Katherine

I can help you out on a couple of things.

> * Being able to keep chapters as separate documents, and yet have the
> numbering continue from chapter to chapter. The Table of Contents and Index
> should still be able to produce correct page information automatically.

You can use the include feature (Inset, then  Include File).  I did this for my
thesis.  Had a seperate file for each chapter.

> * Word count. Remember, dissertations and their specific sections are required
> to have certain word counts. I have simply turned my file into text on a
> regular basis to make such a count, but it seems wasteful.

I used the spell checker to count the number of words.  You get a count at the
end.
  
> * Markup for sub-titles. Title and sub-title need to be separate if
> someone wants to use headings at the top of their pages. My numbers have
> frequently been run off the side of the page. 

This can all be done with raw latex (but don't ask me how).
 
> * Top corner numbering without a heading. I see no option for this that I can
> find.

You have full control over your headers.  Please take a look at the attached
layout file which I used for my thesis (it's a piece of crap but it did the
job), specifically the preamble section.

> * Formats set up for CD-ROMs, URLs and computer programs in GBib.

You can try tkbibtex.  This has these options (I think)
http://www.cat.csiro.au/dmt/programs/autom/pic/tkbibtex.html

> * Automatic alphabetical ordering by key, author or title in GBib.

Try tkbibtex.

I think if you plan to get full control over the formatting of your doc then you
need access to a latex manual.  I eventually got myself one when writing my
thesis and was a great help.

Hope the suggestion help.

Ciao
Ben 
--
_________________________________________

Ben Cazzolato

Fluid Dynamics and Acoustics Group
Institute of Sound and Vibration Research
University of Southampton,
Southampton, SO17 1BJ
UK

Email:  [EMAIL PROTECTED], or
        [EMAIL PROTECTED], or
        [EMAIL PROTECTED], or

Work:   +44 (0)1703 594 967
Fax:    +44 (0)1703 593 190
Mobile: +44 (0)790 163 8826

Web Page : http://www.soton.ac.uk/~bscazz/
_________________________________________

#% Do not delete he line below; configure depends on this
#  \DeclareLaTeXClass[book]{PhD Thesis}
# Report textclass definition file. Taken from initial LyX source code
# Author : Matthias Ettrich <[EMAIL PROTECTED]>
# Transposed by Pascal Andr� <[EMAIL PROTECTED]>
# Heavily modifed and enhanced by serveral developers.

#This is to keep styles in a logical order
Style Standard
 End
Style Chapter
 End
Style Section
 End
Style Subsection
 End
Style Subsubsection
 End
Style List
 End
Style Description
 End
Style Itemize
 End
Style Enumerate
 End
Style TitlePage
 End
Style Bibliography
 End
Style Definition
 End
Style Lemma
 End
Style Theorem
 End
Style Proof
 End
Style Note
 End
Style Paragraph
 End
Style Subparagraph
 End
Style LaTeX
 End
Style Example
 End
Style Appendix
 End
 
# Input general definitions
Input stdclass.inc

# Global parameters.
Sides           2
PageStyle       Fancy
# I had to comment these out cause they fucked up the numbering style
# SecNumDepth     3
# TocDepth        2


# a few changes to the bibliography
Style Bibliography
  TopSep		4
  LabelString		Bibliography

  # label font definition
  LabelFont 
    Series		Bold
    Size		Huge
  EndFont
End

Style TitlePage
  LatexType		Environment
  LatexName		mytitlepage
End


Style Chapter
  LatexType		Command
  LatexName		chapter
  TopSep		4
  # label font definition
  Font 
    Series		Bold
    Size		Huge
  EndFont
End


Style Appendix
  LatexType		Command
  LatexName		appendix
  TopSep		4
  # label font definition
  LabelType             Counter_Chapter
  LabelString           "Appendix "
  LabelStringAppendix   "Appendix "
  Font 
    Series		Bold
    Size		Huge
  EndFont
End

# Including the maths stuff
#Input phd-maths.inc

Preamble
\usepackage{amsmath,amsthm}
\usepackage{amsfonts}

\theoremstyle{plain}
\newtheorem{thm}{Theorem}[chapter] %% Comment out for sequentially-numbered

%\numberwithin{equation}{section} %% Comment out for sequentially-numbered
%\numberwithin{figure}{section} %% Comment out for sequentially-numbered

% This line makes the Figure title use Fig.
%\def\figurename{Fig.}
 

\newenvironment{mytitlepage}
 {
  \thispagestyle{empty}
  \center
 }

%\newcommand\mychapternum
% {
%  \if@openright\cleardoublepage\else\clearpage\fi
%  \ifnum \c@chapter<1 \pagenumbering{arabic}\fi
%  \thispagestyle{plain}%
%  \global\@topnum\z@
%  \@afterindentfalse
%  \secdef\@chapter\@schapter
% }

%\newcommand\mychapter[1]
% {
%  \chapter*
%   {
%    #1
%    \@mkboth{\MakeUppercase{#1}}{\MakeUppercase{#1}}
%   }
%  \addcontentsline{toc}{chapter}{#1}
% }


