Brief mention in Map-making on a budget

Some of the R code I have previously posted here for working with NOAA’s optimal interpolated sea surface temperature (OISST) datasets made its way into a recent piece in a Nature news and commentary piece on open-source map-making tools by Jeffrey Perkel. The article details the expansion of open-source tools for visualizing spatial data that have become more prevalent and more powerful in open-source programs like R and Python. The author merged the sea surface temperature data with a leaflet map and hurricane track data from the National Hurricane Center.

The R code to merge the datasets and generate … Continue Reading

Waterproofing sensors for mussel monitoring

We have recently published two new papers in the Journal of Experimental Biology detailing the results of field experiments we carried out. Our goal was to monitor the behavior and internal temperatures of sea mussels (Mytilus californianus) on the shoreline, and link their recent experiences to their physiological status. There can be substantial variation in the environmental experience of mussels sitting only a few centimeters away from each other, and this project was an attempt to catalog that variation for the first time in a wave-swept rocky intertidal environment. This project involved the development of a new datalogger system (MusselTracker) … Continue Reading

Field work at Bodega Marine Lab

Last week was the kickoff a new project looking at diversity and productivity effects of nutrient and temperature alterations in high intertidal pools. This work is being done in collaboration with Matt Bracken’s Marine Biodiversity Lab group at UC Irvine. Pictured below are Dylan Projansky from SJSU, Matt Bracken (center), Genevieve Bernatchez (UCI), and Samuel Bedgood (UCI, bending over reading the YSI DO sensor).

Evening sampling in the high intertidal zone.

A solar-powered tide clock using Arduino tide prediction libraries

Robert Werner has developed a solar-powered tide clock using my Arduino tide prediction libraries (GitHub link) I previously described here and here. The Instructables page shows how Robert used a servo motor to actuate a pair of hands on a dial face. The red and blue hands give you the time of the next high tide and low tide, respectively.

In Robert’s tide clock, an Arduino programmed with the tide prediction library for Anchorage Alaska keeps time with a real time clock (RTC) chip. At set intervals, the Arduino checks the current time, and makes a … Continue Reading

Processing Rmarkdown documents with Eclipse and StatET

Processing R markdown (Rmd) documents with Eclipse/StatET external tools requires a different setup than processing ‘regular’ knitr documents (Rnw). I was having problems getting the whole rmarkdown -> pandoc workflow working on Eclipse, but the following fix seems to have resolved it, and I can generate Word or HTML documents from a single .Rmd file with a YAML header (see image below).

A .Rmd document with YAML header set to produce a Microsoft Word .docx output file.

For starters, I open the Run > External Tools > External … Continue Reading

R plotmath functions combined with variable values

Getting certain special symbols into R plots, combined with values that are currently stored in variables, has been an ongoing headache of mine. In particular, plotmath symbols such as the plus-minus sign (±), for which the plotmath command is %+-%, had always caused problems due to my inability to parse the R help documentation. For an example, I was trying to get the following simple value (a mean ± 1 SE for a temperature difference) inserted into a plot (a minimalist example):

It turns out that the plotmath operators that are surrounded … Continue Reading

Conference live tweets revisited

Having just returned from the 100th Anniversary meeting of the Western Society of Naturalists meeting in Monterey, it seems like a fine time to generate some new summary data of trends in live-tweeting meetings. I originally addressed this some time last year in this original post: Since that time, there’s been new iterations of the WSN meeting and the Ecological Society of America meeting. I’ve scraped the Twitter archives for the relevant meeting hashtags (#wsn100 and #esa2016), and removed all retweets, so that only ‘original’ tweets are tallied here.
WSN 2016
Shown first below are the meeting totals for the … Continue Reading

Student poster presentation at WSN 2016

It was the 100th anniversary of the formation of the Western Society of Naturalists this year. While WSN was originally a society with fairly broad interests in the terrestrial and marine realms, in the last few decades it has very much become focused on marine habitats, with the occasional estuarine or terrestrial presentations popping up. I try to make a point of going every year, since it’s a great way to catch up on marine science along the west coast of North America (and elsewhere on the globe), and it’s a very student-focused meeting, with at least half of the … Continue Reading

“Robomussels” in the New York Times

Robomussel in mussel bed at Hopkins Marine Station, Pacific Grove, CA.

Robomussel in a mussel bed at Hopkins Marine Station, Pacific Grove, CA.

For several years, starting first at UC Santa Barbara around 1999/2000, and then in the mid 2000’s and early teens at Hopkins Marine Station, I would spend one or two low tides per year going out to the seashore and gluing fake plastic mussels into the middle of real mussel beds (as shown above). These ‘robomussels’ were originally created by Brian Helmuth (now of Northeastern University), … Continue Reading

rtide: a R package for predicting tide heights (US locations only currently)

Joe Thorley at Poisson Consulting has released a new R package, rtide, (on which I am listed as a co-author) that provides the ability to predict future (and past) tide heights for 637 different tide stations in the United States and associated territories. The underlying data, consisting of tide harmonic constituents, are collected and released by the National Oceanic and Atmospheric Administration. The author of the definitive open source tide prediction software, XTide, collates those harmonic data into a usable format, and we have harvested the data to create the … Continue Reading

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