Author: Luke Miller

• September 2, 2012

  Tide height prediction with the Arduino

  A collaborator of mine, Dr. Jeremy Long at SDSU, approached me with the idea of building a system to recreate rising and falling tide heights in his aquaria. One of the keys to making this work was having some way to specify what the tide height should be at any given time. While there is…
• July 11, 2012

  R scripts for downloading iButton Thermochron dataloggers

  Last time, I posted some R code to help quickly launch many iButton Thermochron temperature dataloggers with the same mission parameters. The R code makes use of a publicly-available command line utility released by the iButton’s manufacturer, Maxim.  Of course, Maxim also has a command line utility for downloading the data from those iButtons that…
• March 23, 2012

  Launching iButton Thermochrons with the help of R

  Maxim’s iButton Thermochron temperature dataloggers are little silver doo-dads the size of a large watch battery that can record up to 2048 time-stamped temperature values. The internal battery is usually good for a few years of use. Maxim supplies a Java-based application for talking to iButtons to start recording or to download results. This program,…
• March 11, 2012

  Plotting stuff on an image

  Recently, I needed to figure out how many extension cords I was going to need to buy in order to reach parts of my field site. Wandering around in the field with a surveyor’s tape was an option, but so was plotting distances on an aerial image I had of my site. What follows is…
• January 25, 2012

  ncdf4 R package binaries for Windows

  David Pierce has made available a pre-packaged Windows binary version of his ncdf4 package for R. Go to his ncdf page to download the zip file you need. The current file at the time of this writing is ncdf_1.8.1.zip. http://cirrus.ucsd.edu/~pierce/ncdf/ After downloading the zip file to your Windows computer, you can install this R package…
• January 12, 2012

  Eclipse and StatET 2.0 Install For Running R

  The Eclipse IDE with StatET plugin, developed by Stephen Wahlbrink, is one of the more (maybe the most) full-featured options for running R. I’ve written about this combination before (previous post), but the highlights include a script editor with syntax highlighting, code completion, an integrated graphics window, an advanced debug system, and the best object…
• December 5, 2011

  Loading OSU’s VGPM ocean productivity data in R

  Oregon State University makes a set of ocean productivity data derived from satellite data available for download and use by researchers. The Ocean Productivity website explains the available data and how it was derived. I have put together a few R functions to open a subset of the available data files and plot the data.…
• September 7, 2011

  Digitizing data from old figures with ImageJ

  Following on this earlier post concerning the retrieval of data from figures in published papers with R, here is a method for doing the same with ImageJ. This is a freely available program that should run on Windows/Mac/Linux, just like R. To extract data points from a figure, you’ll need the Figure_Calibration plugin developed by…
• August 19, 2011

  ImageJ paint brush tool keyboard shortcut

  ImageJ is easy to modify if you know a bit of Java. I don’t know any Java. But here’s what I did to add keyboard shortcuts for the paint brush tool and the line selection tool. The code is based off this help file from the ImageJ website: http://rsbweb.nih.gov/ij/docs/guide/userguide-32.html The first step was to figure…
• August 12, 2011

  Measuring leaf or algae blade area in a digital photo with ImageJ

  The following is a tutorial on using the freely available ImageJ program from the National Institutes of Health for estimating the area of a leaf or algae blade (or anything else). The process is straightforward once you understand the various steps. You must begin with a photograph of your object, flattened and dried off as…