American Naturalist BibTeX BST style file

The American Naturalist, a University of Chicago Press - Journals Division journal, specifies that AASTeX should be used to typeset submissions; however, it does not provide any BibTeX BST bibliography style file. That means that authors still have to manually manage their reference list rather than using BibTeX and a central BIB bibliography database.

The BST: I've tried to remedy this by creating amnatnat.bst, a natbib-compatible BibTeX Bibliography STyle (BST) file for the American Naturalist.

As far as I can tell, this BST will generate a properly formatted BBL file that should not require modifications. Note that American Naturalist requires authors to upload their BBL files and NOT their BIB files (i.e., they don't have the ability to run BibTeX on the server).

ONE CAVEAT: If you have titles that contain colons in them, you will have to manually (either in the BIB or the BBL) change the case of the letter following the colon. For example, if "Some Title: Subtitle" is the title, change the "S" in "Subtitle" to "s". A feature/bug of BibTeX is that its sentence case keeps letters following colons capitalized. This does not match the sentence case definition used by many journals, which considers the words after a colon being at the middle of a sentence rather than the start of a new sentence. As far as I know right now, there is no easy way to change the BST file to do this automatically for you.

FYI: This BST file was generated using amnatnat.dbj (for more details, see amnatnat_full.dbj) and amnatnat.patch.

LaTeX for generating Behavioral Ecology manuscript

UPDATE: Check out a more complete math-oriented template/example, that I posted as behavecol_math_template.tex. This is ready to use out of the box. It has comments. It is setup for AMS math. It has table, figure, and autoreferencing examples too.

IMPORTANT NOTE: If using amsmath environments, be sure to check out my information on making lineno compatible with amsmath environments.

UPDATE: I have put behavecol_template.tex and behavecol.bst on-line so that you don't have to do any of the following to get them.

The Oxford Journal Behavioral Ecology is not setup for LaTeX manuscript submissions. This baffles me.

So, I spent some time putting together some macros and a BibTeX style file to get up and running with this journal.

First, a template (that uses the article document class), which fixes incompatibilities between figcaps, caption, and anything that uses \ref (see behavecol_template.tex for what is below, or see behavecol_math_template.tex for a more complete example):

\documentclass[12pt]{article}

\usepackage[paper=letterpaper,margin=1.5in]{geometry}
\usepackage{setspace}\doublespacing

\usepackage{graphicx}

\usepackage[%
            labelsep=newline,
            justification=RaggedRight,
            singlelinecheck=false,
            labelfont=bf,
            tableposition=top,
           ]{caption}
\captionsetup[table]{textfont=bf,position=above}
\makeatletter
\let\oldmakecaption\@makecaption
\makeatother

\usepackage[figon,printfigures]{figcaps}
\def\figurecapname{Figure legends}
\def\tablepagename{Tables}
\def\figurepagename{Figures}
 
\makeatletter
% This lets figcaps work with \ref
% However, forces \label outside of \caption
\def\phantomsection{\relax}
\let\oldfigurepage\@figurepage
\def\@figurepage{%
        \@ifundefined{tf@pof}{}{%
        \let\oldlabel\label%
        \let\oldinput\@input%
        \def\@input{\def\label{\oldlabel}\oldinput}%
        \phantomsection%
        \addcontentsline{toc}{section}{\figurepagename}}%
        \oldfigurepage%
        }
\let\@makefcaption\@makecaption
\let\oldtablepage\@tablepage
\def\@tablepage{%
        \@ifundefined{tf@pot}{}{%
        \clearpage%
        \phantomsection%
        \addcontentsline{toc}{section}{\tablepagename}}%
        \oldtablepage%
        }
\makeatother
\usepackage[subrefformat=subparens,labelformat=parens]{subfig}
\captionsetup[subfloat]{position=top}

\setcounter{secnumdepth}{0}

% Lines are numbered, starting at 1 
% (add pagewise to reset at each page)
%\usepackage[modulo,pagewise,mathlines]{lineno}
\usepackage[modulo,mathlines]{lineno}
\modulolinenumbers[1]
\firstlinenumber{1}
\linenumbers

\usepackage{natbib}
\bibliographystyle{behavecol}
\setcitestyle{%
        authoryear,round,semicolon,%
        aysep={},%
        yysep={,},%
        notesep={, }%
        }

\usepackage{tocbibind}
\def\tocbibname{\refname}

\usepackage{varioref}
\labelformat{equation}{\textup{(#1)}}
\labelformat{enumi}{\textup{(#1)}}

\usepackage[%
            pdftitle={},
            pdfsubject={},
            pdfauthor={},
            pdfkeywords={},
            pdfstartview=FitH,
            bookmarks=true,bookmarksopen=true,
            breaklinks=true,
            colorlinks=false,
            pdfpagelabels=true,hypertexnames=true,
            plainpages=false,naturalnames=false,
            %draft,
            ]{hyperref}

