More field sampling in Sitka

The process of sampling all of our experimental tide pools in Sitka is slowly coming to an end for this trip. We carried out several rounds of water sampling for water chemistry during the daytime and nighttime, along with surveying diversity in the pools and prepping the pools for the future summer experiment.

Taking water samples for the pH and alkalinity measurements that go into assessing acidification in the pools is incredibly tedious, since it requires a certain amount of care. We draw water up from the bottom of the pool, then slowly distribute … Continue Reading

Alaska in January

In collaboration with Cascade Sorte and Matt Bracken from UC Irvine, and Kristy Kroeker from UC Santa Cruz, we are currently up in Sitka Alaska carrying out seasonal sampling for our NSF-funded project “Collaborative Research: Effects of Multiple Aspects of Climate Change on Marine Biodiversity and Ecosystem Functioning”. Much of the current trip’s work centers around sampling water chemistry conditions in our focal tide pools and surveying what’s living in them (algae and invertebrates).

Water sampling is hard when the tidepool is frozen.

We have a … Continue Reading

Tidepool nutrient cycling manipulations

Summer number 1 of our collaborative research project with the Bracken and Martiny lab groups at UC Irvine is proceeding nicely. Our teams have been manipulating mobile grazers, such as limpets, littorine snails, chitons, and hermit crabs, in experimental tidepools in order to measure the growth responses of the photosynthetic algae in these pools (among many other variables we are measuring). Those algae need to take up nutrients from the tidepool water in order to grow, including nitrogen products, which the herbivore grazers just happen to be recycling through their urine as they eat other algae in the pools.

[caption id=”attachment_2440″ … Continue Reading

We’ve moved

As of August 2018, I relocated my lab, and everything else in my life, to San Diego. I have joined the San Diego State University Biology Department as an Assistant Professor.

If you are a student interested in undergraduate, masters, or Ph.D. research opportunities in marine ecophysiology, biomechanics, and climate change impacts on rocky shore and nearshore communities, feel free to contact me at my school email (the email is real hard to figure out, so good luck).

For non-academic inquiries about content on this site, please continue to use the … Continue Reading

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