cPbL's LaTeX page

• March 2009:
  • Here's a recipe for writing your UBC thesis using LyX!
• January 2009:
  • Here's a "complete solution" for writing a manuscript-based thesis at U.B.C..
• Circa 2004-2008:
  • Composing a projected presentation / overhead / slides.
    
  • How to deal with large/wide/long tables, especially tables of regression coefficients for econometrics. See cpblTables.sty and my cpblStata.py code, and some comments in my Software page.
  • Writing a university thesis/dissertation, especially at U.B.C., using LyX, including sectionated bibliographies (for U.B.C.'s manuscript-based thesis style). I'm doing this right now, so ask me!
  • Writing a thesis/dissertation at U.B.C., using the ubcthesis class with landscape portions, long/large tables, doublespace of body text only, etc
• Circa 2000-2002:
  • Writing a university thesis, especially at Stanford (and producing a hyperlinked PDF copy of it),
  • Writing technical papers for any AGU journal,
  • Writing any LaTeX bibliography for works in the physical (or other?) sciences,
  • Using a bibliography in the VLF group, STAR Lab, Stanford, or in a community doing related research.
  • Composing a conference poster on material that is already in LaTeX form, if you have access to a poster-sized (e.g. format A0) printer

Introduction

An update [2006]: I now use the LyX interfact to LaTeX nearly exclusively. I am also facing another dissertation, and may be able to do it most of the way this time in a recent version of LyX.

Feel free to ask me questions on material below; I haven't written everything here. Also feel free to send me an email if something was especially useful.

Stanford University Thesis style

One bug exists with the suthesis-2e style as of 2001. That is that if you make a 2-sided printout and the preface ends on an odd page, an extra blank page is needed and missing. Hugh Holbrook (Stanford) provides the following solution, which is implemented in my copy (old?) of suthesis-2e.sty:

Add the three lines
denoted with '+' below to the afterpreface macro in suthesis-2e.sty to
force a clearpage at the end of the preface.

        \fi
+       \if@twoside
+               \cleardoublepage
+       \fi
        \pagenumbering{arabic}
        \pagestyle{headings}}

What I have to offer is help on modifying the font size of the chapter and section headings from this style, as they are large and ugly.  As I write my thesis, I am keeping style changes in cpbl.sty.

From this, you can see how to adjust the look of these headings, as well as several other key modifications / fixes to the standard software. So, the beginning and end bits of my thesis looks as shown below. Note: there are many things listed here, but they are mostly commented out, and the indexing stuff (and more) can be eliminated. My thesis is available on my home page in pdf, hyperlinked pdf, and HTML versions, so you can see whether you like what I got.

\documentclass[11pt,openright,twoside]{report} % draft 
%\documentclass[10pt,draft]{report} % draft, twoside,openright
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% STANDARD LATEX PACKAGES
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[dvips]{graphicx} % Standard. Inclusion of .eps graphics
%\usepackage[pdftex]{graphicx} % Standard. Inclusion of .pdf graphics
\usepackage{makeidx} % Standard.  Indices
% Note on Index: I find that Emacs justifies a paragraph, it inserts extra
% space in multi-word index entries which are line-wrapped. This
% causes multiple entries when using makeindex. Solution is to clean
% up after Emacs! Terrible.
%
% I prefer the first paragraph of each section to be indented, which is not the LaTeX default (see the Companion, p. 28)
\usepackage{indentfirst} % Standard
\usepackage{afterpage} % Standard utility. Used here for
                       % \afterpage{\clearpage}. Actually, not used. (?)
%\usepackage{float} % Included in MiKTeX. Allows ``H'' specifier for floats.
%\restylefloat{table} % See page 150 of the companion. This if or float package.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% STANFORD THESIS AND CPBL CUSTOMIZATIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{suthesis-2e} % Stanford Thesis style
% Change the font size of chapter and section headings, define fig style etc:
\usepackage{cpbl} %Most of my customizations stored here with comments
%\usepackage[light]{draftcopy} % Turn this on for drafts, but Yap
                               %  won't work.
% Don't use the following. If you want different margins, use vpage package!
%\usepackage{cpblMIT} % Drafthead doesn't work in this, but it sets
                     % margins
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHOOSE SECTION NUMBERING DEPTH  ( erase this section: not needed)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Default is that everything down to subsection gets numbered. Below
% lines can change this.
%\addtocounter{secnumdepth}{1} % Number even the subsubsections.
%\addtocounter{tocdepth}{1} % And also show the subsub's in the TableOfContents
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% BIBLIOGRAPHY FORMAT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[square]{natbib}% From CTAN. Used with a huge variety of .bst biblio formats
\citeindextrue % Automatically put reference authors in the index!!!!!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CUSTOMIZE CAPTIONS WITH CAPTION2 PACKAGE
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[small,bf]{caption2}% This is caption2, supported from
                           % CTAN. Customize caption width, font, etc.
\setlength{\captionmargin}{20 pt}
%\abovecaptionskip
%\belowcaptionskip
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% LOAD UP AMS-LATEX TO HELP WRITE MATRICES, ETC
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{amsmath} 
\usepackage{amssymb}% Include extra symbols: \gtrsim and \lesssim
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% EMPLOY AUTOMATIC LINKS, AND ENABLE HYPERREFERENCING, IN PDF OR LATEX
% OUTPUT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\usepackage[pdftex,colorlinks,citecolor={blue},linkcolor={blue}]{hyperref}
%\usepackage[colorlinks,citecolor={blue},linkcolor={blue}]{hyperref}     
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Load xspace package, useful for defining shortcut commands
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{xspace}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHANGE FOOTNOTE SYMBOLS FROM ARABIC NUMBERS TO INTERESTING SYMBOLS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\renewcommand{\thefootnote}{\fnsymbol{footnote}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% INDEXING FEATURES
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\usepackage{index} This is a David Jones package which I haven't
%                    got. See the companion for info.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% TURN OFF DOUBLE-SPACING FOR DRAFTS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\setstretch{1} % Remove this line for non-draft