% \Autoref is for the beginning of the sentence
\let\orgautoref\autoref
\providecommand{\Autoref}
    {\def\equationautorefname{Equation}%
     \def\figureautorefname{Figure}%
     \def\subfigureautorefname{Figure}%
     \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\Itemautorefname{Items}%
     \def\tableautorefname{Tables}%
     \orgautoref}
 
% \autoref is used inside a sentence 
% (renew of the standard autoref)
\renewcommand{\autoref}{\Autoref}
 
% \autorefs is plural for inside a sentence
\providecommand{\autorefs}{\Autorefs}

\let\oldsection\section
\newcommand{\uppercasesection}[2][]{%
    \oldsection[#1]{\MakeUppercase{#2}}}
\newcommand{\uppercasesectionstar}[1]{%
    \oldsection*{\MakeUppercase{#1}}}
\makeatletter
\def\section{%
    \@ifstar{\uppercasesectionstar}%
            {\@dblarg{\uppercasesection}}}
\makeatother

\hypersetup{%
        pdftitle=
        {The title},
}
\title{The title}
\author{}
\date{}
     
\begin{document}
    
\maketitle
     
\begin{abstract}
% ...The abstract...
        \textit{Key words:} Keywords separated with comma+space, 
                            List ends with period.
        \hypersetup{%
        pdfkeywords=
        {Keywords separated with comma+space, 
         List ends with period},
        }
\end{abstract}
\newpage
     
% ...The document...
     
% The following line loads the references
\bibliography{the_bib_database_name}
     
\end{document}

Of course, remember to put table captions before the actual table insertion. In fact, it is important that the inside of a table environment has caption first, then label OUTSIDE of the caption, then the actual table content. Additionally, subfigures should be inserted (within a figure environment) with something like:

\subfloat[]{
% ... something like an \includegraphics ...
\label{fig:a}
}

Also, when you're ready to submit, get rid of the % on the %draft, line of the hyperref options. This will turn off all hyper linking, which will prevent strange little unlinked boxes from being drawn in your autogenerated proof.

Next, the bibliography style file, which I may end up posting later separately. As of right now, it has to be constructed from pieces. First, save the following as behavecol.dbj (see behavecol_full.dbj for more details):

%% Driver file to produce behavecol.bst from merlin.mbs
%% Generated with makebst, version 4.1 (2003/09/08)
%% Produced on 2007/08/23 at 12:02
%% 
\input docstrip
 
\preamble
----------------------------------------
*** Bibliography style for _Behavioral Ecology_. ***
 
\endpreamble
 
\postamble
End of customized bst file
\endpostamble
 
\keepsilent
 
\askforoverwritefalse
\def\MBopts{\from{merlin.mbs}{%
  ay,nat,nm-rvx,ed-rev,jnrlst,keyxyr,dt-beg,yr-per,note-yr,jxper,%
  jttl-rm,thtit-a,vnum-x,pp-last,num-xser,btit-rm,bt-rm,add-pub,%
  pre-edn,in-col,pp,abr,ednx,ord,jabr,xand,etal-xc,nfss,}}
\generate{\file{behavecol.bst}{\MBopts}}
\endbatchfile

and then run latex behavecol.dbj. Next, save the following to behavecol.patch:

--- behavecol.bst 2007-08-29 12:07:40.000000000 -0400
+++ behavecol_new.bst 2007-08-29 12:08:01.000000000 -0400
@@ -89,7 +89,7 @@
 FUNCTION {output.nonnull}
 { 's :=
   output.state mid.sentence =
-    { ", " * write$ }
+    { ". " * write$ }
     { output.state after.block =
         { add.period$ write$
           newline$
@@ -144,6 +144,9 @@
 FUNCTION {add.blank}
 {  " " * before.all 'output.state :=
 }
+FUNCTION {add.semicolon}
+{  ";" * before.all 'output.state :=
+}
 
 FUNCTION {date.block}
 {
@@ -248,7 +251,7 @@
 { "in" }
 
 FUNCTION {bbl.pages}
-{ "pp." }
+{ "p." }
 
 FUNCTION {bbl.page}
 { "p." }
@@ -260,10 +263,10 @@
 { "Tech. Rep." }
 
 FUNCTION {bbl.mthesis}
-{ "Master's thesis" }
+{ "[Master's thesis]" }
 
 FUNCTION {bbl.phdthesis}
-{ "Ph.D. thesis" }
+{ "[PhD thesis]" }
 
 FUNCTION {bbl.first}
 { "1st" }
@@ -488,6 +491,16 @@
     }
   if$
 }
+FUNCTION {format.book.pages}
+{ pages "pages" bibinfo.check
+  %duplicate$ empty$ 'skip$
+  empty$ 'skip$
+    { add.semicolon 
+      add.blank 
+      pages "pages" bibinfo.check 
+      " " * bbl.pages * }
+  if$
+}
 FUNCTION {format.note}
 {
  note empty$
@@ -950,6 +963,10 @@
     }
   if$
 }
+FUNCTION {format.university.address}
+{ school "school" bibinfo.warn format.org.or.pub
+}
+
 FUNCTION {format.publisher.address}
 { publisher "publisher" bibinfo.warn format.org.or.pub
 }
@@ -1148,12 +1165,11 @@
   author format.key output
   format.date "year" output.check
   date.block
-  format.title
-  "title" output.check
-  new.block
+  format.title "title" output.check
+  add.blank
   bbl.mthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
+  format.university.address output
+  format.book.pages output
   new.block
   format.note output
   fin.entry
@@ -1178,12 +1194,11 @@
   author format.key output
   format.date "year" output.check
   date.block
-  format.title
-  "title" output.check
-  new.block
+  format.title "title" output.check
+  add.blank
   bbl.phdthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
+  format.university.address output
+  format.book.pages output
   new.block
   format.note output
   fin.entry

