Code Comments

Simple Multi-Threading Example in Java

This week I spent some time figuring out how to use multiple threads in Java. Well, really, I just learned the basics. But it was enough to get a functional example working, and it took me less time than I anticipated. I won’t go into a lot of detail on how to do this because [...]

How to Add a Footnote With No Number in LaTeX

In LaTeX, it is very easy to create footnotes. The simplest way is to use this syntax: \footnote{put text here} In some cases, you might want to suppress the number on a footnote. I looked around the web, and a few suggestions were out there, but the simplest one I could find was the following: \let\thefootnote\relax\footnotetext{put text here} Depending [...]

Adding Math/Greek Symbols in LaTeX Text Mode

One of the strengths of LaTeX is that it handles special symbols quite well and is well suited for mathematical annotation in general. However, sometimes you need to add special symbols to the main body of your document and it doesn’t make sense to do it in math mode. Two examples of this are when [...]

Putting Labels Above Bars in Barplots in R

Let’s say you are creating a barplot in R. Sometimes you want to label the bars below the X axis. But sometimes you might also want to put a label above the bars. This is pretty easy to do but a little hidden. Below is a working example based on randomly generated data that illustrates [...]

Creating a Shortcut to Open Terminal in Specific Directory in Ubuntu

I finally made the leap to doing most of my research on computers that run on Linux. The distribution I’m using is Ubuntu. So far I’ve found it quite good. One thing I do frequently is open a Terminal (command) window in a specific directory. However, when you open the Terminal, it by default opens [...]

Solving “cannot find xml2-config” on Ubuntu 9.10

I was trying to install some packages in R recently that depended on the XML package. I used the nifty install.packages() command, but I was getting an error: “cannot find xml2-config” This error was preventing these other packages from being installed properly. It turns out that I needed to install a library called libxml2-dev. In my case, [...]

How to Create a Simple ROC Curve

I’m using the R statistical package and the ROCR package within that. Both of these are free and very flexible. Sometimes with that flexibility comes ambiguity as to what you should do to accomplish a relatively simple task. I am doing a data-mining (machine-learning) project in which I predict a cancer patient’s prognosis. The algorithms [...]

How to Access Slots in S4 Classes in R: Area Under Curve Example

In the R statistical package, you have various ways of representing and packaging data. The most simple is in a single variable. More complex representations include vectors, lists, matrices, and data frames. An even more complex representation is S4 Classes, which are intended to simulate object-oriented programming in R. I was using an R package that [...]

How to Restart Figure and Page Numbering in LaTeX

When you’re creating a document with LaTeX, you sometimes want to restart the page numbering. In my case, it’s because I have an appendix (supplementary methods) section in a paper I’m writing. I want to be able to reference the figures in this section starting at 1 rather than starting at the number of the [...]

Dynamically Invoke a Function in Python

In this post, I referred to an article that explains how to invoke methods dynamically (when you have the name of the method as a string object). Today I ran into a problem where I needed to do this, but the methods were not contained within a class. I just had them declared in my [...]