Guidelines and Examples for Preparing Math Clinic Report in LaTeX

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1 Guidelines and Examples for Preparing Math Clinic Report in LaTeX Stephen Billups October 9, 2007 Abstract This document explains how to prepare your Math Clinic Report in LaTeX, and gives some concrete examples of how to do various things in LaTeX. 1 Introduction This document has two main purposes: 1) to give specic instructions on how Math Clinic reports should be prepared in LaTeX (to ensure consistency), and 2) to provide some examples of how various things can be done in LaTeX (so you can imitate the commands in your report). In preparing this document, I followed the instructions I am giving now, so you can use this document as a template for creating your own report. (see the input les grp9.tex, grp9-body.tex, and grp9-bib.bib). You can recreate this document using the following instructions: 1

2 1. Copy the following les into your working directory. (You can download these les from www-math.cudenver.edu/ billups/courses/guides). clinicpreamble.tex clinicmacros.tex grp9.tex grp9-body.tex grp9-bib.bib grp9-pic1.png 2. Type the following commands: > latex grp9 > bibtex grp9 > latex grp9 > pdflatex grp9 Note that you have to call latex multiple times in order to get all of the references correct!! Section 2 gives specic instructions regarding le formats, naming conventions, and creating your bibliography, which will be required for all clinic reports. Following that, Section 4 gives examples of how to do various things in LaTeX (such as including graphics, making tables, formatting algorithms, and including computer code.)

3 2 Clinic Instructions 2.1 Files All les that you create for your clinic report should be named starting with 'grpx', where X is your team number. For example, if you are in team 9, your le names should start with 'grp9'. Your report will consist of at least the following three les: File Name grpx.tex grpx-body.tex grpx-bib.bib Description A short header le The body of your report Your BibTeX le The header le sets things up to format your report as a standalone article (using double spacing). When I prepare the nal combined report for the class, I will use a dierent header le (so that each team report will be incorporated as a separate chapter in the combined report). To prepare your header le, all you need to do is edit the title and author commands, and change all occurences of 'grp9' to whatever your group ID is. The body le holds your report. This le should not have a preamble (\documentclass,\begin{document},\end{document}, etc), since those commands are provided in the header le. The BibTeX le will be described in Section 3.1 below. In addition to the three les above, you may also create graphics les. The le names for these should also begin with 'grpx-'. As noted in Section 4.1, I recommend that you use the.png format for graphics.

4 Table 1: Referencing Commands Entity xxx Referencing Command Section (or subsections) sec \secref Appendix app \appref Chapter chap \chapref Equation eq \eqref Figure g \figref Table tab \tabref Theorem thm \thmref Lemma lem \lemref Denition def \defref Corollary cor \corref Proposition prop \propref Assumption ass \assref Algorithm alg \algref Problem prob \probref 3 Labeling and Referencing commands When labelling sections, gures, tables, etc., your labels should have the format xxx:gggg-zzzzzz, where xxx is a string that identies the type of entity you are labeling (see denitions in Table 1, gggg is your group id (e.g., grp1, grp2, etc.), zzzzzz is a string describing what you are labelling. To reference the labelled entities, you can use the appropriate referencing command, shown in Table 1. For example, you might label your introduction as follows:

5 \section{introduction}\label{sec:grp1-introduction} And then you can reference your introduction with the command \secref{grp1-introduction}. 3.1 BibTeX Your bibliography must be prepared using BibTeX, using the plain-annote bibliography style. To do this, you need to create a le called 'grpx-bib.bib'. This le will include entries for each of your references: For example, here is a sample author title = "R. Mifflin", = "Semismooth and semiconvex functions in constrained optimization", journal = "Siam Journal on Control", year = "1977", volume = "15", pages = " ", annote = "{This is the first appearance in the literature of the concept of a semismooth function. Semismooth functions are closed under addition and composition, and also guarantee the local convergence of nonsmooth generalizations of Newton's method.}" }

6 The above entry species a journal article. But there are many other choices in BibTeX: book, techreport, phdthesis, unpublished, etc. Depending on the type of publication, you will need to specify dierent information in the BibTeX entry. To get more examples on specifying.bib les, you can look at the grp9-bib.bib le that you copied to your directory. The BibTex Key: Each BibTeX entry must be identied with a unique string, called the key, which is specied on the rst line, immediately following the "". In the above example the key is "miin:semismooth". You should use the following convention in creating keys: Single author: <last name>:<keyword> (Example: miin:semismooth) Two authors: <1st author>.<2nd author>:<keyword> (Example: billups.watson:probabilityone) More than two authors: <1st author>.<2nd author>.ea:<keyword>. (Example: billups.dirkse.ea:comparison). In the above, <keyword> species the rst nontrivial word in the title. The key is referenced in a \cite command in LaTeX to reference the citation. For example: \cite{mifflin:semismooth}. Nocite. If you want a reference to appear in your bibliography, but don't actually cite it anywhere in your document, you can use the \nocite command (for example, \nocite{billups.watson:probability-one}). If you want all references from your.bib le to appear in the bibliography le, you can include the command \nocite{*}.