Then run

patch < behavecol.patch

from the same directory that you ran the DBJ command in. That should generate the behavecol.bst file that is needed for the above template to work.

lineno and amsmath compatibility

UPDATE 2 (READ THIS!): As Ulrich Diez points out, this can be made more compact. Here's the result (place this in the preamble, probably anywhere):

\newcommand*\patchAmsMathEnvironmentForLineno[1]{%
  \expandafter\let\csname old#1\expandafter\endcsname\csname #1\endcsname
  \expandafter\let\csname oldend#1\expandafter\endcsname\csname end#1\endcsname
  \renewenvironment{#1}%
     {\linenomath\csname old#1\endcsname}%
     {\csname oldend#1\endcsname\endlinenomath}}% 
\newcommand*\patchBothAmsMathEnvironmentsForLineno[1]{%
  \patchAmsMathEnvironmentForLineno{#1}%
  \patchAmsMathEnvironmentForLineno{#1*}}%
\AtBeginDocument{%
\patchBothAmsMathEnvironmentsForLineno{equation}%
\patchBothAmsMathEnvironmentsForLineno{align}%
\patchBothAmsMathEnvironmentsForLineno{flalign}%
\patchBothAmsMathEnvironmentsForLineno{alignat}%
\patchBothAmsMathEnvironmentsForLineno{gather}%
\patchBothAmsMathEnvironmentsForLineno{multline}%
}

This is all that is needed for the standard AMS math environments. However, if you want to add environment BLAH, you can add

\patchAmsMathEnvironmentForLineno{BLAH}

before the closing curly brace. If you want to add environments BLAH and BLAH*, you can add

\patchBothAmsMathEnvironmentsForLineno{BLAH}

before the closing curly brace.

UPDATE 1: If you use the mathlines lineno option, you may notice that amsmath environments like align may create strange double numbers at the end of the environment. I haven't looked into why this is the case. If you really need mathlines loaded, you may want to consider ways of using equation or equation* exclusively. Keep in mind that you will still need to load at least the equation and equation* lines:

\AtBeginDocument{%
%
\let\oldequation\equation%
\let\endoldequation\endequation%
\renewenvironment{equation}%
  {\linenomath\oldequation}{\endoldequation\endlinenomath}%
%
\expandafter\let\expandafter\oldequationstar\csname equation*\endcsname%
\expandafter\let\expandafter\endoldequationstar\csname endequation*\endcsname%
\renewenvironment{equation*}%
  {\linenomath\oldequationstar}{\endoldequationstar\endlinenomath}%
}

You may think that the displaymath option of lineno will do this for you, but loading amsmath seems to prevent that. I haven't looked into why.

A comp.text.tex post gives some history behind this fix.

It's well-known that lineno and amsmath don't play well together. After loading amsmath, the paragraph that precedes an equation, equation*, align, align*, or any of the other amsmath environments will cease to get line numbers. The ugly fix to this is to wrap every math environment with a linenomath environment. That's pretty annoying. Here's a fix that redefines the equation environment and the amsmath environments so that they'll work with noalign. Yes, it even handles the starred versions of these.

