The Geomblog

I've been forcing myself to learn enough R and ggplot to make nice looking plots. It's taking me painfully long to learn to do even the most basic things, and +Carlos Scheidegger has been a big help !

What makes learning ggplot hard is grasping its underlying design philosophy. There's a notion of layers in a plot that I'm still getting used to. Once you get the hang of it it's quite elegant, and makes modifying plots very easy -- once you get the hang of it.

All of which makes me a little more sympathetic to people who struggle with using LaTeX. LaTeX has many of the same unnatural design principles, starting with the lack of a WYSIWIG interface (and no, LyX doesn't really count). It's an incredibly powerful interface (like ggplot), but it's darned hard to do simple things.

In fact, I've been wishing for a "Word equivalent" for ggplot2. Just like overleaf.com is now trying to make LaTeX easier for the general public, I would love to see some kind of interactive interface to ggplot2 that can generate the code automatically for standard tasks.

Here's the talk announcement:

Did you know that every time you use $..$ to italicize text, or use \\ to force a newline, Leslie Lamport cries out in agony and Don Knuth starts another fascicle of Volume IV of TAoCP ?

Come and learn about how to use LaTeX, and use it well. Your collaborators will love you, your advisors will love me, and you'll realize that the most awfully written drivel looks awesome when typeset well.

This will be interactive!! I'll be using a shared space for editing and viewing latex documents, and there will be class activities, so please do bring your laptops/tablets/other editing device so you can follow along and participate.

For this talk I solicited comments from colleagues as to what they'd like their students to learn. Probably the most useful comment I got was from +Robert Ricci and +Eric Eide: to whit,

• You should really use some kind of IDE to write and build your documents
• Version control is your friend
• *sections should be separate files.
• Text should be readable.
• Use macros where convenient
• Don't reinvent: use the many many built-in packages at ctan.org
• Use tex.stackexchange.com to learn how to hack whatever you need in LaTeX.

A corollary: to see a theoretician editing LaTeX close to a STOC/FOCS/SODA deadline is to realize that theory folk are AWESOME programmers.

At this point, mostly everyone is aware of how to use beamer to make presentations in LaTeX. However, many fewer people (mostly only geometry folk) are aware of Ipe, a kind of next-generation xfig.

You may stop reading right now if

• you always use powerpoint for slides OR
• you rarely have to use LaTeX in slides OR
• you really hate non-WYSIWYG presentation software

Still here ? ok...

I wanted to share a workflow tip that I found quite useful when making slides with step-through animations. Suppose you have a sequence of slides in a presentation that unfold a figure step by step, or animate some algorithm execution etc. Ipe, coupled with a few LaTeX commands, provides a really nifty way of rendering the animation without jumps, misalignments, or misdrawings.

Ipe (and many other drawing programs) has the notion of a layer. More powerfully, Ipe also has the notion of a 'view', which you can think of as a (sub)set of layers. For example, if you have a drawing with layers 1,2,3,4,5, then view 1 might consist of {1,2,3}, and view 2 might consist of {1,2,5}, and so on.

What this means is that when you want to do step-animation, it's really easy. Each time you move to a new step, you create a new view in Ipe (which also usually creates a new layer), and you can select whichever subset of the current set of layers you want to render, as well as drawing new ones.

Ipe stores all the views as separate pages in a PDF file, so your final animation consists of a multi-page PDF file. And now comes the cool part.

Suppose you want to include this sequence of views in a beamer slide, with each view appearing after the next in response to a mouse click. You need two things:

• pdftk (which comes standard in most linux installations), which allows you to split a PDF file into multiple files (one per page), with any format for the filename that you specify. For example, I have a command called 'splitpdf' that does this:

  pdftk 1ドル.pdf burst output 1ドル-%d.pdf

  
  which takes a file name.pdf and splits it into name-1.pdf, name-2.pdf and so on.
  


• Next, you need the (standard) LaTeX package 'xmpmulti' which gives you the command \multiinclude. It allows you to include multiple figures that share a common prefix. So for example, to include all the figures created by the previous pdftk command, you merely write

  \multiinclude[start=1,format=pdf]{name}

  .The 'start=1' starts counting from 1 instead of 0, and you can also specify an end-counter.
  

But the best part is when you instead use

\multiinclude[<+>][start=1,format=pdf]{name}

Now, the files are included with an automatic 'replace each by the next' mode (<+> is standard beamer notation for this). At this point, you have a sequence of animations ready to go. In fact, when I give lectures, I have a number of slides that just look like this:

\begin{frame}
\frametitle{Title}
\mi{name}
\end{frame}

where \mi is a macro I defined for the above multiinclude. Ipe does all the layering and viewing work for me, and multiinclude takes care of the rest. This has made making complicated animations really simple and fast.

p.s if you're still wondering why one should use Ipe instead of xfig, the LaTeX integration in Ipe is superb. No nonsense with special flags, and pstex_t and craziness like that. You get WYSIWYG LaTeX inside Ipe, you can use whatever macros you have in your text, and the various nifty alignment tools make an Ipe drawing look really clean.

I try not to write BibTeX by hand any more: too easy to introduce errors. So I usually use either DBLP or the ACM digital library to get BibTeX for papers. Sometimes the journal has BibTeX, or some format that can be converted. As an aside, IEEE is extremely lame: you have to login to their digital library even to get a citation !