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Adjust behaviour of float placement (see LaTeX companion)
% using float package.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\floatpagefraction{0.7}
%\renewcommand{\topfraction}{0.75}

\makeindex
\begin{document}

% SOME DEFINITIONS FOR THROUGHOUT DOCUMENT.

%\newcommand{\draftComment}[1]{ {\tiny #1} }  % For drafts
\newcommand{\draftComment}[1]{}               % For non-drafts

\renewcommand{\text}[1]{{{\rm #1}}}  % For use within math mode.

% BELOW ARE INDEXING SHORTCUTS AND TEXT SHORTHAND
\newcommand{\Sections}{Sections\xspace}
\newcommand{\sections}{Sections\xspace}
\newcommand{\figures}{Figures\xspace}
\newcommand{\Index}[1]{#1\index{#1}} % Shorthand. See Companion, p352
\newcommand{\Sindex}[2]{#1\index{#1#2}} % Shorthand. See Companion, p352
\newcommand{\nn}[1]{#1n} % Used to denote that a index ref is in a footnote.

\input{preface} % Load all the data that serves the suthesis-2e style.
% Even the following doesn't work:
\newpage{\pagestyle{empty}\cleardoublepage} % See companion, page 93. This doesn't work, and if the preface ends on an odd page and you're printing 2-sided, you may have to print the preface separately from the body...

\chapter[Introduction]{Introduction}

This work describes optical measurements of high altitude discharges

\chapter{Conclusions and Suggestions}

\section{Conclusions}

The major results of this work may be grouped as follows.

\section{Further Research}

\begin{singlespace}
{\small
\newpage\cleardoublepage \addcontentsline{toc}{chapter}{Bibliography}
  \bibliography{elves,inan,spriteAGU98,sprites,recent,pre1968,bluejets,spriteAGU96,flashes,books,lightning,runaway,spriteAGU99,nitrogen,theses,astronomy}
  \bibliographystyle{aguCpbl} }
\end{singlespace}

\begin{singlespace}
\newpage\cleardoublepage \addcontentsline{toc}{chapter}{Index}
\printindex
\end{singlespace}

\end{document}

\title{\sc Fast Photometric Imaging of High Altitude Optical Flashes Above Thunderstorms}
\author{Christopher Paul Barrington-Leigh}
\dept{Applied Physics}
\principaladvisor{Umran S. Inan}
\firstreader{Sebastian Doniach}
\secondreader{Martin Walt}
\submitdate{September 2000}
\copyrightyear{2001}

\beforepreface

\dedication{To the god of fire.}

\prefacesection{Abstract}

Lightning in the Earth's troposphere is among the largest impulsive
...

\prefacesection{Acknowledgements}

How can I adequately thank everyone who has made the past five years
the most fun period of my life? 
...

\figurespagetrue
\tablespagefalse        % change to \tablespagetrue if you have tables
\afterpreface

[Added May 2001; brief:] Please see the hyperlinked PDF version of my thesis, mentioned above. This is incredibly easy to make, since LaTeX inherently knows about cross-references. Just use the pdflatex program rather than latex to compile your code, and use the PDF compilation options, above and in cpbl.sty, and invoke the hyperref package, as above. Make sure to upgrade to the very latest version before you use this. [I should mention that I have run into a "! TeX capacity exceeded, sorry [pool size=68177]. ...after \ifx \csname br@\x \endcsname" problem running in one implementation, but not in another.] However, some problems are that the colorlinks option of hyperref conflicts with the doublespace package (I have fixed this -- contact me!) and that you will have to have all your .eps figures available as .pdf files. The latter is solved easily with the clever Perl script epstopdf; in Unix I use a C-shell script makePDF.csh to convert all my figures using this program. Other methods of making PDF figures or PDF documents have caused me great and varied frustrations.