% To deal with amsmath, must redefine math environments later
\AtBeginDocument{%
%
\let\oldequation\equation%
\let\endoldequation\endequation%
\renewenvironment{equation}%
  {\linenomath\oldequation}{\endoldequation\endlinenomath}%
%
\expandafter\let\expandafter\oldequationstar\csname equation*\endcsname%
\expandafter\let\expandafter\endoldequationstar\csname endequation*\endcsname%
\renewenvironment{equation*}%
  {\linenomath\oldequationstar}{\endoldequationstar\endlinenomath}%
%
\let\oldalign\align%
\let\endoldalign\endalign%
\renewenvironment{align}%
  {\linenomath\oldalign}{\endoldalign\endlinenomath}%
%
\expandafter\let\expandafter\oldalignstar\csname align*\endcsname%
\expandafter\let\expandafter\endoldalignstar\csname endalign*\endcsname%
\renewenvironment{align*}%
  {\linenomath\oldalignstar}{\endoldalignstar\endlinenomath}%
%
\let\oldflalign\flalign%
\let\endoldflalign\endflalign%
\renewenvironment{flalign}%
  {\linenomath\oldflalign}{\endoldflalign\endlinenomath}%
%
\expandafter\let\expandafter\oldflalignstar\csname flalign*\endcsname%
\expandafter\let\expandafter\endoldflalignstar\csname endflalign*\endcsname%
\renewenvironment{flalign*}%
  {\linenomath\oldflalignstar}{\endoldflalignstar\endlinenomath}%
%
\let\oldalignat\alignat%
\let\endoldalignat\endalignat%
\renewenvironment{alignat}%
  {\linenomath\oldalignat}{\endoldalignat\endlinenomath}%
%
\expandafter\let\expandafter\oldalignatstar\csname alignat*\endcsname%
\expandafter\let\expandafter\endoldalignatstar\csname endalignat*\endcsname%
\renewenvironment{alignat*}%
  {\linenomath\oldalignatstar}{\endoldalignatstar\endlinenomath}%
%
\let\oldgather\gather%
\let\endoldgather\endgather%
\renewenvironment{gather}%
  {\linenomath\oldgather}{\endoldgather\endlinenomath}%
%
\expandafter\let\expandafter\oldgatherstar\csname gather*\endcsname%
\expandafter\let\expandafter\endoldgatherstar\csname endgather*\endcsname%
\renewenvironment{gather*}%
  {\linenomath\oldgatherstar}{\endoldgatherstar\endlinenomath}%
%
\let\oldmultline\multline%
\let\endoldmultline\endmultline%
\renewenvironment{multline}%
  {\linenomath\oldmultline}{\endoldmultline\endlinenomath}%
%
\expandafter\let\expandafter\oldmultlinestar\csname multline*\endcsname%
\expandafter\let\expandafter\endoldmultlinestar\csname endmultline*\endcsname%
\renewenvironment{multline*}%
  {\linenomath\oldmultlinestar}{\endoldmultlinestar\endlinenomath}%
%
}

The pattern is pretty clear. You can use it along with any of your own environments. For example, add this at the end (before the closing curly brace) to fix your BLAH environment:

\let\oldBLAH\BLAH%
\let\endoldBLAH\endBLAH%
\renewenvironment{BLAH}%
  {\linenomath\oldBLAH}{\endoldBLAH\endlinenomath}%

and drop this at the end (before the closing curly brace) to fix your BLAH* environment:

\expandafter\let\expandafter\oldBLAHstar\csname BLAH*\endcsname%
\expandafter\let\expandafter\endoldBLAHstar\csname endBLAH*\endcsname%
\renewenvironment{BLAH*}%
  {\linenomath\oldBLAHstar}{\endoldBLAHstar\endlinenomath}%

I hope that's useful for someone.

cleveref incompatibilities with Elsevier and Springer

elsart problems: If you try using cleveref with any of the elsart packages, you may get this error:

! TeX capacity exceeded, sorry [input stack size=5000].
\cl@part ->\cl@part 
                    \@elt {section}

This is due to a flaw in the elsart packages. They setup some part counters even though part isn't defined. This confuses cleveref. To fix this, add the following anywhere in your preamble:

\makeatletter \let\cl@part\relax \makeatother

Later, you can use cleveref's poorman option to strip all of the cleveref stuff from your document. After that, you can remove this line.

svjour problems: Similarly, if you try combining cleveref with Springer journal support files, you may get this error:

! TeX capacity exceeded, sorry [input stack size=5000].
\cl@chapter ->\cl@chapter
                          \@elt {theorem}

Again, this is due to a flaw in the Springer packages. They setup some chapter counters even though chapter isn't defined. To fix this, add the following anywhere in your preamble:

\makeatletter \let\cl@chapter\relax \makeatother

Again, this can be removed after cleveref's poorman procedure is applied.

Source and acknowledgments: The Springer solution was given by "Dan" in a comp.text.tex post. I used it to generate the elsart solution.

Tech. Cheat Sheets!

Check out the recent "Developer’s Alarm: 200+ Hotkeys To Boost Your Productivity" from Smashing Magazine for more hotkeys. This focusses on Windows apps, but there are some apps that have cross-platform support, and so this isn't an entirely worthless post.

In the spirit of previous posts [1, 2, 3], here are some more!

I found TechCheatSheets.com, which includes some nice reference sheets, and some broken links. However, it got me thinking about "cheat sheet," which got me searching, and I found these popular links:

• Mozilla Firefox Cheat Sheet (HTML, PDF)
• Mozilla Thunderbird Cheat Sheet (HTML, PDF)

That last one probably beats my Thunderbird quick reference (PDF, LaTeX). However, those do not replace my Camino quick reference (PDF, LaTeX).

My (Reference) Desk

Now that I have compiled all of these quick references [1, 2, 3], I can put them together to surround myself in easy-to-access information. In fact, I will. I did. Here it is! From left to right (pictures taken with my wonderful phone and stored in a flickr photoset)...

Hot Key References

NOTE: The two updates below may serve as good LaTeX examples featuring the use of multicol.

UPDATE 2: I have used the Thunderbird list to make a Thunderbird quick reference PDF (LaTeX source available).

