Phase Portrait

Thanks, Microsoft, for SP3. I was getting tired of being happy.

2008-05-12T14:51:00.005-04:00

What a stupid fucking bug (KB951446) posted on May 6 with no indication that it will ever be fixed.

So, if you have a single computer (e.g., a laptop) connected to your ICS machine via a crossover cable, every time you disconnect that single computer, your ICS is going to die. The next time you reconnect, you have to restart the ICS service MANUALLY.

Remember that scene in High Fidelity where Rob explains to Barry that he just wants noise on in the background that he can ignore? That's the way I feel about Windows. I don't use it. I don't need it. I don't want it. I just have to have it for a few tedious things, and so I'd like it to sit back and do its thing without getting in my way. Right when I start forgetting that it's there, Microsoft goes ahead and does something to remind me it's still around. It's like some disease that just won't go away.

I've also heard a rumor that XP3's ICS restricts you to sharing your connection with no more than 10 other computers. That's pretty dumb too.

(Am I Just) Fooling Myself

2008-04-14T14:17:00.002-04:00

NPR Song of the Day (April 11, 2008): "Eli 'Paperboy' Reed Channels Soul's Giants" by Marc Silver

Just who does Eli "Paperboy" Reed think he is? The reincarnation of the wicked Wilson Pickett? A skillful James Brown imitator? Winner of the Austin Chronicle's award for "best Otis Redding impersonation by a 23-year-old Jewish boy from Massachusetts"?

Song: "(Am I Just) Fooling Myself"
Artist: Eli "Paperboy" Reed
CD: Roll with You
Genre: Soul

Hear the track at the story page.

Haverin on LiveJournal

2008-03-12T09:35:00.003-04:00

From xkcd/77:

Because it drives me nuts...

2008-03-12T09:21:00.004-04:00

From xkcd/394:

On a serious note, "kB" is "kilobyte" and "kb" is "kilobit." An uppercase "K" is "Kelvin," and so it should never be paired with either "B" or "b". For most modern machines, a "B"yte is 8 "b"its, but there is NO GOOD REASON to assume this case. The meaning of "kilo" is context-dependent, though it's computationally convenient to use 1024 rather than the standard 1000 (because computers address things in base-2).

Snow Wall in Columbus, Sno-hio

2008-03-10T09:54:00.009-04:00

If you didn't hear, over Friday night and Saturday morning, 20 inches of snow were dumped on Columbus, OH. That made driving a little rough Saturday, but the main roads cleared up substantially Sunday. Nevertheless, nearly every school is closed today and Ohio State sent out an e-mail warning people that parking might be a little hairy today.

So, I came to work early this morning not knowing what to expect. After previous big snow weekends, the parking lot would get a little smaller because the plowed snow gets pushed to the edges of the lot causing it to contract. However, as you can see, the lot really looks very good:

So, where did all the snow go?! Well, if I turn 180 degrees around, here's what I see:

Now, I walk a little to my left:

So, you're probably thinking that they just plowed all the snow to one end of the parking lot. However, I'm leaving out a big part of the story. If I KEEP walking, you see this:

and this:

and this:

In other words, they've put a SEVEN FOOT SNOW WALL in the MIDDLE of the parking lot, separating one LARGE parking lot into two smaller lots.

Happy melting!

Fixing Vim-LaTeX Compiler Error Messages

2008-03-05T16:48:00.004-05:00

If you use Vim-LaTeX, you've probably noticed that sometimes errors will cause Vim to open up a completely unrelated file on top of your current file. This is Vim's way of bringing you to the source of the error, but it parsed the latex return text improperly.

The problem is that LaTeX status messages keep track of which file is being used with parentheses over multiple lines. So, in order to figure out where an error is, Vim has to match opening parentheses with closing parentheses over multiple lines. Unfortunately, Vim's compiler error message features cannot do this if multiple parentheses are on one line.

