Early Open Wave Height Logger battery tests

The Open Wave Height Logger prototype stack.

The Open Wave Height Logger prototype stack.

Following on the previous post about the Open Wave Height Logger project, I’ve been conducting a simple battery life test. One of the prototype OWHLs was powered by a 3 D-cell alkaline battery pack and shoved in the freezer for 32 days. The image below shows the collated daily data files for that time period, during which the data logger was sampling 4 times per second continuously. The black line is pressure in millibar, … Continue Reading

Open Wave Height Logger

OWHL – The Open Wave Height Logger
OWHL is a project originally dreamed up by Jarrett Byrnes and Ted Lyman at UMass Boston. Early on they contacted me for my thoughts on how to accomplish the goal of making a cheap, long-life pressure sensor data logger that could be used to record ocean wave heights near shore. I joined the effort during the initial specification stages. Ideally this device could be mounted on the seafloor at ~10 meters depth offshore, and record surface waves at 4 Hz for many months, with data saved to a micro SD card in a … Continue Reading

Lizards

Smug looking lizards.

Papoose_narrows_lizard_13

Midday, 100mm f/8

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100mm f/8

They seem awfully contented.

Thomson Reuters Web of Science is still using OCR text recognition for new citations?

A co-author emailed me the other day to point out that somehow my name had been misspelled in the Web of Science citation database on our recent paper in Ecological Applications.

The Web of Science listing has my first name listed as “Luice”, which judging by the name of this here website, isn’t how you spell my first name. Thomson Reuters managed to replace the “k” in my name with an “ic”. That looks suspiciously like an optical character recognition (OCR) error , which you might have run into if you’ve ever scanned in an old document and … Continue Reading

Arduino code for MS5803 pressure sensors

I have recently been developing a library for the Measurement Specialties MS5803 line of digital pressure sensors. These sensors are available in several different pressure ranges from 1 to 30 bar, they are submersible if installed in a proper housing, they communicate via I2C or SPI, and they cost around US$35. It’s fairly straightforward to interface the MS5803 with a microcontroller like the Arduino that can also communicate via the I2C or SPI protocols. They are a surface-mount style chip, meant to solder onto a 1.27mm pitch SOIC-8 layout (like the green board I used in the picture below). … Continue Reading

NOAA OISST v2 High Resolution daily sea surface temperatures with R

Update, 2015-11-30 It appears that NOAA has gone through and upgraded all of the OISST files to the newer version of the NetCDF file format. As a result, the functions outlined in this post don’t work any longer. Instead, see the updated functions in my newer post, http://lukemiller.org/index.php/2014/11/extracting-noaa-sea-surface-temperatures-with-ncdf4/. The concepts are the same as described here, but the newer functions use the ncdf4 package to access the newer NetCDF file format.

The National Ocean and Atmospheric Administration generates freely-available world-wide estimates of mean daily sea surface temperature, and has been doing so back to 1981. The data are on … Continue Reading

Part 2: Make your R figures legible in Powerpoint/Keynote presentations

In the previous post, I outlined some tips for increasing the size of figure labels for figures that are meant to be displayed on a projector. The previous post used the base R plot() function, but the procedure when plotting with ggplot2 is different and usually quite a bit simpler than the stock R plotting functions. As before, I’m outputting the figures here as 1024×768 PNG image files, since they’re sure to work in whatever version of PowerPoint or Keynote you’re stuck using.

I’ll begin by generating some random data and dates to use in the plots. … Continue Reading

Make your R figures legible in Powerpoint/Keynote presentations

Having just returned from the SICB 2014 meetings, the appearance of many people’s Powerpoint figures is fresh on my mind. The sheer number of tiny figure labels (tick marks, axis titles, legend text etc) is disappointing. If we want to point fingers, MATLAB users are clearly the worst offenders because of the microscopic default label sizes in that program, but there are plenty of illegible R and matplotlib figures out there as well. Excel is obviously its own special class of terrible, but we will speak of it no more. The default settings in most of these programs … Continue Reading

Seastar wasting syndrome

2013 is turning out to be a bad year for seastars (starfish) along the west coast of North America. As documented by this UC Santa Cruz monitoring webpage, a wasting disease of unknown origin (possibly caused by bacteria or a virus) is causing seastars of several species to fall apart. The map provided by the monitoring group shows all of the places where affected seastars have been found. Seastars on the seashore and below the surface are being found with the disease.

I happened upon a Pisaster ochraceus in the mid-intertidal zone at Hopkins Marine Station today … Continue Reading

Measuring respiration rates

Here’s what the last month of my life was like.

This video shows the process of measuring limpet respiration using a fluorescence-based oxygen measuring system and a custom-built 15-well respiration chamber. The water bath maintains the desired temperature, and the user’s only job is to sit there and move the fiber optic probe to each well and take a reading for ~10 seconds. This goes on for two hours, and then you get to clean up, weigh all the animals, and move on with your life

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