Writing papers for AGU journals

LaTeX Bibliography

I never need to enter any bibliographics information by hand.  Here is the process I have been going through:

1. Periodically search INSPEC, which is available for Stanford students from library.stanford.edu, for any publications since 1968 that are of interest.  When you have sought some references (e.g. "find abstract sprites") you can export your findings into a format which we can convert to a .bib file.  (I  believe this format is also used by EndNote, and thus I suspect that bibliographic databases analogous to Inspec for other fields could also export into this format. If not, you will need to modify a Perl program below.)  For instance, I use

mail all export to cpblnova

to send the search results to myself in the EXPORT format (and then save the text file as "inspec.txt" from my email inbox) or better, if I'm using SAMSON (a Stanford telnet program), I can just type

save all export to c:/inspec.txt

to save it to disk on a p.c.
2. Next, run a modified version of Dave Lauben's program, to be run on Unix.  His package includes export2bib which calls cit2let2bib.pl, and I run it like this:

export2bib inspec.txt > sprites.bib

This produces a file in standard format (see Lamport's "LaTeX", section B.1) which can be read by BibTeX.  Not standard is the algorithm for choosing a keyword associated with each reference.  You could change that easily by editing the cit2let2bib.pl file.  I am using a key such as InanApr99 for a work published by Inan (and others) in April of 1999.
3. To make use of this bibliography database, I now include the line

\usepackage{natbib} % From CTAN.  Used in association with a huge variety of .bst bibliography formats.

in the preamble of my LaTeX file and at the end of the document write:

\bibliography{sprites,elves} % Include references in sprites.bib, elves.bib
\bibliographystyle{aguCpbl}      % Use the brilliant author-year referencing system of agu.bst

The latest versions of the natbib.sty package and agu.bst package are available from CTAN. Without all the documentation, etc, all you need is natbib.sty and agu.bst.   However, as you can see in the \bibliographystyle line above, I use aguCpbl.bst, in which I have made a small modification so that it doesn't de-capitalize title words. Now when I need to reference a source, I can use one of the varieties of the \cite command documented in agu.bst to make a reference mid-sentence, at the end of a sentence, in a list, or whatever (honestly -- any formulation I could need!), and to automatically add the item to the printed bibliography.  If there are references with identical author/year designations, they will automatically have a, b, c, etc appended to the designations.

VLF Group Bibliography Database

There are only two important issues for creating and maintaining such a database. One is the format of the citation key. I have decided that Dave Lauben's method of FirstauthorMonthYear (e.g. SmithApr99) is the best alternative. This could be made YnK-compliant. The second is how to organise and update the various database (.bib) files. This is still an open question. The good thing is that they can be multiply redundant when listed (see above) in a \bibliography command. So feel free to suggest new subjects for .bib files... I will be happy to do the INSPEC search and conversion if you can't.

Please help contribute something, and suggest changes. There are a number of things that need working on.

Composing a poster

psresize -H46.78in -W33.05in -pletter bigposter.ps onepage.ps

psresize -H46.78in -W33.05in -pA4 bigposter.ps onepage.ps

Composing "slides" for digital or overhead projection

• if material does not fit on a page, it does not disappear; an extra page gets created (like the ancient slitex slides.sty). That is, pagination is automatic. Like in other document classes, you can start a new page (slide, with title, etc) when you want, but you don't need to worry about things fitting on a single page if you don't want to.
  • The title is repeated on these extra slides (ie subsequent slides without a new title). They appear in smaller text on the right, above a header line. Alternatively, they could appear with a ``cont'd'' suffix or etc.
  • The point is that I'd like to be able to use an existing (e.g. article) document and convert it to slides very easily.
• I'd like to be able to use LyX with it.
• I'd like to be able to use not-so-huge fonts, and turn off all glitz, but
• it should generate PDF bookmarks/TOC etc, and be able to give PDF directives like ``fullscreen'' when compiled to PDF
• some smart image sizing would be nice

So, to use it in LyX: Under document layout, set document class to "foiltex", options to "dvips,headrule,color", and pagestyle to "foilheadings", and under document paper, choose "landscape". Under document preamble, enter:

\usepackage{cpblFoils}
\usepackage[cspex,bbgreekl]{mathbbol} % Eek! This is necessary for expect %mathbb symbol in foils...?!