Adventures with TeX Live

Since I use the Linux Mint operating system, the obvious (if not only) choice for a LaTeX distribution is TeX Live. (If you are not familiar with, or are not interested in, the LaTeX typesetting system, you have already read too far in this post.) On Mint, Ubuntu and other Debian-type operating systems, you typically …

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Surviving an nVidia Driver Update

Scenario: I’m running Linux Mint 17.3 Rebecca (based on Ubuntu 14.04) on a PC with a GeForce 6150SE nForce 430 graphics card. My desktop environment is Cinnamon. The graphics card is a bit long in the tooth, but it’s been running fine with the supported nVidia proprietary driver for quite some time. Unfortunately, having no …

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Hovering Over Shiny Plots

I’m following up on yesterday’s post, “Formatting in a Shiny App“. One of the features I added to my Shiny application was the ability to identify a point in a plot by hovering over it. Since I wanted to do this in several different plots, and did not want to reproduce the logic each time, …

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Formatting in a Shiny App

I’ve been updating a Shiny (web-based interactive R) application, during the course of which I needed to make a couple of cosmetic fixes. Both proved to be oddly difficult. Extensive use of Google (I think I melted one of their cloud servers) eventually turned up enough clues to get both done. I’m going to record …

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Some R Resources

(Should I have spelled the last word in the title “ResouRces” or “resouRces”? The R community has a bit of a fascination about capitalizing the letter “r” as often as possible.) Anyway, getting down to business, I thought I’d post links to a few resources related to the R statistical language/system/ecology that I think may …

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Connecting Bluetooth Headphones

I recently picked up a pair of Bluetooth headphones (Mixcder ShareMe 7) for use with my laptop (which runs Linux Mint). Getting them to connect properly was a bit of an adventure. After I had things (mostly) sorted out, I decided to script the steps necessary to get them working so that I could just …

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Finding the Kernel of a Matrix

I’m working on an optimization problem (coding in Java) in which, should various celestial bodies align the wrong way, I may need to compute the rank of a real matrix and, if it’s less than full rank, a basis for its kernel. (Actually, I could get by with just one nonzero vector in the kernel, …

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MathJax Whiplash

Technology is continuously evolving, and for the most part that’s good. Every now and then, though, the evolution starts to look like a random mutation … the kind that results in an apocalyptic virus, or mutants with superpowers, or something else that is much more appealing as a plot device in a movie or TV …

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Selecting the Least Qualifying Index

Something along the following lines cropped up recently, regarding a discrete optimization model. Suppose that we have a collection of binary variables $x_i \in B, \, i \in 1,\dots,N$ in an optimization model, where $B=\{0, 1\}$. The values of the $x_i$ will of course be dictated by the combination of the constraints and objective function. …

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Alternative Versions of R

Fair warning: most of this post is specific to Linux users, and in fact to users of Debian-based distributions (e.g., Debian, Ubuntu or Mint). The first section, however, may be of interest to R users on any platform. An alternative to “official” R By “official” R, I mean the version of R issued by the …

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The Monty Hall Evolver

The Monty Hall problem is very famous (Wikipedia, NYT). It is so famous because it so easily fools almost everyone the first time they hear about it, including people with doctorate degrees in various STEM fields. There are three doors. Behind one is a big prize, a car, and behind the two others are goats. …

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An SSH Glitch

Something weird happened with SSH today, and I’m documenting it here in case it happens again. I was minding my own business, doing some coding, on a project that is under version control using Git. After committing some changes, I was ready to push them up to the remote (a GitLab server here at Michigan …

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Coding for kids

I’ve been trying to get my kids interested in coding. I found this nice game called Lightbot, in which one writes simple programs that control the discrete movements of a bot. It’s very intuitive and in just one morning my kids learned quite a bit about the idea of an algorithm and the notion of …

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Thunar Slow-down Fixed

My laptop is not exactly a screamer, but it’s adequate for my purposes. I run Linux Mint 17 on it (Xfce desktop), which uses Thunar as its file manager. Not too long ago, I installed the RabbitVCS version control tools, including several plugins for Thunar needed to integrate the two. Lately, Thunar has been incredibly …

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Parsing Months in R

As part of a recent analytics project, I needed to convert strings containing (English) names of months to the corresponding cardinal values (1 for January, …, 12 for December). The strings came from a CSV file, and were translated by R to a factor when the file was read. The factor had more than 12 …

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Python usage survey 2014

Remember that Python usage survey that went around the interwebs late last year? Well, the results are finally out and I’ve visualized them below for your perusal. This survey has been running for two years now (2013-2014), so where we have data for both years, I’ve charted the results so we can see the changes …

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RStudio Git Support

 One of the assignments in the R Programming MOOC (offered by Johns Hopkins University on Coursera) requires the student to set up and utilize a (free) Git version control repository on GitHub. I use Git (on other sites) for other things, so I thought this would be no big deal. I created an account on …

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Estimate whether your sequencing has saturated your sample to a given coverage

This recipe provides a time-efficient way to determine whether you’ve saturated your sequencing depth, i.e. how much new information is likely to arrive with your next set of sequencing reads. It does so by using digital normalization to generate a “collector’s curve” of information collection. Uses for this recipe include evaluating whether or not you …

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Updated Benders Example

Two years ago, I posted an example of how to implement Benders decomposition in CPLEX using the Java API. At the time, I believe the current version of CPLEX was 12.4; as of this writing, it is 12.6.0.1. Around version 12.5, IBM refactored the Java API for CPLEX and, in the process, made one or …

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Being a release manager for khmer

We just released khmer v1.1, a minor version update from khmer v1.0.1 (minor version update:220 commits, 370 files changed. Cancel that — _I_ just released khmer, because I’m the release manager for v1.1! As part of an effort to find holes in our documentation, “surface” any problematic assumptions we’re making, and generally increase the bus factor of the khmer project, …

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Learning R

I have recently dedicated myself to learning R, a programming language and environment for focusing largely on statistical analysis and computing. The benefit of using R over other statistical computing packages is that it is free, open-source, and has a hugely active community around its use.  R can be used cross-platform  (PCs, Macs, and Linux) …

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A Java Slider/Text Combo

A few years back I was coding (in Java, of course) the <shudder>GUI</shudder> for a research program. I needed to provide controls that would let a user specify priorities (0-100) scale for various things. Two possibilities occurred to me, with pretty much diametrically opposed strengths and weaknesses. Sliders have a few virtues. Grabbing and yanking …

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CP Optimizer, Java and NetBeans

After years of coding CPLEX applications in Java, I’ve just started working with CP Optimizer (the IBM/ILOG constraint programming solver) … and it did not take me long to run into problems. As with CPLEX, you access CP Optimizer from Java through the Concert API. As always, I am using the NetBeans IDE to do …

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