Book Review: Mixed Effects Models and Extensions in Ecology with R


Mixed Effects Models and Extensions in Ecology with R
Zuur, A.F., Ieno, E.N., Walker, N., Saveliev, A.A., Smith, G.M.
Springer, 2009

Somewhere along the line you probably realized that your undergraduate statistics classes didn’t quite cover the breadth of topics you’d end up needing for dealing with your data. The time constraints of a typical quarter or semester-long biostats class often leave you only scratching the surface of all of the issues you need to consider when analyzing a typical ecological data set. That’s … Continue Reading

Time lapse of fall 2010

The video above is a series of photos, taken around 8am daily between Oct 10, 2010 and Jan 1, 2011. The view is of the backyard of my current abode. Taken with a Canon 5D (try the HD version on youtube), 35/1.4, Av mode at f/8, ISO 200. My ocean view, such as it is, reappeared around Thanksgiving, and the first snow hits December 21st.

Additionally, below is a 1-day time lapse of the snow storm that hit Boston on January 12, 2011. The images were … Continue Reading

Book Review: A Beginner’s Guide to R

A Beginner's Guide to R

A Beginner’s Guide to R

Alain F. Zuur, Elena N. Ieno, Erik H.W.G. Meesters
Springer, 2009

So you’ve decided to start learning R. Probably because someone in your institution, typically a gentleman with an unkempt beard who likes to rail on about open source software, has convinced you to abandon the comfortable GUI-driven statistics program you learned in undergrad. But it quickly becomes apparent that leaving the familiar point-and-click interface of JMP or Minitab or (horrors) Excel for the text-driven world of R isn’t as simple as downloading … Continue Reading

Book Review: R in a Nutshell

R in a Nutshell
R in a Nutshell
Joseph Adler
O’Reilly Media, 2010

If you’re looking for an introduction to the R computing language and statistical platform, R in a Nutshell, by Joseph Adler, may be worth a look. This book is a member of O’Reilly Media’s “In a Nutshell” series that may be familiar to you if you dabble in programming. The goal of the book is to introduce the reader to many aspects of the R language, from the basic architecture and syntax of R to some of the many available … Continue Reading

Book Review: Practical Computing For Biologists


Practical Computing for Biologists
Steven H. D. Haddock and Casey W. Dunn
Sinauer, 2010

Practical Computing for Biologists is an ambitious book that primarily aims to demystify many of the problems that most biologists will hit at some point in their research that can be solved with a bit of simple programming. The book does an admirable job of achieving this goal by exposing the reader to a number of freely available programs and techniques for dealing with text files and other data types. Much of the book (Parts 1-4) … Continue Reading

R 2.12.0 and Eclipse with StatET installation


A while back I outlined the setup process for running R under the Eclipse integrated development environment with the help of WalWare.de’s StatET plugin for Eclipse, in Windows 7. This post is an update on that procedure for the newer versions of each of the programs now available.

Specifically, this information pertains to an installation of Eclipse 3.6 (Helios), StatET version 0.9.1.b201011060900E36sw, and R 2.12.0, under Windows 7 64-bit (circa December 2010). The process for making R work within Eclipse has become a bit more … Continue Reading

Sorting out Sweave in Eclipse/StatET

Using Sweave to produce pretty-looking documentation for R is awfully handy. It takes a little tweaking to get set up in Eclipse and StatET though. I followed the information in Jeromy Anglim’s webpage to originally get Sweave set up. The following is my experience getting it working with Eclipse 3.5, StatET 0.9.1.b201011060900E35sw, Sweave Add-on for StatET 0.9.0.b201011060900E35sw, MiKTeK 2.9, and R 2.12.0 i386 on Windows 7 x64 circa November 2010.

I initially wrote a .Rnw file to be run through Sweave and converted to a pdf. I then set up Eclipse to process the .Rnw file using Sweave. I … Continue Reading

Altering Eclipse user name

Using StatET’s code generation templates is handy, but the standard Eclipse variable for ${user} just inserts the currently logged-in user’s account name. If you want a different name to appear when ${user} is called, one method is to alter the eclipse.ini file.

Specifically, add the line
-Duser.name = Your full name
at the end of the .ini file.

For instance, my eclipse.ini file looks like this:
-startup
plugins/org.eclipse.equinox.launcher_1.0.201.R35x_v20090715.jar
–launcher.library
plugins/org.eclipse.equinox.launcher.win32.win32.x86_1.0.200.v20090519
-product
org.eclipse.epp.package.jee.product
–launcher.XXMaxPermSize
256M
-showsplash
org.eclipse.platform
–launcher.XXMaxPermSize
256m
-vmargs
-Dosgi.requiredJavaVersion=1.5
-Xms40m
-Xmx512m
-Duser.name=Luke Miller

When I open a new R-script file in Eclipse now, StatET automatically inserts that user name.

You can further alter the generated code in the Eclipse Preferences window. Go to Window>Preferences and you’ll get the following window.

[caption id=”attachment_502″ align=”aligncenter” … Continue Reading

Current temperature conditions at the Marine Science Center

Updated December 2013: The seawater temperature monitoring is no longer functional since I moved away and someone turned off the computer. The data I collected for 2010, 2011, and part of 2012 are available as one csv file: 2010-2012_MSC_temps.csv  The time stamps are all in Eastern Standard Time (UTC-5, no daylight savings time) and the water and air temperatures are in degrees Celsius.

I put together a temporary monitoring system for the seawater temperature and air temperature here at Northeastern University’s Marine Science Center in Nahant, Massachusetts.

The monitoring system is was running using some homebrewed Labview code … Continue Reading

Analyzing gels and western blots with ImageJ

The following information is an updated version of a method for using ImageJ to analyze western blots from a now-deprecated older page.

If you’re looking for a more comprehensive workflow option for your western blot analyses, please visit my tutorial on using Image Studio LiteIS_lite_icon, a free software package from LI-COR Biosciences. The Image Studio Lite software can be downloaded for free from www.licor.com/islite. In addition to the functionality described below for ImageJ, Image Studio Lite provides additional … Continue Reading

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