UPDATE 1: I have used the Camino list to make a Camino quick reference PDF (LaTeX source available).

I have been posting about quick references a lot lately [e.g., 1, 2]. I found another good quick reference site, allhotkeys.com. It has lots of software hotkey quick references. For example,

• Mozilla Firefox hotkeys
• Mozilla Firefox extensions hotkeys
• Mozilla Thunderbird hotkeys
• Camino hotkeys
• Safari hotkeys
• Microsoft Word hotkeys
• Microsoft Excel hotkeys
• Microsoft PowerPoint hotkeys
• Remote Desktop hotkeys
• Mac OS X Keyboard shortcuts
• iTunes hotkeys
• GMail hotkeys
• UNIX and Linux hotkeys
• Command line keyboard shortcuts
• ...and lots more...

So that's potentially helpful. But right now the pages are really slow to come up, so I have no idea what they look like. Nor do I know if I can easily get them onto a landscape sheet of paper that I can tape to the wall somewhere...

Traditional way to change cleveref defaults

UPDATE: cleveref also includes a set of defaults for the ntheorem package when the ntheorem option is given. I've just put those defaults into cleveref_nthoerem_defaults.tex. Include it with \input{cleveref_ntheorem_defaults.tex} after (or instead of) including the other file.

Because it will probably be a long time until a simpler way of changing cleveref defaults gets implemented, I needed a way to change these defaults without adding tens of lines to my LaTeX source. I came up with cleveref_defaults.tex, which basically contains all of the default lines from the cleveref documentation, plus a set of table defaults. You can include it with:

\input{cleveref_defaults.tex}

Then, go ahead and modify cleveref_defaults.tex to match your conventions (e.g., change the four "eq." to "Eq." and the four "eqs." to "Eqs.").

Protype for simplifying changing cleveref defaults

UPDATE: I have created crefntheoremdefaults.tex, which does this same stuff to the ntheorem package. You have to be sure to include the crefdefaults.tex file first. The files crefntheoremdefault_constants.tex and crefntheoremdefault_formats.tex play a similar role as the analogous ones below.

I think the package cleveref is great. In fact, I think it has much of what has been missing from LaTeX for a long time. See its documentation for more information about the package.

My only gripe about cleveref is that it is tedious to change something like all of the default "eq." and "eqs." to "Eq." and "Eqs.", respectively. So I put together these scripts as a kind of proof of concept (they also setup cleveref to handle table references, something that is not done by default at the moment):

• crefdefaults.tex
• crefdefault_constants.tex
• crefdefault_formats.tex

The first script, crefdefaults.tex, is simply crefdefault_constants.tex concatenated with crefdefault_formats.tex. Therefore,

\input{crefdefaults.tex}

is equivalent to

\input{crefdefault_constants.tex}
\input{crefdefault_formats.tex}

However, if the poorman option is used and the corresponding sed script is applied, the resulting file will need to have the content of crefdefault_formats.tex removed; crefdefault_constants.tex should not be removed. In other words, if you are planning on using poorman, use the 2-line include and comment the crefdefault_formats.tex line out of the script that results from the sed script.

What's the outcome of this? I can now do

\renewcommand{\crefenumilabelformat}[3]{\textup{(#2#1#3)}}

in order to change every item reference so that it is surrounded by upright round braces. Additionally, changing "eq." to "Eq." and "eqs." to "Eqs." is as simple as it was in hyperref (for use with \autoref); that is, it is these two lines:

\renewcommand{\crefequationname}{Eq.}
\renewcommand{\crefpluralequationname}{Eqs.}

Unfortunately, the output of the poorman sed filter is a little messy. However, if these are someday integrated into cleveref, that could be fixed. There are other shortcuts built into crefdefaults.tex as well. It probably requires documentation, but it's just a prototype for now.

Good idea? Bad?

MATLAB Quick Reference Cards (and more)

UPDATE: I list an AMSTeX reference card below. There is also an AMSLaTeX reference card available at refcards.com.

This is meant to be a follow-up to the "TeX Reference Card (and others)" post.

I found a list of a bunch more quick reference cards, which include applications/packages like MATLAB, MATLAB toolboxes, Perl, MFC, MySQL, Linux, UNIX, Vi, Vim, Windows, AMSTeX, TeX, and a bunch more...

However, I was just looking for MATLAB quick reference cards. So, here are these (some of which did not come from the above site):

• MATLAB quick reference
• MATLAB toolboxes quick reference
• MATLAB reference card meant for an ENG101 class
• MATLAB reference card
• An edited MATLAB reference card

So, that's nice. I recommend one of the bottom two [i.e., 1, 2].

Using Skim with MATLAB

I found a hint for using TeXShop as a MATLAB previewer on OS X, primarily because plots look better in PDF and TeXShop auto-updates files from disk. This was a tip from back in 2005. Since then, MATLAB's OS X plotting has gotten a lot better. Additionally, Skim has been invented.