%\renewcommand\listoffigures{%
%    \if@twocolumn
%      \@restonecoltrue\onecolumn
%    \else
%      \@restonecolfalse
%    \fi
%    \chapter*{\listfigurename
%      \@mkboth{\MakeUppercase\listfigurename}%
%              {\MakeUppercase\listfigurename}}%
%    \addcontentsline{toc}{chapter}\listfigurename
%    \@starttoc{lof}%
%    \if@restonecol\twocolumn\fi
%    }

%\renewcommand\listoftables{%
%    \if@twocolumn
%      \@restonecoltrue\onecolumn
%    \else
%      \@restonecolfalse
%    \fi
%    \chapter*{\listtablename
%      \@mkboth{%
%          \MakeUppercase\listtablename}{\MakeUppercase\listtablename}}%
%    \addcontentsline{toc}{chapter}\listtablename
%    \@starttoc{lot}%
%    \if@restonecol\twocolumn\fi
%    }

%\renewenvironment{thebibliography}[1]
%     {\chapter*{\bibname}
%%        \@mkboth{\MakeUppercase\bibname}{\MakeUppercase\bibname}}%
%      \addcontentsline{toc}{chapter}\bibname
%      \list{\@biblabel{\@arabic\c@enumiv}}%
%           {\settowidth\labelwidth{\@biblabel{#1}}%
%            \leftmargin\labelwidth
%            \advance\leftmargin\labelsep
%            \@openbib@code
%            \usecounter{enumiv}%
%            \let\p@enumiv\@empty
%            \renewcommand\theenumiv{\@arabic\c@enumiv}}%
%      \sloppy
%      \clubpenalty4000
%      \@clubpenalty \clubpenalty
%      \widowpenalty4000%
%      \sfcode`\.\@m}
%     {\def\@noitemerr
%       {\@latex@warning{Empty `thebibliography' environment}}%
%      \endlist}


\pagenumbering{roman}



%**********************************************************
% The stuff below here is all formatting
%**********************************************************






% Use the table of contents package
\usepackage[nottoc]{tocbibind}
% Rename the Bibliography to References
\renewcommand{\tocbibname}{References}

% This is to enable me to make an index
\usepackage{makeidx}
\makeindex

% This is so I can use Harvard style citations
\usepackage{harvard}
%\usepackage{natbib}
%\renewcommand{\cite}{\citep}
%\newcommand{\citeasnoun}{\citet}
%\renewcommand{\citename}{\citeauthor}

% This is to force duplex printing on the HP5Si
\special{header=/home/bscazz/latex/printing/dup_on.ps}

% The following line allows the tables to expand to accomodate sub and superscripts
\usepackage{tabls}

% This allows user to define font type for Chapter/Section labels
\usepackage{sectsty}
\allsectionsfont{\fontfamily{phv}\selectfont}

% The line below defines a font type (Helvetica)
\newcommand{\helv}{%
\fontfamily{phv}\fontsize{10}{11}\selectfont}

% These two lines change the header style, ie lowecase
\lhead{\nouppercase{\rightmark}}
\rhead{\nouppercase{\leftmark}}

% The following line removes the ruler line in the header
\renewcommand{\headrule}{}

% The follwing lines define where the stuff goes in the headers
\fancyhf{}
\fancyhead[LE,RO]{\helv \bfseries \thepage}
\fancyhead[LO]{\rightmark}
\fancyhead[RE]{\leftmark}

% This is an attempt to remove the page no from the footer
\fancyfoot{}

% Definition for the Thumb index - Size of blob
\setlength{\unitlength}{18mm}
\newcommand{\blob}{\rule[-.2\unitlength]{2\unitlength}{.5\unitlength}}

% Define right blob
\newcommand\rblob{
  \begin{picture}(0,0)
    \put(1.0,-\value{chapter}){\blob}
  \end{picture}}

% This line allows two types of header definitions: one for the chapter pages and one for normal
\pagestyle{fancyplain}
% The [] indicates the even pages.
%The first term in \fancyplain is the plain style (for chapters) and the second is for the normal pages 
\cfoot[\fancyplain{}{}]{\fancyplain{\helv \bfseries \thepage}{}}
\rhead[\fancyplain{}{\helv \nouppercase \leftmark}]{\fancyplain{}{\helv \bfseries \thepage}}
% Put this line at the begining of Chapter 1 if you want thumb marks
%\rhead[\fancyplain{}{\helv \nouppercase \leftmark}]{\fancyplain{\rblob}{\helv \bfseries \thepage \rblob}}
\lhead[\fancyplain{}{\helv \bfseries \thepage}]{\fancyplain{}{\helv \nouppercase \rightmark}}
%


% The following line is to remove headers/footer for the blank pages
%++++++++++++++++++++++++++++++++++++++++++++++
%
%   This part puts a sentence on a blank page
%
\makeatletter
\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
    \hbox{}
    \vspace*{\fill}
    \begin{center}
%        \fbox{This page intentionally contains only this
%        sentence.}
    \end{center}
    \vspace{\fill}
    \thispagestyle{empty}
    \newpage
    \if@twocolumn\hbox{}\newpage\fi\fi\fi}
\makeatother
%++++++++++++++++++++++++++++++++++++++++++++++


EndPreamble

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