Little screws

This is for no one else’s benefit but my own. These are the little screws from McMaster-Carr that are useful for screwing into the mounting holes in Pelican cases and similar knock-off watertight gear boxes.

Accessing NOAA tide data with R (updated 2021)

It’s been a decade since I wrote a script to retrieve observed tide height data from NOAA’s CO-OPS server, which lets you grab up to a month of tide data for a given tide station at a time. In that time, they’ve migrated over to a new server and slightly different API, so it’s probably time to update the script.

The updated version of this script is available in my miscellaneous public R Github as “coops_tide_ht_retrieval_monthly_v3.R”. The current version is copied below. To use it, you’ll need to install the … Continue Reading

Open Wave Height Logger paper

After a prolonged period of development, we’ve finally put out an article in Limnology and Oceanography: Methods detailing our Open Wave Height Logger project (OWHL). This paper walks through the motivations for the project (low-cost, long-duration water pressure data logging so that we can know what the waves were like at a field site) and the variety of tests we went through during development.

The paper itself is freely available via open access here: Reading

Salvaging a microSD card

Opening up a watertight box and finding this inside is never encouraging.

This box was likely dragged up to 2 meters below the water’s surface for several hours during a maybe-historic rainfall and outflow event in Los Penasquitos Lagoon in San Diego during April 2020. Photo by Shane Finnerty.

The toxic soup trapped inside the box wasn’t doing any favors to the batteries or electronics, and the data logger was dead on arrival. But we pulled the microSD card to see if … Continue Reading

Updated OWHL assembly video

I have revised the Open Wave Height Logger electronics assembly video as of March 2020 to include narration (uh-oh) and more information about the programming process and error codes. This video outlines the entire assembly process for soldering the components to the 3 circuit boards of the OWHL Revision C design. The current designs and software to run the OWHL can be found at the OWHL Github repository.

A permanently archived copy of this video can … Continue Reading

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