Because of the advances in MATLAB, this may not be a useful hint anymore, but give this a try sometime:

figure(1);
set(gcf, 'Visible', 'off');
plot(x, y);
print(gcf, '-dpdf', 'figure1.pdf');
system('open -a Skim figure1.pdf');

Now, I believe there's a way to do this without having to plot first. That is, I think there's a way to plot to PDF without first generating that figure.

What's cool about this is that any future updates of the PDF will cause Skim to update automatically. Therefore, Skim becomes your plot viewer. That might be nice, right?

Using Skim, PDFSync, and TeXShop

UPDATE 3: I have updated the script to support command-line options that will prevent TeXShop from doing things like refreshing text (and trashing your unsaved changes), activating (taking your focus away), and opening (possibly getting in front of your view). Try the -h option for details.

UPDATE 2: There is a related Skim revision that will make it easier to use AppleScript for PDFSync interfacing. This change will prevent having to make UNIX shell scripts that must be modified with chmod.

UPDATE 1: As you can see in the Skim revision history, future versions of Skim will include their "Application Support" directory (e.g., ~/Library/Application Support/Skim/) as well as a "Scripts" subdirectory in their path. When that occurs, scripts like the one below can be stored there and executed from Skim without specifying the full path name.

I know there are ways to change TeXShop's previewer; however, I don't know how to do them. Additionally, I don't use TeXShop, so I have little incentive to look those things up.

However, I do use Skim, which is compatible with pdfsync, and recently someone asked me how they could get Skim to call up TeXShop at a particular line (as someone would want to do when using pdfsync).

For that, I generated a texshop script that looks like this (an earlier version of this can be found on the Skim wiki):

fileName="$1"
lineNumber="$2"
gotoString=""

[ "${fileName:0:1}" == "/" ] || fileName="${PWD}/${fileName}"
[ "${lineNumber}" == "" ] || gotoString="goto line ${lineNumber}"

exec osascript \
  -e "set texFile to POSIX file \"${fileName}\"" \
  -e "tell application \"TeXShop\"" \
    -e "activate" \
    -e "open texFile" \
    -e "tell front document" \
      -e "refreshtext" \
      -e "${gotoString}" \
    -e "end tell" \
  -e "end tell"

To use this script, follow these steps:

1. Save that file as something (preferably in the PATH somewhere, but this is not necessary) like

   /usr/local/bin/texshop

   or anywhere you would like (e.g., /Users/username/bin/texshop). However, if you place it somewhere differently, be sure to update the red text in these instructions.


2. Next, chmod it 0755, as in

   chmod 0755 /usr/local/bin/texshop

   This can be done from the Terminal.


3. Finally, tell Skim's PDFSync preferences (under Preferences->LaTeX or Preferences->Sync depending on your Skim version) to use a "Custom" editor with

   Command: /usr/local/bin/texshop
   Arguments: "%file" %line

   Make sure you click AWAY (e.g., onto a different tab) from the PDFSync settings before you close the Preferences. Otherwise, one of your text boxes may not get saved.

After this is done, doing Shift+Command+CLICK in Skim on a location in the PDF will bring up the source in TeXShop located at the that generated that point in the PDF.

Note that if you have saved texshop somewhere in your PATH, then you should be able to drop the /usr/local/bin/ from the front of the Command: line.

Great 2-port USB KVM switch: IOGEAR GCS632U MiniView Micro USB Plus

A while ago I made a couple of posts about KVM switches [i.e., 1, 2]. In that case, I was searching for a PS/2 KVM switch that supported 5-button mice. Several KVM switches failed me, including a switch from Belkin that looked great on paper but was awful in practice. In the end, it was the cheapest switch that worked like a charm. Well, here's how things went this time.

• Again, Belkin makes crap: Last week I went through virtually the same process with 2-port USB KVM switches. This time I needed a USB switch to go back and forth between my Apple PowerBook and my Dell Workstation (I'm spanning the PowerBook's second monitor onto the Windows machine). Because it looked to be the cheapest, I tried the Belkin F1DK102U 2-Port USB KVM Switch with Built-In Cabling first. It said it supported OS X and XP. Strangely, it also required software to be installed in order to use it. This should have been my first clue that I was wasting my time and money with this awful Belkin product. I don't remember the last time I was pleased with a Belkin product (I suppose I had some UPS's from them that weren't that bad). Despite being OS X compatible, booting with the product connected caused the PowerBook to crash pretty bad. It gave me that little black window of death on bootup. Again, because it required software in order to use, that made uninstalling it (while the monitor was still connected to it) was a pain. PLUS, when it was connected, it wasn't able to emulate my monitor and mouse and keyboard, and so Windows and OS X weren't convinced that I was using the monitor, mouse, and keyboard that I was using. Oh, and on TOP of that, one of its attached cables (you can see this in the picture) is only about a foot long, and it's the DEFAULT PORT! This was a lousy product.


