Phi \sum \int \oint \prod cos \cos sin \sin tan \tan log \log ± \pm \le \ll \ge \gg \bullet \circ \diamond \approx \sim \simeq \propto \equiv \in \leftarrow \rightarrow For a comprehensive list of all of the Latex symbols that are available see 7

8 Super and sub-scripts Subscripts and superscripts are made, respectively, with the commands _ and ˆ. Sums and integrals (under symbols on previous page) have upper and lower limits. We can use the symbols _ and ˆ to introduce these limits. The command \sum_{i=1}ˆ{n} produces n i=1 and the command \int_{a}ˆ{b} produces b a Two special considerations must be kept in mind when type setting integrals. 1. There should be a little extra space between the differential operators, e.g. dx and the integrands preceding it. Thus \intˆ{b}_{a} f(x) dx should be \intˆ{b}_{a} \ dx 2. According to the International Standards Organization the d in dx should be upright. This means that if we want to be compliment with the world we need to type \intˆ{b}_{a} f(x) \ \mathrm{d}x Useful mathematical stuff Roots: The command for the n-th root of an expression is \sqrt[n]{expression} For example \sqrt[3]{2} produces 3 2 In the case of a square root you do not need the [2]. Fractions: The command for a fraction is 8

9 \frac{expression_a}{expression_b} For example, \frac{aˆ2+bˆ2}{y+x} yields a 2 + b 2 y + x Automatic sizing of brackets: Mathematics often contains bracketing symbols, usually in pairs that enclose part of the formula. Obviously when we print the text we want these brackets to be scaled appropriately with respect to the mathematical expression(s) they surround. This is accomplished by typing \left lbrack expression \right rbrack where lbrack indicates [,\{,( and rbrack indicates ],\},) and we note that the brackets {,} require a \. The math environments: The math environments have the basic structure \begin{environment} commands here \end{environment} The math environments that we will use are called array, eqnarray, and figure. As you will see the first two environments allow you to include systems of equations, matrices, etc into your text and the last one introduces figures. There is also a math environment that introduces tables; however, we will not use this environment in this course. The array environment: One of the most useful mathematical environments is the array environment. A single argument specifies the number of columns and the alignment of items within the columns. For each column, there is a single letter in the argument that specifies how items in the column should be positioned: c for centered, l for flush left and r for flush right. Within the body of the environment, adjacent rows are separated by // and adjacent items within a row are separated by an & character. It should be noted that array is activated in math mode (in contrast to eqnarray). For example, the array environment 9

10 \[ \begin{array}{clcr} a+b+c & uv & x-y & 46 \\ a+b & u+v & z & 1234 \\ a + 3u/v & uvˆ2 & 5176 \end{array} \] generates a + b + c uv x y 45 a + b u + v z 123 a u/v uva 5436 Now the reason why array is so important is that we can use it in so many different ways. For example how can be rewrite the above equation as a matrix a + b + c uv x y 45 a + b u + v z 123 a u/v uva 5436 All we need to do is type the commands \[ \left( \begin{array}{clcr} a+b+c & uv & x-y & 45 \\ a+b & u+v & z & 123 \\ a & u/v & uva & 5436 \end{array} \right) \] A frequent problem is to type set equations of the following form { y if y > 0 x = z + y otherwise The becomes in LaTeX \[ x= \left\{ \begin{array}{ll} 10

11 y & \mbox{if $y>0$} \\ z+y & \mbox{otherwise} \end{array} \right. \] where we see how to type words inside of math mode (use \mbox{}) and what to do if you include only one member of a bracket pair (type a. where the missing lbrack or rbrack should be). The eqnarray environment: The eqnarray environment is especially useful for typing multi line equations. In many ways the eqnarray environment works the same way that the array environment works. Here are some useful examples (note adding the * deletes the equation number). \begin{eqnarray} x & = & 17y \\ y & > & a \nonumber \\ & & b + 78 \end{eqnarray} generates x = 17y (1) y > a b + 78 (2) where we see that the addition of \nonumber removes the equation number from the line it is typed on. On the other hand if we replaced eqnarray by eqnarray* no equations numbers would appear. If the formula is too long to put into a single line, then we must tell LaTeX that the - or + is a binary operator. This is done by starting the formula with an invisible first term, produced by \mbox{} with a null argument. Thus the commands \begin{eqnarray*} y & = & a + b + c + d + e + f + g \\ & & \mbox{} + h + j + k + l \end{eqnarray*} 11

12 generates y = a + b + c + d + e + f + g + h + j + k + l Another way to divide an equation across multiple lines is to split it as follows \begin{eqnarray*} \lefteqn{a+b+c+d =} \\ & & e+f+g+h+ \\ & & j + k + l + m + n \end{eqnarray*} where we obtain a + b + c + d = e + f + g + h + j + k + l + m + n The figure environment In order to introduce figures into our article we need to pay attention to the following points: 1. We must include the user package graphicx in the preamble of your La- TeX file. 2. The figure must be in the form of either a *.eps file or a *.png file. 3. Both types of files can be produced by MATPLOTLIB (Pylab). 4. When you use *.png, then you must use the command pdflatex. This approach is good since you can use Adobe Acrobat Reader (can be downloaded for free from the Internet) to print out your article on your own printer. 5. If you have access to a postscript printer (most of us do not), then you can use *.eps figures and the LaTeX command to process your article. The environment has the form 12

13 \begin{figure} \includegraphics[width=.9\textwidth]{filename.eps} \caption{your text here} \label{your label here} \end{figure} 13