So, I shamelessly borrowed an solution from Luc Hermitte's VIM Macros. Specifically, I was inspired by the vim-tex.sh, which pipes TeX output through a filter that corrects any problems that could confuse Vim. However, I didn't like that his script needed to create a temporary file, so I then borrowed a shell script tip off of a UNIX forum that copies file descriptors around so that actual disk files aren't needed.

The result is vimlatex, a shell script that post-processes TeX output so that it's in a form that Vim likes. To use it, just put it in your PATH and make it executable (i.e., chmod it 0755) and then add vimlatex in front of any compiler command you have. For example, if you have a compiler line in your .vimrc or in your Makefile that starts with latex, insert vimlatex (and a space) in front of the latex (i.e., change latex to vimlatex latex).

Alternatively, any output piped to vimlatexpipe will get properly sanitized for Vim too.

Vim-LaTeX, Vim 7.0, and the filetype plugin

2008-03-05T11:30:00.006-05:00

It's strange to me that this isn't better documented. On the other hand, Vim-LaTeX hasn't been maintained for AGES...

If you're using Vim-LaTeX with Vim 7 or higher, you should make sure you have this somewhere in your .vimrc:

" Prevents Vim 7.0 from setting filetype to 'plaintex' let g:tex_flavor='latex'

Otherwise, your .tex files will not automatically kick off vim-latex on opening!

So, if you're having problems getting Vim-LaTeX to load when Vim opens a .tex file, try making that change (as well as all of the filetype plugin changes to your .vimrc that are documented).

Get Your Head Around my Blue Morning

2008-02-22T11:16:00.004-05:00

Recent NPR Song of the Day tracks for you:

You can stream them from NPR's site (which is linked from each song). I've sent Pandora an e-mail suggesting that they add the songs to their database. On that note, I always get a personal response from one of the people at Pandora whenever I send them a song suggestion. I think that's pretty cool.

Showing your Grandview Colors...

2008-02-10T15:39:00.000-05:00

Outside the Window at Stauf's, a white car was pulled over by a Grandview cop. The white car pulled over near a light, so the cop car stopped in the middle of the intersection. After about five minutes, the cop came out and walked toward the car. A black female was driving the car. After a few minutes of talking to the woman, they asked her to come out of the car, put cuffs on her, and put her in the cop car. She cooperated. No struggle. No argument. No violence.

By this time, two other cop cars had arrived. You can see all three of them in this picture (click for larger).
Here's a zoomed in version that shows the cop car blocking the intersection... (click for larger)
Eventually, the passenger (a black male) moved into the driver's seat, and another cop came and talked to him. After many minutes of talking to him, they asked the black male to get out of the car, and they frisked him (in 14 degree Fahrenheit weather). Eventually they let him get back into the car, but he had to get back into the passenger seat. Evidently, they didn't think he'd be going anywhere anytime soon.

During this whole time, a black child with a little red hat with a light blue winter jacket bounced around in the back seat, trying to figure out what was going on with the adults in the car.

During this whole event, two Stauf's regulars behind me recollected on how the Grandview cops only pull over "ratty cars" and "cars with black people in them". The word "profiling" was used.

Traffic has started to form behind the cop car blocking the intersection.

It'll be interesting to see how long this lasts. Good thing there are three police cars, at least two of which carry multiple police officers.

Like reading my horoscope...

2008-02-10T15:11:00.000-05:00

In a comment on a previous post, I got a complaint that all of my new posts are about computer stuff only. Evidently, I'm much more entertaining when I talk about life.

A little after I left my job in Austin to start grad school, my boss left his job to go to grad school. His most recent post really resonates with me. As a bonus, Clay was always more entertaining than me, so I figured forwarding "you all" to his post would be even better than me taking the time to report on life in general.

From Clay's post:
Sundays are tough at the Menlo Park outpost of the Daigle/Box family. The psychology of it all is as follows: LL takes Sundays pretty badly because it means the weekend is almost over. So she regrets how, yet again, we failed to do anything fun or get any skinnier. For example, last night (which was a Saturday), she wanted to go see a movie, but instead we stayed home and ordered Chinese food, which accomplished neither the fun nor skinny parts of her goals. It is also on Sundays that LL notices the apartment isn't tidy and sometimes that can compound the feelings of not getting stuff done.