For the most part, I don't need to go beyond ACM or DBLP, which is great. But here's the problem: their formats are different ! I needed the BibTeX for a recent paper of mine, and found it on both sites. Here's what ACM gave me:

@inproceedings{1516372,
author = {Ahmadi, Babak and Hadjieleftheriou, Marios and Seidl, Thomas and Srivastava, Divesh and Venkatasubramanian, Suresh},
title = {Type-based categorization of relational attributes},
booktitle = {EDBT '09: Proceedings of the 12th International Conference on Extending Database Technology},
year = {2009},
isbn = {978-1-60558-422-5},
pages = {84--95},
location = {Saint Petersburg, Russia},
doi = {http://doi.acm.org/10.1145/1516360.1516372},
publisher = {ACM},
address = {New York, NY, USA},
}

and here's what DBLP gave me:

@inproceedings{DBLP:conf/edbt/AhmadiHSSV09,
author = {Babak Ahmadi and
Marios Hadjieleftheriou and
Thomas Seidl and
Divesh Srivastava and
Suresh Venkatasubramanian},
title = {Type-based categorization of relational attributes},
booktitle = {EDBT},
year = {2009},
pages = {84-95},
ee = {http://doi.acm.org/10.1145/1516360.1516372},
crossref = {DBLP:conf/edbt/2009},
bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/edbt/2009,
editor = {Martin L. Kersten and
Boris Novikov and
Jens Teubner and
Vladimir Polutin and
Stefan Manegold},
title = {EDBT 2009, 12th International Conference on Extending Database
Technology, Saint Petersburg, Russia, March 24-26, 2009,
Proceedings},
booktitle = {EDBT},
publisher = {ACM},
series = {ACM International Conference Proceeding Series},
volume = {360},
year = {2009},
isbn = {978-1-60558-422-5},
bibsource = {DBLP, http://dblp.uni-trier.de}
}

So as you can see, we have a problem. The formats are not consistent, which means that if I need to get some references from DBLP, and others from the ACM, my references file is going to look very irregular.

Other critiques:

• I have never understood why DBLP splits up the conference and the paper: with BibTeX, if you cite three or more papers that use the same crossref, the crossref is included itself as a reference, which is just strange.
• Unless you use double curly braces, capitalizations inside a string get removed, which is mucho annoying: It's "Riemannian", not "riemannian".
  
• The DBLP name for the conference is too cryptic: who'd even know what EDBT is outside the database community. On the other hand, the ACM citation is clunky, and is a page-length disaster waiting to happen.

Thoughts ?

Dear journal,
If it isn't too much of a problem, could you possibly attach a BibTeX link to each article that you list ? For the sake of my cruelly abused fingers ? Could you ? PLEASE ?

According to the hyperref documentation, the algorithm package should be loaded after hyperref:

algorithm:
\usepackage{hyperref}
\usepackage[chapter]{algorithm}% eg.

According to the hyperref documentation, all packages should be loaded before hyperref:

In most cases, therefore, you should load your package before you load hyperref, and hyperref will patch things up so that they work, so you can utilise your (patched) package after loading both:

If you do the first, you get this annoying set of warnings:

! pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored

If you do the second, you get an error:

undefined control sequence \theHalgorithm

Clearly, the first is preferable to the second, but even the first is terribly annoying. Does anyone have any ideas on how this can be fixed ?

Update: It works ! A comment from Iain Murray points out that in the hyperref README, one is told to include the float package BEFORE hyperref , and only then include algorithm (after hyperref).

A rather long time ago, I had asked how to track changes in Emacs/LaTeX, along the lines of what Word can do. There were many suggestions at the time, along the lines of using CVS, and one person had even mentioned 'texdiff'.

I actually got around to trying latexdiff today, and it actually works quite well. Given an old and new LaTeX document, it will output a "diff" TeX file that when compiled marks changes in coded colors; blue for insertions, red for deletions. People I know use this all the time for managing changes with collaborators.

The program itself can be run as a standalone Perl script, so it's quite portable. I plan to use it more often.

This is a neat plugin. And just to test it, here's the Johnson-Lindenstrauss Lemma:

For any and any integer n, let be a positive integer such that
Then for any set of points of n points in , there exists a map such that for all ,


Not bad at all !

File this under 'late-night LaTeX griping':

Is there any way of stripping metadata from a PDF file ? I'm writing a referee report for a journal, and used PDFLaTeX to create the report. When I scan it in acroread, there's all kinds of meta data that could identify me.

Now pdftk is a useful package that can strip out some of the simple metadata like 'creator'. However, pdftex adds "Advanced" fields, and one of them is the full pathname of the original LaTeX file. If your filesystem (UNIX) is anything like mine, then a part of that pathname is the /<username>/ section, which in many instances is an almost unique identifier. This also happens with dvipdfm, which uses the gs backend to create the PDF file, and with ps2pdf. pdftk cannot strip out these fields, because it doesn't appear to see them.

I suspect that if I owned a copy of the very-not-free Acrobat, I could meddle around with this metadata. Obviously I could submit the review as a Postscript file, but in general I prefer to maintain PDF. Further this problem also occurs if I want to do due diligence when submitting to conferences with double blind review, and sometimes I don't have the option to use PS.

This is puzzling me, and I am hoping my readers might help:

I want to add a reference to this entry:

@article{ref,
author = {First Last and First M. Last, III},
title = {Insert Title Here},
journal = {Int. J. Comput. Sci.},
volume = 1,
number = 1,
year = 2010,
pages = {137--154},
}

and it comes out looking like this (in my .bbl file):

\bibitem{ref}
{\sc Last, F., and First M.~Last, I.}
\newblock Insert Title Here
\newblock {\em Int. J. Comput. Sci 1}, 1 (2010), 137--154

As you can see, there are two problems:

1. The second name is not formatted in the style of the first
2. The second author has been replaced by their grandparent (!) (the III has been replaced by I).
   

This is using the acm.bst style file. I tried using plain.bst, and the problem persists: the second author is listed as III First M. Last.

I tried standard tricks like enclosing the III in braces, placing commas in certain places, removing them etc. No luck.