7 Referencing web pages. Referencing web pages is a bit risky because the web page may change, move, or even be deleted. So it is generally preferable nd other references whenever possible. But if you believe the web page is stable and the information is not easily available any other way, then go ahead and reference the web page. An example of such a web page is [2]. Also, some publications are available in print, but are also available online. See [1] for an example. 4 Examples This section demonstrates how to do various things in LaTeX. 4.1 Graphics You can include graphics les with either and.eps or.png sux using La- TeX. (NOTE: the clinicpreamble.tex le includes the command 3 \usepackage{graphicx}, which enables the inclusion of graphics les). Whenever possible, I recommend using the.png sux, because this is also compatible with Powerpoint. Here is an example of how to do it. Comments about Figure 1: Notice how I labeled the gure: the '\label' command is inside of the '\caption' command. It wasn't necessary to include the graphics within a gure, but it is good practice.

8 Figure 1: Cell Cycle There are a variety of ways to specify the size of the graphic. The command I used here '[width=.5\textwidth]' says to make the graphic ll up 50% of the width of the text. You could do something similar using heights (e.g. '[height=.5\textheight]'. You can also specify absolute sizes (e.g. inches, etc.), but that is not good practice. 4.2 Algorithms The standard way to format algorithms in LaTeX is using the tabbing environment. See the grp9-body.tex le to see how the following algorithm is formatted: j=1 while j <= maxit xj = x+alpha*d;

9 phij = feval(fun,xj,1); % phij= phi(x+alpha*d) if (phij > phi0+c1*alpha*phider0 (i>1 && phij >= philo)) ahi = alpha; end; end; Notice that I had to add backslashes in front of some symbols to get things formatted correctly. As you can see, this can get a bit tedious, so if you have a lot of code you want to include in your report, I recommend using the verbatim environment (as shown in Appendix A). 4.3 Tables Here is a table that demonstrates various formatting options. Dimensions Problem Inputs Outputs Comp Summation of n 1 θ(n) Ω(n) Ω(n 1/2 ) Ω(n 1/3 ) n numbers Multiply two 2n 2 n 2 θ(n 3 ) Ω(n 2 ) Ω(n) Ω(n 3/4 ) n n matrices Solving an n n n 2 + n n θ(n 3 ) Ω(n 2 ) Ω(n) Ω(n 3/4 ) linear system (by G.E.) Accountant's n + 1 n θ(2 n ) Ω(2 n/2 ) Ω(2 n/3 ) Ω(2 n/4 ) Nightmare

10 4.4 Math max i T x iv i (t i ) subject to b i t i e i d i if x i = 1 t i + d i + s ij t j if x i = 1, x j = 1 and y ij = 1 y ij + y ji = 1 d i 0 x i, y ij {0, 1} for all i, j. (1) 5 More resources This document provides examples of just a few things you can do in La- TeX. For more information, here are a couple of free resources about LaTeX available for download o of the web: LaTeX quick start guide. Harvey Greenberg's Concise Introduction to LaTeX. A Computer Code Sample j=1; while j <= maxit xj = x+alpha*d; phij = feval(fun,xj,1); % phij= phi(x+alpha*d) % test first Wolfe condition at current value of alpha

11 if (phij > phi0+c1*alpha*phider0 (i>1 && phij >= philo)) % alpha is too big, so desired step % length is in the interval (alo,alpha). ahi = alpha; phihi = phij; % phihi = phi'(ahi) break; % proceed to zoom end; end; References [1] S. C. Billups, L. Lana, and P. Gee. Clustering gene expression proles via permutation vectors. Ccm technical report, University of Colorado at Denver and Health Sciences Center, Available for download at Presents an algorithm for clustering gene expression proles based on using permutation vectors. [2] H.J. Greenberg. Mathematical Programming Glossary. INFORMS Computing Society, An extensive glossary of terms used in the mathematical programming literature.

Note for the LaT E X version of this Document

Note for the LaT E X version of this Document BibT E XisaLaT E X facility for creating bibliography les. The LaT E X manual, which is available through the bookstores, contains a section that explains