I on the other hand, don't mind Sundays that much. My low point actually comes on Friday when, yet again, I feel like I didn't make very much progress that week on school or research or whatever else.
(...continues...)

So, go read about Clay and LL's "Furniture repair!".

I've finally done it...

2008-02-08T12:22:00.001-05:00

After 15 years, I've finally done it.

I've put set -o vi into my profile.

(Sam Cooke's "A Change Is Gonna Come," performed by James Taylor as in the West Wing episode, plays in the background)

MacAlly ICEKey and IOGear MiniView KVM Switch

2008-01-27T15:58:00.000-05:00

Unfortunately, the MacAlly ICEKey USB Slim Keyboard and the IOGear MiniView Micro USB Plus (GCS632U) KVMP switch cannot work together to give you the full functionality of the keyboard.

If you want to use this keyboard with this switch, you have to live with the fact that your volume and eject keys will never work on the keyboard.

There is a method of emulating the special keys using combinations like pressing and releasing "control" and then pressing and releasing "1".

Interestingly enough, the MacAlly iKeySlim keyboard works great with this KVMP switch. Additionally, while the ICEKey requires driver installation, the iKeySlim does not.

So, there you have it. You've been warned.

NOTE: You may have some luck with this tip I found on macosxhints, but I didn't. Let me know if you get something figured out.

Geek Squad sucks

2008-01-14T10:26:00.001-05:00

UPDATE: On January 14, I received a response:
Who sent this to me from info@geeksquadcentral.com?

Thank you!

Sara Yanari
Agent 191
Mission Specialist
Geek Squad Operations - Corporate
Agent191@geeksquad.com
Cell: (612) 919-4855/Office: (612) 291-9689

"Serving the Public, Policing Technology, and Protecting the World"

Want to know more about Geek Squad? Or keep up on the latest info?
Geek Squad Photo Blog: http://www.flickr.com/groups/geeksquad/
Idea Festival: http://www.geeksquad.com/ideafestival
Squad Cast: http://forums....squadcast

There are two possible reasons for this response:
"Agent 191" doesn't understand "Reply-To" and delegating of support messages.
"Agent 191" might think that my message was some internal joke played on her by other people at Geek Squad.
Either way, "Agent 191" looks a bit like an idiot or an ass (or both). When you see those Geek Squad commercials, these are the people you're dealing with.

I sent a snarky response back (one to info, and one to Agent 191 directly), but I haven't received anything else. So, now when I teach classes to my young engineers, I refer to "Geek Squad" where I used to say "lay people." Snap! (or something)

An e-mail I just sent to Geek squad:

Subject: Complaint: Packaging information of CAT-6 crossover cable

"Geek" squad --

     I purchased a CAT-6 crossover cable of yours yesterday. The packaging surprised me. You advertise yourselves as some sort of elite group of geeks, but the printing on the packaging makes me wonder if any of you know anything about technology at all.

     There are several examples on the front of the package, but one sentence in particular is especially troubling:

"Your geek squad network crossover cable uses an RJ45 connection allowing you to connect between similar types of equipment without the use of a hub; one PC to another PC for example."

     The difference between a crossover cable and a standard patch cable has nothing to do with the "RJ45 connection." For one, both cables use a type-45 "registered jack (RJ)". "RJ45" describes the PHYSICAL connector. That is, it describes the PLASTIC end that mechanically snaps into place when the male version is inserted into the female version.

     The difference between a crossover cable and a standard patch cable is the 8P8C (i.e., "8 position 8 contact") termination type. A patch cable has a T568A termination at one end and a T568B termination at the other end.

     It would be wise for you to change the wording to something like:

"Your geek squad network crossover cable uses an T568A-to-T568B termination allowing you to connect between similar types of equipment without the use of a hub; one PC to another PC for example."
Otherwise, it just simply doesn't look like you know what you're doing.

