Perils of Data-based Birding

As a birder-scientist, not only do I have the joys of exploring farmlands and forests for novel encounters, but I also have the “joys” of exploring fields…. as in data fields.

As part of my PhD program, to become more knowledgeable about birds, I have to spend more time away from real birds (much of the current knowledge transfer system is based on similar logic…e.g. to improve learning we should spend less time learning and more time testing).  For the spring semester, I opted to do a rotation in the lab of Dr. Gareth Russell.

The Russell Lab does fascinating work looking at animal choice and response to their environment by modeling behavior and movement.  Current and recent work has followed Grizzly Bears in Alaska, Big Horn Sheep in California, Baleen Whales social networks in the Atlantic Ocean, Elephants in Africa.  The modeling element comes in when scientist try to interpret why the animals made the choices they did.  What elements of the environment most resonated with the animal causing its behaviour?

Turns out since you can’t actually ask the animals, you can use a computer to figure it out.

For my project, I can share the details later, I obtained  USGS banding records for songbirds along the east coast to determine movements over time.  My goal was to use this data to answer questions about their migratory movements in the fall.

As it goes with a venture into any new area, there’s a steep learning curve as you get to know the landscape.  You have weird experiences such as when I reloaded the data set and every bird name involving a color (say yellow warbler and white-throated sparrow) became {#*code#) warbler and (#&code#(-throated sparrow.

Twitter Screen Capture.

Twitter Screen Capture.

So after months of learning to program in Mathematica (mixed success), I managed to create a map! This beautiful rendered map shows 50+ years worth of records where in the birds presented:

  • were banded and recaptured after July 1,
  • were banded and recaptured in the same year,
  • were recaptured in a new location.
Mathematica output.

Mathematica output: Apparently one bird didn’t get the memo and went west, not south.  H1: That bird can’t read a compass. H2: That bird is a rebellious juvenile.

However, as beautifully colored as it is and as important as it looks, it’s only ~800 pieces of data across 44 species and 50+ years, not enough for a solid analysis. Back to the drawing board.

When after significant hours of effort, you’re still coming up with nothing, you doubt yourself, even when other people have faith. “There aren’t any birds here!”

Twitter Screen Capture.

Twitter Screen Capture.

Then you do something really basic, like identifying an American Robin, or writing a function which figures out how many days into a year it is.

Twitter Screen Capture.

Twitter Screen Capture.

Now you know there are birds there, and you’re just not finding them.  You feel conflicted about that.

Three weeks to go and we’re still “exploring the data”.  The sun is nearly setting.

Mathematica output: Tree swallow presence (blue) and absence (white) data with years as the x axis and days into the year as the y axis.

Mathematica output: Tree swallow presence (blue) and absence (white) data with years as the x axis and days into the year as the y axis.

So, finally we made a graph.  This graph, for Tree Swallows, shows presence (blue) and absence (white) data with years as the x axis and days into the year as the y axis.  Think January at the bottom and December at the top.

Now that I’d found one bird surely I could find them all, but could I do it by family?

Yes… Probably… How hard could it be?… Maybe… If I had more time… Impossible… Wait, what?… No… Maybe… Nope… Did I get it?

After a very dark night:

Mathematica output.

Mathematica output: 10 families of songbirds tracked over the years for arrivals and departures. years are represented on the x axis and days into the year as the y axis.

 

I actually succeeded as the sun rose.  Talk about symbolism!  I’ll have a chance to share this in my next meeting on Friday. Hopefully we can call this success.

Can only imagine what’s next?  3D versions?

Stay tuned for Rotation 2 news coming Summer 2015 when I return to real fields (or forests anyway)!

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Cavorting at Cape Florida

This post could also be called “A Reason to Return”.  There are two reasons, so settle in for a long story.

On our first conference free day, Tara and I decided to venture over to the Gulf Coast to visit J. N. Ding Darling NWR.  However, Our foray was not meant to be.

What we didn’t realize when we arrived is that there are three classes of roads in Florida.  There are the streets with a light at every possible intersection (very slow going!), the freeways (highways without a cost, also very slow going!), and the tollroads (much faster going!).  However, Florida has switched over to a mandatory automated toll payment system based on either a tag or your license plate (no more cash/coin payments!).  If you inadvertently drive through without the tag, they sent the fee to the address associated with the license, no big deal and no big cost, unless you happen to be in a rental vehicle.  If you are in a rental, then you are charged a ~$50 surcharge for each day you go through tolls.   If you wish to rent a tag in addition to the vehicle, it’s $10/day.  Neither option is ideal.  So our solution was avoid toll roads.  Which doesn’t work if you want to go to Disney World or travel across the state.  We didn’t want Disney but we did need to cross southern Florida.  We searched and searched, but couldn’t figure out a route after accidentally getting on the toll road and getting right off again. (Had we just kept going we would have had the fine either way and very different birds to share, oh well!).

