Author: Luke Miller

• December 19, 2012

  Generating polygon boundaries for plotting simple time series data with missing data

  Every so often I want to plot some data with pretty upper and lower error bounds, such as temperature data through time, perhaps with the maximum and minimum temperature range or standard error bounds for averaged data. The polygon( ) function can make those sorts of pretty plots. However, I’ll often have chunks of missing…
• December 16, 2012

  Adventures in kludgy software – Diving PAM edition

  As a general rule, expensive pieces of lab equipment must come with software of questionable quality. In this case, I just want the raw data off a $20,000 submersible DIVING-PAM fluorometer, which can be used for measuring the photosynthetic yield of algae and plants out in the field, away from a computer. But downloading the…
• December 11, 2012

  Waterproofing iButtons, and reading waterproofed iButtons

  iButton temperature dataloggers are tiny, long-lived temperature sensors that are great for all kinds of environmental and biological monitoring, but they’re a long ways from waterproof. Old farts will regale you with tales of a bygone era when you could leave a bare iButton submerged in seawater for months at a time without problems, but…
• November 17, 2012

  The new definitive guide for setting up Eclipse, StatET, and R on Windows 7

  Quite a while back I wrote some tutorials on getting the StatET plugin for Eclipse running, so that you can write R code and run it within the Eclipse development environment. The developers of all of these pieces of software have kept marching on with the development process, so my walk-throughs are getting a little…
• October 31, 2012

  Have some squid

  You might be forgiven for thinking that the ocean is an endless bounty of edible goodies when you walk outside and find squid just strewn everywhere on the beach, waiting for you to pick them up and eat them. This happened the other day at work, when a group of juvenile Humboldt squid (Dosidicus gigas)…
• October 17, 2012

  Adding p values and R squared values to a plot using expression()

  I was fooling around with including a p-value and R2 value on a plot I was putting together, and found myself quickly descending into the world of R graphics esoterica. I wanted to be able to include the values on the fly using values extracted from a linear model summary object, and I wanted to…
• October 8, 2012

  Another R + iButton script

  Previously I’ve detailed R scripts that automate the launching and downloading Maxim iButton thermochron data loggers. I’m typically doing the launching and downloading at separate times in my workflow, since I have duplicate iButtons to swap out, so separate scripts work for me. Ryan Knowles recently contributed a combined version of these scripts that downloads…
• October 6, 2012

  ATtiny84 LED display and heater project

  Here’s a little project that uses an ATtiny84 microcontroller, programmed with the Arduino software, to build a thermostatically-controlled heater. It allows the user to choose a temperature setpoint, and then displays the current temperature using an Adafruit 4-digit 7-segment LED display over I2C. The youtube video below demonstrates part of the project, where an ATtiny84…
• October 3, 2012

  USB extension cables

  Here’s a standard USB webcam sitting on top of 30 meters of USB extension cables (three 10 meter cables). Three cables daisy chained together with the webcam attached to the end seems to be the functional limit. Adding a 4th 10-meter cable results in the camera not being recognized. These 10 meter extension cables, also…
• September 2, 2012

  Using Arduino tide predictions

  In the previous post, I outlined some Arduino code to generate tide height predictions for a NOAA tidal reference station. Now let’s do something useful with this newfound functionality. In the experiments I run, it’s useful to keep intertidal animals like snails and limpets on a natural tidal cycle. In addition, some animals like high-shore…