     When I picked up the cable and saw the text above, I was seriously worried that it would have the 500 MHz bandwidth I needed. Unfortunately, because it was the only one available and I didn't want to terminate my own and risk the crosstalk, I had to buy your expensive cable. My computers came up with gigabit link, so I'm guessing things are fine, but I wonder what I'd find if I walked down the hall and tested these things on a network analyzer.

     Clean up your act, Geek squad.

     Thanks for your understanding --
     Ted Pavlic

A bit much? (yes, I realize there's a typo... I said "patch" once where I clearly meant "crossover")

File Associations and PATH with MacVim

2007-12-30T13:19:00.001-05:00

UPDATE: The newest release of MacVim has a preference pane that lets you "Launch Vim processes in a login shell." If turned on, it should solve the PATH problem suffered by some Vim users.

If you use Vim for OS X or the nascent MacVim, you may have noticed that

your PATH is not set correctly (i.e., compilations fail) and
Vim is not associated with all of your text files (i.e., it doesn't show up in the "Open With" context menu)

A while ago, I realized that the gvim.app available for download from the OS X Vim site had the potential to solve both of these problems, and so I hacked it to produce:

gvim.app (for Vim for OS X) and
mvim.app (for MacVim; maybe unneeded if "Launch ... login shell" preference turned on)

To install one of these files, download the archive, unzip it, and move the application into your /Applications folder. If you start Vim from that application, it will open as usual but will have the PATH set as if you were in the Terminal (i.e., it executes a bash login before exec'ing Vim). You should also notice that the new launcher application shows up in your "Open With" menus. Finally, if you put the launcher in your Dock, you can use it to generate new Vim windows, even if Vim is already open.

PDFSync Inverse Searches in MacVim

2007-12-29T16:48:00.000-05:00

Remember the post on doing inverse searches in Vim on OS X? The idea was to drop gvim-pdfsync into

/usr/local/bin

(or somewhere else in your PATH) and then execute

gvim-pdfsync "%file" %line

to do inverse searches in Vim for OS X just like you can in Windows or in other UNIXes. For example, in Skim, under the PDFSync section of the Sync tab of the Preferences, you can put

Preset: Custom
Command: gvim-pdfsync
Arguments: "%file" %line

For MacVim

I thought it might be nice if I published how to do the same thing in the nascent MacVim, which supports servers just like Vim for Windows. Provided that you've installed the mvim shell script somewhere in your PATH, you can setup Skim with

Preset: Custom
Command: mvim
Arguments: --remote-tab-silent +":%line;foldo!" "%file"

or, if you don't like tabs

Preset: Custom
Command: mvim
Arguments: --remote-silent +":%line;foldo!" "%file"

Retro-Approach

Alternatively, if you really liked the gvim-pdfsync approach and want something similar for mvim, put mvimtab-pdfsync or (if you don't like tabs) mvim-pdfsync in your PATH (e.g., in /usr/local/bin) and then setup Skim for:

Preset: Custom
Command: mvimtab-pdfsync
Arguments: "%file" %line

or (if you used mvim-pdfsync)

Preset: Custom
Command: mvim-pdfsync
Arguments: "%file" %line

I hope that helps.

Frum rhymes with Doom

2007-11-18T17:50:00.001-05:00

On the November 15, 2007 episode of Marketplace, they aired a commentary called "Learn a Lesson from the Dark Ages" by conservative demagogue David Frum. I couldn't help but send a response.

This correspondence is regarding "Learn a lesson from the Dark Ages" by David Frum, which aired on Thursday, November 15, 2007.

The argument offered by Mr. Frum is called the "environment Kuznets hypothesis," which is an application of the classic Kuznets hypothesis to conservation. The "environmental Kuznets curve" is a "U"-shaped curve on a plane with conservation on the vertical axis and economic growth on the horizontal axis. That is, with economic growth, conservation decreases until some critical point and then increases.

