BACKGROUND: The origins of this post are a Phase Portrait post, Preamble for Journal of Mathematical Biology. See that post for the history behind this issue.

UPDATE 4: The updated svglov2.clo and svglov3.clo are not needed if the preamble is used below (i.e., if the \RequirePackage{fix-cm} line is added before the documentclass line.

UPDATE 3: See the section that redefines \autoref. Changed definition to support starred commands that are unlinked.

UPDATE 2: See the section starting with the comment "%% Level 1 Subsections". It forces subsections to show up like sections in the PDF bookmarks; this is a (strange) JMB convention. In the comment I make some suggestions for improvements.

UPDATE 1: See the small commented section "%%%% Table Support". If the LaTeX code is uncommented there, there is no need for the \noalign{\smallskip} stuff around \hline horizontal table rules. It uses the tabls package to do this.

I've been trying to fix and modernize some of the Springer LaTeX support files for the Journal of Mathematical Biology (JMB). I've come up with these...

• svglov2.clo - document class option for svjour2.cls. I used fix-cm to get rid of some of the warnings about not being able to scale the Computer Modern fonts. This is not needed if the preamble below is used (i.e., with the fix-cm line before the documentclass line).


• svglov3.clo - document class option for svjour3.cls. I used fix-cm to get rid of some of the warnings about not being able to scale the Computer Modern fonts. This is not needed if the preamble below is used (i.e., with the fix-cm line before the documentclass line).


• spmpsci.bst - BiBTeX bibliography style file for JMB. The original version of this did not reverse the first and last name of the editors as required; I fixed that.


• spmpscinat.bst - natbib compatible BiBTeX bibliography style file for JMB. Be sure to include natbib with numbers and sort&compress options.

%%%% Journal of Mathematical Biology (JMB) setup

% Allow Computer Modern fonts to be scaled (must be before svjour3)
\RequirePackage{fix-cm}

% Use running heads
\documentclass[runningheads]{svjour3}

% The journal's name
\journalname{Journal of Mathematical Biology}

% use Times fonts
\usepackage{mathptmx}

% flush right qed marks (Halmos square), 
% e.g., at end of proof
\smartqed

% Use natbib for \citet, \citep, etc.
% (JMB: numbered citations that are sorted and compressed)
\usepackage[numbers,sort&compress]{natbib}
%\bibliographystyle{spmpsci}
\bibliographystyle{spmpscinat}

%%%% Some useful packages

% Allow for smarter labeling of enumerations and itemizations 
% (consider using enumitem instead)
\usepackage{paralist}

% Provides \labelformat, which changes how \ref references look
\usepackage{varioref}

% Mathematical symbols, etc.
\usepackage{amssymb,amsfonts,amsmath}

%%%% Table Support

% UNCOMMENT THE FOLLOWING LINES TO GET RID OF
% \noalign{\smallskip} STUFF AROUND \hline's IN
% TABLES
%
% % The following three lines remove the need for 
% % the \noalign{\smallskip} around the \hline's 
% % in the _Journal of Mathematical Biology_ LaTeX
% % template
% \usepackage{tabls}
% \addtolength\extrarulesep{\smallskipamount}
% \addtolength\extrarulesep{1pt}

%%%% Graphics and Figure Support

% Use subfig for subfigures
\usepackage[nearskip=-3pt,captionskip=4pt,
            listofformat=subsimple,
            labelformat=simple]{subfig}

% Make sure subfigures have parentheses around them everywhere
\renewcommand\thesubfigure{(\alph{subfigure})}

% Use graphicx for including graphics
\usepackage{graphicx}

% When picture environments are used, use 
% pict2e for better resolution and flexibility
\usepackage{pict2e}

