Category Archives: San Juan salmon tracking

Chinook salmon and southern resident killer whales occupy similar depths in the Salish Sea

New paper by UW colleagues entitled “Interpreting vertical movement behavior with holistic examination of depth distribution: a novel method reveals cryptic diel activity patterns of Chinook salmon in the Salish Sea” shows some results from Vemco receivers I deployed in the San Juan Islands. Young adult Chinook favor depths less than ~30 meters, with some seasonal variability in their diel activity patterns. Overall, they go deeper and vary more in the depths at night.

Dive profiles for two Salish Sea Chinook salmon during the summer and fall.

Dive profiles for two Salish Sea Chinook salmon during the summer and fall.

Interestingly, according to a report to NOAA/NWFSC by Baird et al, 2003 (STUDIES OF FORAGING IN “SOUTHERN RESIDENT” KILLER WHALES DURING JULY 2002: DIVE DEPTHS, BURSTS IN SPEED, AND THE USE OF A “CRITTERCAM” SYSTEM FOR EXAMINING SUB-SURFACE BEHAVIOR) SRKWs spend >97% of their time at depths of less than 30m.

This suggests any future deployment of horizontal echosounders should aim to ensonify a depth range centered on ~25m (e.g. 5-45m or 10-40 m).  Compared to the estimated orientation and surveyed depth range of our 2008-9 salmon-SRKW echosounder pilot studies, we may want to measure inclination more carefully to (a) center the survey on the mean summertime depth range of Chinook and (b) avoid ping reflections from surface waves, boats, and bubbles (which may have confused interpretations of targets >100 m from the transducer).  Here’s my diagram for the situation in 2008-9 in which we were centered on 15 m and ensonified a maximum depth range of ~0-30m (in other words, we may have been aiming a little high):

Screen grab from the 2009 ASA presentation showing echosounder geometry

Screen grab from the 2009 ASA presentation showing echosounder geometry



Hydra: a step towards marine telemetry data sharing

Today I finally was able to log on to Hydra a web site that facilitates data sharing among researchers who track the movements of aquatic animals in the Pacific Northwest, U.S.

Hydra logo

The whole proprietary tag/receiver technology maintained by Vemco leaves a *lot* to be desired from an open science perspective.  By all rights they should be the ones making it easy for their users to share data.  But Vemco has dominated the market and played defensively for so long that the community here in the progressive Northwest was forced to create Hydra to enable some degree of organized collaboration and data sharing.

As we finish up the final field work for our study of how adult (lackmouth) salmon move in the San Juan Islands, today I’m cleaning up receivers, offloading data, uploading detection files to Hydra, and preparing the receivers to be returned to their owners.  Also, I organized and uploaded to Flickr a bunch of photos from the project.

Data management progress:

  • Reset Panasonic toughbook clock to NIST
  • All metadata in Google spreadsheet of San Juan Fish telemetry study
  • Verified data offloaded from Iceberg and Patos receivers (101004, 110848) and prepared for storage
  • Offloaded data from previous batch of recoveries (9 receivers) and backed up all data to cloud
  • Still need to offload data from latest batch of recoveries (5 receivers)
  • Still need to try uploading to Hydra…
  • When interpreting results, be sure which time Vue exports: local or GMT!  Checking in the Vue software options, I see time is set to UTC.

More progress on 11/14/13:

  • Uploaded yesterday’s csv files to Hydra after verifying that drift was no more than 5 minutes for any deployment during our study.
  • Updated metadata, including: made new sheet to match Receiver Deployment upload format, copied metadata to it, then converted recover dates to End_Date column; then converted all lon/lat pairs to decimal degree format (and checked/corrected all for accuracy via Google map of deployments)
  • At first attempt at deployment metadata upload, I got “Manufacturer” error.  I tried re-formatting Google spreadsheet date as YYYY-MM-DD, removed a () from a site name, removed all blank lines before downloading the .csv file, and then simplified the file name (no spaces) before re-uploading.  That got me this error:
    Unable to parse start date: Date string was 2011-11-15, and did not match YYYY-MM-DD HH:MM:SS or MM/DD/YYYY (time data '2011-11-15' does not match format '%Y-%m-%d %H:%M:%S')
  • Then I tried switching back to the Google date format of MM/DD/YY even though the output CSV file does not display double digits for the first 9 months or days (e.g. 3/4/2013 not 03/04/2013).  Hydra didn’t seem to mind about that though –
  • receivers-recovered-mmddyyyy.csv processed successfully, Deployment File, 32 rows, 0 rejected.
  • Finished offloading data from last batch of 5 receivers (but did not open cases as they still need final cleaning): 101589, 100914, 101594, 101621, 108402.

More progress on 11/15/13:

  • Backup and upload 5 most recent data files.
  • Experiment with Hydra mapping and sharing functionality (seems to leave a lot to be desired wrt figuring out anything about the actual fish whose tags we’ve detected), finish feedback email to Hydra administrators, and send it.
  • Emailed Anna+ with updates, links, and .zip of latest data files
  • Upload to Google workbook and compare 2012-2013 tag list with rough notes on detections (column P).  I find zero overlap.  Bummer!

Towards open science at Beam Reach

Herein begins my first open science notebook.  Inspired by my friend, Eli Holmes, who shared her open notebook during the recent Federal furlough, I started reading about open notebooks and decided that maintaining one would fit into my on-going efforts to refine and open my scientific workflow.

As 2013 ends I’ll be working on three projects.  Collaborating with Val Veirs and Jason Wood, I will finish a paper on the underwater noise made by ships within the summer habitat of southern resident killer whales.  I will daft a synopsis of sound (noise and signals) in the Salish Sea for the Encyclopedia of Puget Sound.  And I will wrap up a salmon tracking project in the San Juan Islands that was organized by Tom Quinn (UW) and Kurt Fresh (NOAA/NWFSC) with Anna Kagley and others.  These projects will supplement the teaching and research (wiki) and blogging I conduct through my non-profit, the Beam Reach Marine Science and Sustainability School.

Along the way, I expect to continue exploring tools that boost my scientific productivity and support my long-term goal of opening science.  I am writing in Open Office and maintaining my references, bookmarks, and notes with Zotero, while keeping an eye on tools like ShareLaTeX.  I use GMT to make maps and we are using R to generate figures for the ship source level paper.  While surveying our open access publication options, we are watching the release of Libre (this November!?) in the hopes of engaging its open peer-review process.