It's interesting that Mr. Frum uses the Kuznets hypothesis to argue that our salvation comes from focussing on globalization. In fact, the Kuznets hypothesis only matches observational data when looking locally. In developed countries, we do see that economic growth leads to cleaner air and water and increased conservation; rich people embrace their local nature. Unfortunately, the conservation of developed countries comes at the cost of the destruction of the rest of the world. Global energy use and human population growth is still on the rise and global conservation is still falling. Additionally, every species we drive to extinction is lost permanently, so it's hard to imagine that the global conservation-growth curve can ever slope upward.

I worry that Mr. Frum's optimism is not simply outdated but is dangerous. I encourage him to consider taking a more conservative approach to the environment.

In retrospect, I could have said "which erred on ..." instead of "which aired on ...," but I would never want to be accused of sounding snarky...

Journal Reviewer Review

2007-10-02T08:45:00.000-04:00

A recent paper of mine was rejected from Journal of Theoretical Biology. For fun, lets compare and contrast and selection from the reviewer comments ("MS" = "manuscript"):

From Reviewer #1:

Overall I really liked the work presented in this MS - by generalising the traditional models of the ecological economics underpinning solitary foraging behaviour the authors offer a very interesting (& in retrospect) intuitively appealing justification for accepting that the concorde fallacy may not always be fallacious.

From Reviewer #2:

This result seems to be of significance in biology, psychology, economics, and business, and I think that the paper is deserving of publication in JTB. The paper is also very well written, and the mathematical presentation is clear and precise.

Those two were pretty nice, and suggest that I should resubmit the paper with a couple tiny revisions and I'll be off and running. Great! Wait... What's this?

From Reviewer #3:

I regret to say I have no idea what this paper is about. The mathematical lingo is completely unfamiliar to me (after about 50 years of teaching and research in maths)...(details omitted)...(I recently had a grad student who wrote in this vein. When I asked him to explain in ordinary math, he gave up.) I didn't read any further. My advice is reject.

HUH?!

Removing WiFind

2007-09-18T08:54:00.000-04:00

The WiFind application from TastyApps has potential, but in the end it falls short and is not worth all of the bother. WiFind will slow down your computer nearly to a halt in some cases. Because the developers made it an input manager without a preference pane, it cannot easily be turned off. Even when it's running well, it still takes a click or two in order to get it to display the information you need.

The free application coconutWiFi is almost identical to WiFind, but because it's an application, it's much easier to install, load, unload, and uninstall.

Getting rid of WiFind can be a major pain (especially if it's in the process of grinding your machine to a halt at the time). The developers gave it an installer (because it's an input manager and not an application), but despite Apple's guidelines that all programs with installers must have uninstallers, they did not give it an uninstaller.

So, here's how I went about turning OFF WiFind. WiFind uses this InputManager called "SIMBL" to modify the wireless menu directly (rather than putting up its own menu, like coconutWiFi). So, you can either remove SIMBL or remove WiFind from SIMBL so that while SIMBL loads, WiFind will not.

To remove WiFind only, look for the folder

/Library/Application Support/SIMBL/Plugins

or the folder

~/Library/Application Support/SIMBL/Plugins

where ~ is your home directory. Inside that folder, you'll find a WiFind.bundle. Move it somewhere else (or delete it) and logout (or restart) to disable/remove WiFind.

Alternatively/additionally, you can remove SIMBL. Look in the folder:

/Library/InputManagers

~/Library/InputManagers

where ~ is your home directory. There should be a SIMBL folder inside one of these. To remove SIMBL, delete the SIMBL folder. To disable it, remove the SIMBL folder. Again, be sure to logout or restart after making this change. When you're logged back in, SIMBL should not be loaded.

If you think you will want to turn this off later, simply move the SIMBL folder out of the InputManagers folder and into some other folder that you create (I created an InputManagersOff folder in my /Library). Next, if you logout (or restart), WiFind will not be started. At some time, you should probably also get rid of the folders

/Library/Application Support/SIMBL/

and

~/Library/Application Support/SIMBL/

where ~ is your home directory.

You might notice that there are files dropped in /Library/Receipts (or maybe ~/Library/Receipts) from WiFind (or wifind) and SIMBL. You may consider removing these files too, but it won't hurt to leave them there.