• IOGEAR is lovely as always: Luckily, I had to go back to the store for a different reason, and I noticed that they had four IOGEAR GCS632U MiniView Micro USB Plus 2-port KVM switches, and two of those switches were marked at a price CHEAPER than the Belkin piece of crap. I had someone check, and the correct price was the low price. So I took the Belkin back and got the IOGEAR instead. This switch said it was Mac compatible (Mac mini compatible, even). Heck, it even said it was SUN compatible! It also had ANALOG AUDIO support, which is kinda nice. Finally, right on the box it said, "USB sniffing technology allows complete USB mouse and keyboard emulation for error-free boot-up." This feature was one of the major things I LOVED about the old QVS PS/2 switch. Plus, I figured this meant that it would crash my PowerBook like the Belkin thing did. Both of its cables were the same length (6'), and it would choose a "default" port based on what was powered on. Oh, and did I mention it didn't require software?

The result? The IOGEAR GCS632U, the cheapest 2-port USB KVM switch that was available to me, worked EXACTLY as I wanted it to. It's beautiful. It's slick. I love it. I love IOGEAR.

NOTE: IOGEAR also has a PS/2 version of this switch that I'm guessing works as superbly as the QVS KVM-12CK (the PS/2 switch from the previous posts) that is still working great today.

OptOutPrescreen.com - stop getting credit card offers!

This was suggested on NPR's Day to Day today to opt out of getting credit card and insurance offers in an effort to save money while also saving paper.

Go to OptOutPrescreen.com to do this. They'll submit your request to the credit bureaus, and eventually that'll stop creditors and insurers from sending you CRAP.

Skim automatic refreshes and simpdftex

UPDATE: I've updated the script so that it works with OS/X Leopard. See comments for details.

The OS X PDF viewer Skim has the ability to automatically refresh files after they have been updated on disk. In Skim version 0.4.1 and below, this was done by polling a file every second to see if it has been changed. In Skim version 0.5 and up, this feature is implemented using kqueue events. This is a much better way of doing things. However, if the file that is open gets deleted and a new file created with the same name, events for that new file will not be received by Skim.

Unfortunately, the script simpdftex that comes with a number of LaTeX distributions (e.g., gwTeX) deletes a PDF before updating it. This means that autorefreshes won't work when regenerating a PDF from its LaTeX source using simpdftex.

So, motivated by the history in a Skim bug report, I've put together a simpdftexnodel script that fixes this problem (based on the 2007/05/07 gwTeX simpdftex). To use this file:

• Place the script somewhere (probably in your PATH).
• chmod the file 0755.
• Make sure that your distillers and TeX program (or at least symlinks to them) exist in the same directory.
• Stop using simpdftex and start using simpdftexnodel.

I hope that helps!

Women more dominant than men

WebMD : Wives Wield Decision Power in Marriage

Balance of Problem-Solving Power Weighs in Favor of Women

Men may rule the world but women rule the roost, according a new study that shows women wield considerably more decision-making power than men within marriages.

Researchers found that wives, on average, displayed more power than their husbands during problem-solving discussions, regardless of who brought up the topic of discussion.

And it’s not simply a case of women talking more than men.

“It wasn’t just that the women were bringing up issues that weren’t being responded to, but that the men were actually going along with what they said,” researcher Megan Murphy, assistant professor of human development and family studies at Iowa State University, says in a news release. “They were communicating more powerful messages, and men were responding to those messages by agreeing or giving in.”

“There’s been research that suggests that’s a marker of a healthy marriage – that men accept influence from their wives,” Murphy says.

TeX Reference Card (and others)

UPDATE 3: I found the source of the popular LaTeX cheat sheet. It includes a PS version, a PDF version, PNG views [Page 1, Page 2], and the LaTeX source. It's nice that the source is available. That makes it easier to shift from A4 to letter paper and back.

UPDATE 2: More reference cards can be found in the follow-up to this message.

UPDATE 1: Check out refcards.com and the old version old.refcards.com. There are lots of useful cards, including some of the ones I linked below. This TeX card and this Vim card look familiar. There are other EMmacs and Vim cards in the editors section. There is also a typesetting section that includes a LaTeX cheat sheet.

The Brown University Center for Fluid Mechanics, Turbulence and Computation (CFM) has a collection of computing tutorials. Buried in there somewhere is a useful Plain TeX reference card in PostScript format. I have generated a PDF version of this reference card.

I stress that this is a Plain TeX reference card, and so there are different ("better"?) ways of doing some of these things using other LaTeX macros (note TeX vs. Plain TeX vs. LaTeX differences: [1, 2, 3, 4, and more]). However, this is still a very useful reference card. It prints out as two landscape-oriented pages (weirdly sized: 11.7" x 8.3"). I plan on printing this out and taping it next to my desk at the office. I also found a useful longer Plain TeX reference sheet that may be helpful to some people. Of course, there are even longer Plain TeX reference documents also available.

Oh, I also found this AUC TeX reference card PDF with available source code. I don't use AUC TeX (I favor VIM-LaTeX), but maybe someone who does could use this. FYI, AUC TeX is a package for EMacs providing extra support for LaTeX (and others).

