Keep on Fighting!

For a long time I’ve been wondering why we are not able to use Enter in the LyX Scrap environment which was set up by Gregor Gorjanc for Sweave. Two weeks ago, I (finally!) could not help asking Gregor about this issue, as I’m using “LyX + Sweave” more and more in my daily work. He explained it here: LyX-Sweave: mandatory use of control+enter in code chunks

After digging into the LyX customization manual for a while, I found a solution which allows us to press the Enter key just as we normally do when typing in a LyX document. The key is to use Environment instead of paragraph as LatexType for the style definition of Scrap. Besides, I used the LatexName as wrapsweave, as a LatexName is required by LyX. The definition for wrapsweave is simple: just two empty lines by \par. (If you define it as \newenvironment{wrapsweave}{}{}, you will run into troubles sometimes; especially when you use indent for paragraphs.)

As we know, LaTeX environment cannot be centered in LyX (only paragraphs can), so I defined a special environment ScrapCenter when I want to insert graphics via Sweave and make them center-aligned.

Since animation 1.0-9, we will be able to create a PDF document with an animation embedded in it; the function is saveLatex(), and its usage is similar to saveMovie() and saveSWF(): you pass an R expression for creating animations to this function, and this expression will be evaluated in the function; the image frames get recorded by a graphics device. In the end, a LaTeX document is written in a directory, and we can get a PDF document by running pdflatex on the document.

In fact, the key point is the LaTeX package named animate, which can be used to insert image frames into a PDF document to generate an animation. The interface of animations created by this package is quite similar to the HTML animation page by the R package animation, moreover, it also uses JavaScript (in PDF) to animate the image frames.

I‘d like to thank Prof Michael Friendly for telling me this: just create a hyperlink to the file with the run protocol and then you can open a file directly from the hyperlink. For example, in LaTeX with hyperref package, you may use \href{run:path/to/some.file}{some link} to open this some.file in your PDF. This is a useful hack that I have been looking for over a long time.

I have spent three days on these two plugins. The first one “animation” is written by myself after a quick view of the instructions on writing plugins for Dokuwiki, as there is no such kind of plugins so far. What I want to say is “Regular expression is really a devil”! It has almost taken me a whole day to understand how to use a correct pattern to match the parameters in the tags…

Then I modified the “math” plugin so that it is much easier and more familiar for us to type LaTeX formulae in the wiki pages: just use $...$ or $$...$$. People who are familiar with LaTeX surely know what they mean.

By the way, Philippe Grosjean has kindly provided me the necessary files for highlighting R code in the Dokuwiki system. That’s really fantastic! See this page for some examples.

So the main infrastructure has been built till now; the next step is to modify my animation package and include more functions which have been in my mind for a long time. Then I will begin to migrate the old web pages in http://R.yihui.name to AniWiki.

I suddenly realized just now that the line breaks for LaTeX code in Rd files are also \cr instead of \\ (which I thought to be in the past). R CMD CHECK will replace your \cr with \\ when producing LaTeX documentation files. If you write \\ directly in Rd files, it will be recognized as “an escape character + a backslash“, which surely is not a line break symbol.

I found such a problem in the documentation file for the function brownian.motion() in my package “animation“. The original code is:

\deqn{x_{k + 1} = x_{k} + rnorm(1)\\
  y_{k + 1} = y_{k} + rnorm(1)}{x[k + 1] = x[k] + rnorm(1)\cr y[k + 1] = y[k] + rnorm(1)}

And actually it should be:

\deqn{x_{k + 1} = x_{k} + rnorm(1)\cr
  y_{k + 1} = y_{k} + rnorm(1)}{x[k + 1] = x[k] + rnorm(1)\cr y[k + 1] = y[k] + rnorm(1)}

I was just to write an email for help but I understood the reason for my problem (by checking the result from R CMD CHECK) before I sent my email.

“Boadilla” is a quite plain theme in beamer class; I like plain styles, but I also want a headline in the top indicating the sections so that I can know where I am when I’m giving a speech. Thus I gave some slight changes to this plain theme: the default headline has been replaced with “infolines“, while the definition of the outer theme “infolines” has also been modified as I don’t have any subsections.

The original headline:

\ifbeamer@secheader\else\setbeamertemplate{headline}[default]\fi

The modified version:

\ifbeamer@secheader\else\setbeamertemplate{headline}[infolines]\fi

Downdload the file here

You may visit http://yihui.name/en/2007/10/jokes-in-statistics-a-talk-to-be-given-in-cueb/ to see the effects of my modifications.

When I was adjusting my slides for a talk (to be given in Oct 16) in the Capital University of Economics and Business, I found the table of contents was a little bit too long to be placed in a single page while the titles of all sections are not so wide, thus I searched for some instructions on multi-column pages in LaTeX, and easily got this Wikipedia page: http://en.wikibooks.org/wiki/LaTeX/Page_Layout. Some codes as follows will just help us separate a part of texts into several columns:

...
\usepackage{multicol}
...
\begin{multicols}{3}    % 3 columns
   If you are using a standard Latex document class,
   then you can simply pass the optional argument twocolumn
   to the document class: \documentclass[twocolumn]{article}
   which will give the desired effect.
\end{multicols}
...

This is what my table of contents looks like now: