R as.Date() and time zones

Here’s a fun quirk to watch out for when playing around in R with POSIX time values and converting them to dates.

I’ll start by creating a time variable, in the POSIXct class, and set it to use my current time zone, which is Pacific Daylight Time (PST8PDT).

mydatetime = as.POSIXct(‘2019-05-29 23:59’, tz = ‘PST8PDT’)

If I then wanted to turn this time into a simple Date, dropping the time information, I would (naively) do the following:

as.Date(mydatetime)… Continue Reading

Building a new bivalve gape sensor datalogger

It’s construction time in the laboratory again. This time we’re building shell gape sensors for oysters, based on a datalogger design derived from the MusselTracker datalogger I designed a few years back.

In this new design, we can have up to 16 gape sensors attached to one datalogger, though we’ll just have 10 to start with right now. These will be deployed on a mooring inside an estuary, so they will primarily need to be protected from a bit of wave splash and rain. But they’ll be built with the same kind of … Continue Reading

Dynamic measurements of black oystercatcher (Haematopus bachmani) predation on mussels (Mytilus californianus)

A black oystercatcher foraging in central California

Myself and co-author Wes Dowd have a new paper out in the journal Invertebrate Biology detailing a set of observations we made of black oystercatchers attacking a set of mussels that were part of an experiment we were running. The mussels in our experiment were wearing a set of sensors, including an internal temperature sensor, a valve gape sensor (aka a ‘valvometer’), and a 3-axis accelerometer and magnetometer sensor. These mussels were part of a bed of live mussels (image below) … Continue Reading

Preparing for the upcoming field season

Production is ramping up for the imminent start of two field experiments in Alaska and California. In both cases we’ll be manipulating tide pool temperatures using heaters to slightly raise water temperatures during low tide. To get ready for that, I’ve been working on soldering and assembling the custom circuit boards that will handle the heating control.

Tide pool heater circuit boards

These boards house a ATmega328P microcontroller and DS3231M real time clock, and they are programmed with an algorithm to calculate tide height for a … Continue Reading

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