Speaking of Vim:

• Here's a cool set of multilingual Vim quick reference cards (again, PDF with 2 landscape-oriented pages) that include their sources and an HTML version.
• Here's a similar Vim quick reference card (PDF).
• Here's yet another Vim quick reference card (PDF).
• Finally, here's VIM-LaTeX's quick start introduction document.

So that's nice.

Correction: TeXnicians (and TeXackers) over TeXperts

I thought this correction to a Brown university TeX tutorial was really cute.

I like you page on TeX, but had to comment that TeX is properly pronounce like the Tech in Technology (Knuth "The TeXbook" page 1) and thus the proper name for a TeX hacker is a TeXnichian not a TeXpert as you stated on your page (http://www.cfm.brown.edu/tutorials/tex.html) in fact the first exercise in the TeXbook is "After you have mastered the material in this book will you be: A TeXpert or a TeXnichian?" to which the correct answer is "A TeXnician (underpaid); sometimes also called a TeXacker." (Knuth, the TeXbook)

Please change this grievous error.

Thanks,

Christopher A Craig (ccraig@cc.gatech.edu)

\cref* and \crefrange*: temporarily disable cleveref hyperlinks

UPDATE: I've e-mail chatted with the author of cleveref, and it sounds like the changes below (the * macros and the new defaults) may get built into the next release. So that's exciting. The author has recently sent me new versions of cleveref that include these suggestions. Only time will tell when it's on CTAN. So that's exciting.

I've also had a chance to reflect on the poorman option of cleveref. It's an interesting idea. When loaded with this option, cleveref will generate a sed script that the author can use on the source files that will change each of the cleveref macros into old-fashioned references with everything typed out. That is, if you have a journal that does not support cleveref, you run sed on your source code before uploading it, and your journal works with the resulting files that are stripped of cleveref code. That's pretty clever.

I think that by the 1.0 version of cleveref package, it will be ready to replace hyperref's \autoref macro.

One thing that hyperref gives you that cleveref does not are starred versions of the referencing commands that disable hyperlinks. For example, in hyperref, \ref* and \autoref* work exactly like \ref and \autoref but are not hyperlinked. That's nice. Of course, there is no \Autoref or \autorefs or \Autorefs.

A major nice thing that cleveref does is let you format your expanded references with more detail than hyperref. For example, you can make an equation reference expand as "Equation (1)" where the "1" gets linked while having a figure reference expand as "Fig. 1" with the whole "Fig. 1" linked. Of course, this assumes that you've loaded both cleveref and hyperref, like this:

\usepackage{hyperref}
\usepackage[hyperref]{cleveref}

Additionally, cleveref does give the equivalent of those special versions of \autoref. cleveref supports single and multiple references, including reference ranges.

So consider the following, which gives you all the nice stuff about cleveref but also adds starred versions of its macros:

\makeatletter

% \cref and \cref*
\let\origcref\cref
\newcommand{\crefstar}[1]
    {\begin{NoHyper}\origcref{#1}\end{NoHyper}}
\renewcommand{\cref}{\@ifstar{\crefstar}{\origcref}}

% \crefrange and \crefrange*
\let\origcrefrange\crefrange
\newcommand{\crefrangestar}[2]
    {\begin{NoHyper}\origcrefrange{#1}{#2}\end{NoHyper}}
\renewcommand{\crefrange}
    {\@ifstar{\crefrangestar}{\origcrefrange}}

% \Cref and \Cref*
\let\origCref\Cref
\newcommand{\Crefstar}[1]
    {\begin{NoHyper}\origCref{#1}\end{NoHyper}}
\renewcommand{\Cref}
    {\@ifstar{\Crefstar}{\origCref}}

% \Crefrange and \Crefrange*
\let\origCrefrange\Crefrange
\newcommand{\Crefrangestar}[2]
    {\begin{NoHyper}\origCrefrange{#1}{#2}\end{NoHyper}}
\renewcommand{\Crefrange}
    {\@ifstar{\Crefrangestar}{\origCrefrange}}

\makeatother

So there you go! That nearly beats \autoref!

Why nearly? Unfortunately, cleveref breaks some Springer journal document classes. The author also doesn't claim that it does or does not support item labels (he mentions that it may or may not, so it's uncertain). Finally, I don't like the default choices for some of the label formats. For example, you shouldn't ever start a sentence with an abbreviation, and the parentheses that go around equation numbers should be surrounded by \textup to keep them from looking silly in an italicized theorem environment. That's why I'm saying that by the 1.0 version (it was 0.6 since June of 2007), it should be a pretty awesome package... especially if the modifications above are built into the package.

MacResearch - Online Community for OS X in Science

This might have potential...

MacResearch - Online Community and Research for Mac OS X in Science

MacResearch.org is an open and independent community for scientists using Mac OS X and related hardware in their research. It is the mission of this site to cultivate a knowledgeable and vibrant community of researchers to exchange ideas and information, build a community knowledge-base, and collectively escalate the prominence of Apple technologies in the scientific research community.