%%%% Hyperlink and Autoreference Support

%% Level 1 Subsections
%
% JMB does this weird thing where all subsection-level PDF 
% bookmarks are displayed as section-level bookmarks. 
% Strangely, they do *NOT* turn on the ``bookmarksnumbered'' 
% hyperref option. I think their articles would be MUCH more 
% readable with all level-1 bookmarks if they were prefixed 
% by their section number. I'm sure they'd argue that since the
% sections are linked within the document, this is not needed.
%
% (note: another option is to set tocdepth=2 and turn on
%        the ``bookmarksopen'' hyperref option)
%
% Anyway, the following redefines \addcontents line to setup 
% the bookmarks like JMB articles. Must do this after hyperref 
% because it redefines \addcontentsline Therefore, just use an 
% AtBeginDocument.
%
\AtBeginDocument{\let\orgaddcontentsline\addcontentsline
\renewcommand{\addcontentsline}[3]{
        \ifthenelse{\equal{#1}{toc}}
                {\ifthenelse{\equal{#2}{subsection}}
                        {\orgaddcontentsline{#1}{section}{#3}}
                        {\orgaddcontentsline{#1}{#2}{#3}}}
                {\orgaddcontentsline{#1}{#2}{#3}}}}

% Include hyperref for link support
%\usepackage[dvipdfmx,   % If need dvipdfmx
%\usepackage[dvips,      % If need dvips
\usepackage[%           % Fine in most cases
            pdfpagelabels,hypertexnames=true,
            plainpages=false,
            naturalnames=false]{hyperref}

% Configure the hyperlink color
\usepackage{color}
\definecolor{darkblue}{rgb}{0,0.1,0.5}
\hypersetup{colorlinks,
            linkcolor=darkblue,
            anchorcolor=darkblue,
            citecolor=darkblue}

% In the future, it would be nice to use the package
%
%    cleveref
%
% Right now, it breaks svjour3 and svjour2, so we just have to use
% autoref and labelformat :(.

% Make sure \autoref puts parentheses around 
% equations and enumeration items (similar to \eqref)
% NOTE: This allows us to use \ref instead of \eqref
\labelformat{equation}{\textup{(#1)}}
\labelformat{enumi}{\textup{(#1)}}

% Make sure equations are numbered by section
\numberwithin{equation}{section}

%% We need to redefine \autoref. We should use 
%% abbreviations inside the sentence and full names 
%% at the beginning of sentences. Additionally,
%% need to handle the plural cases.

% \Autoref is for the beginning of the sentence
\let\orgautoref\autoref
\providecommand{\Autoref}
        {\def\equationautorefname{Equation}%
         \def\figureautorefname{Figure}%
         \def\subfigureautorefname{Figure}%
         \def\sectionautorefname{Section}%
         \def\subsectionautorefname{Section}%
         \def\subsubsectionautorefname{Section}%
         \def\Itemautorefname{Item}%
         \def\tableautorefname{Table}%
         \orgautoref}

% \Autorefs is plural for the beginning of the sentence
\providecommand{\Autorefs}
        {\def\equationautorefname{Equations}%
         \def\figureautorefname{Figures}%
         \def\subfigureautorefname{Figures}%
         \def\sectionautorefname{Sections}%
         \def\subsectionautorefname{Sections}%
         \def\subsubsectionautorefname{Sections}%
         \def\Itemautorefname{Items}%
         \def\tableautorefname{Tables}%
         \orgautoref}

% \autoref is used inside a sentence 
% (this is a renew of the standard)
\renewcommand{\autoref}
        {\def\equationautorefname{Eq.}%
         \def\figureautorefname{Fig.}%
         \def\subfigureautorefname{Fig.}%
         \def\sectionautorefname{Sect.}%
         \def\subsectionautorefname{Sect.}%
         \def\subsubsectionautorefname{Sect.}%
         \def\Itemautorefname{item}%
         \def\tableautorefname{Table}%
         \orgautoref}

% \autorefs is plural for inside a sentence
\providecommand{\autorefs}
        {\def\equationautorefname{Eqs.}%
         \def\figureautorefname{Figs.}%
         \def\subfigureautorefname{Figs.}%
         \def\sectionautorefname{Sects.}%
         \def\subsectionautorefname{Sects.}%
         \def\subsubsectionautorefname{Sects.}%
         \def\Itemautorefname{items}%
         \def\tableautorefname{Tables}%
         \orgautoref}