Ted E.C.E. Bear

2007-09-18T08:42:00.001-04:00

I put this together for my ECE webpage.

That version has a transparent background. I have a version with a white background too.

Cute? Everything except for the bear was actually "drawn" in LaTeX, which I think is pretty cool. The bear is an image I found that Yahoo thought was Creative Commons (CC) licensed. I hope its particular CC license allowed for changes...

American Naturalist BibTeX BST style file

2007-08-31T09:48:00.000-04:00

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.

Viewing man pages and text files in Skim

2007-08-29T13:10:00.000-04:00

As discussed on the Skim wiki, it is possible to view man pages (and more) nicely formatted as a PDF in Skim.

If you use bash, try adding these lines to your .bashrc:

function skimcat () { cat $* | enscript -p - | open -f -a Skim; }
function manp () { man -t $* | open -f -a Skim; }

Alternatively, if you use tcsh, try adding these lines to your .cshrc:

alias skimcat="cat \!* | enscript -p - | open -f -a Skim"
alias manp="man -t \!* | open -f -a Skim"

Then you'll be able to do skimcat to cat files to Skim, and you'll be able to use manp to view man pages formatted in Skim.

NOTE: You can actually pipe anything that is PostScript (or PDF) formatted to Skim (via the open command shown above).

What's wrong with engineers?

2007-08-27T21:47:00.000-04:00

"Love Affair" (Regina Spektor) lyrics

There was a love affair in this building
The kind of love affair
Which every respectable building must keep as a legend
Slowly festering through an innocent "by the way"
Or "have you heard"
He was perfect except for the fact that he was an engineer
And mothers prefer doctors
And lawyers

Yet despite this imperfection
He was clean-looking and respectable-looking
And you'll never find a mother
Who doesn't appreciate a natural man
So he grew healthy aloe vera plants by the window
Healthy teeth in his mouth
Healthy hair on his head
He grew healthy wavy brown hair on his head
The kind, the kind that babies always go for
With sticky little fingers

I have healthy hair and teeth and wavy brown hair. I don't know about the baby thing...

I'm pretty sure my aloe vera plant is dying too...

I suppose it is true that mothers rarely like me...

LaTeX for generating Behavioral Ecology manuscript

2007-08-23T22:16:00.000-04:00

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.

d'Feet ALS Walk Time Again!

2007-08-22T12:15:00.000-04:00

This year, the Columbus d'Feet ALS Walk is on Sunday, September 16, 2007.

My brother has ALS (Lou Gehrig's disease), and we participated in this walk for the first time last year (he was diagnosed last year). There was a great turnout. It was neat to see the support from the community.

So, while it's getting late, I hope people will visit my d'Feet ALS walk page and make a donation or become a walker themselves.

Broken sections in Elsevier elsart1p, elsart3p, and elsart5p

2007-08-08T17:50:00.000-04:00

UPDATE: You should probably add
\def\@seccntformat#1{{\@secnumfont{}\csname the#1\endcsname.}\quad}
around line 128 (i.e., after the \@secnumfont definition) as well. Alternatively, you could add something similar (surrounded by \makeatletter and \makeatother) to your preamble.

Ever notice how section* is broken in elsart1p.cls, elsart3p.cls, and elsart5p.cls from Elsevier? Because of this, the section titles for the acknowledgments (i.e., from \ack) and the references look like normal text. Plus, the references do not show up in the PDF bookmarks. This "feature" is annoying; working with journals generally is.

How to fix this? You have to hack the document class files. In particular, you need to remove (or comment by placing a % on the beginning of the line) a chunk of lines from the document class of interest to you. In particular, remove

elsart1p.cls - lines 144--196
elsart3p.cls - lines 147--199
elsart5p.cls - lines 144--196

These lines redefine the LaTeX internals \@startsection, \@sect, and \@ssect. However, it does not appear there is any good reason why Elsevier has done this, so just stick with the standard ones. This will make your document look much better too.

Until Elsevier does this for you, you should upload your modified document class with your article OR use the elsart document class in the version you send to Elsevier.