By the way, the solution we learned on our way out of Florida is to purchase a tag at a grocery store. It’s a few dollars and prevents the charge going to the lisence and thus through the rental agency.   Now, you know too, and back to the birds.

Since going west was a fail…

“”Go West, young man, go West. There is health in the country, and room away from our crowds of idlers and imbeciles.” “That,” I said, “is very frank advice, but it is medicine easier given than taken. It is a wide country, but I do not know just where to go.” “It is all room away from the pavements. […]” 
                  —Josiah Bushnell Grinnell [3]

We went south.  We drove into Miami-Dade county (home of the 2000 election controversy which was realized as we drove through!) and decided to visit Not Bilbo Baggins, but Bill Baggs Cape Florida SP (Bilbo Baggins would be much better a name!)

Cape Florida: What's a post about Florida beaches without sand or a lighthouse?   Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

Cape Florida: What’s a post about Florida beaches without sand or a lighthouse? Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

Since many more of you know of Bilbo Baggins than Bill Baggs: Bill Baggs was a Miami journalist and editor who did much coverage of racial tensions in Florida during the 50s and 60s as well as opposed the Vietnam War (per Wikipedia).  More relevantly, he supported Florida conservation efforts.  So we ended up at Bill Baggs State Park.

There was a lighthouse (pictured above) and white sand beaches (not pictured), but there were also birds. Not the tons and tons we were hoping for, but quality enough that it made the excursion worthwhile.

Immature Double-crested Cormorant flying   just above the water.  Playing with birds on the move and the telephoto lens. Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Immature Double-crested Cormorant flying just above the water. Playing with birds on the move and the telephoto lens. Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

There’ll be a few photos of Cormorants in this post in part because they were common, but also because they’re super cool!  As we were wandering around the interior, I happened to look up to spot this fellow: Short-tailed Hawk.  Short-tailed Hawk was  on our wish list.

Our only view of a Short-tailed Hawk during our entire visit.  Much more cooperative than the Galapagos Hawk of a year past! Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Our only view of a Short-tailed Hawk during our entire visit. Much more cooperative than the Galapagos Hawk of a year past! Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

I also happened to look up and spot a Magnificent Frigatebird, but no luck on that photo. (I have plenty from Galapagos to tide me over though!).

After seeing what the park had to offer, we decided to move on a bit and try nearby  Bear Cut Preserve at Crandon Park.  Most of the birds were to be found around the Marjory Stoneman Douglas visitor’s center (which was lovely).   We spotted 3 Eurasian Collared Doves around the building.

Eurasian Collared Dove looking mournful it's not a mourning dove.  Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Eurasian Collared Dove looking mournful it’s not a mourning dove. Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

We walked their recommended trail and came across a Yellow-crowned Night-Heron (not pictured) and then walked back along the beach  (frequently ranked in the top 10 of America’s best beaches) where we came across this view:

The only fossilized reefs in the world.  How cool?! Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

The only fossilized reefs in Florida. How cool?! Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

What you’re looking at are fossilized mangrove reefs.  They’re really only inches tall here.  I suspect they’re mostly buried under the sand. And yes, that is Miami in the background. More on fossil reefs can be learned here.

Second photo of the still only fossilized reefs in the world.  Still cool. Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Second photo of the still only fossilized reefs in Florida. Still cool. Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

I’m including the next photo just because I like the alignment of birds.  Some type of gull.

The detail on the photo is rubbish.  But I love the clouds and the alignment of the birds.  Authentic photo, no photoshopping here! Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

The detail on the photo is rubbish. But I love the clouds and the alignment of the birds. Authentic photo, no photoshopping here! Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

As we returned, the tide was creeping out and by just rolling up our pants (in my case because only I go to Florida and still wear pants!) a few inches, could we walk out along  a sandbar to get much closer to the birds.

Glorious detail of Double-crested Cormorant feathers. Double-crested Cormorant feathers are cool.  Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Glorious detail of Double-crested Cormorant feathers. Double-crested Cormorant feathers are cool. Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

Yes, this Cormorant has his back to us, but note the feathers. The feathers are truly amazing.  Feathers of cormorants are truly amazing.  I recently read a paper discussing the unusual feather structure in Great Cormorants.  Any birder familiar with Cormorants knows how they stand with their wings outstretched.  Why?  All birds have fine feather control.  What this means is that there are muscles attached to their feathers that allows the precise rearrangement of each feather.  It is believed that cormorants manipulate their feathers underwater to help them dive.

Consider it this way.  Birds have these amazing adaptations that help them take to the sky: they need to be lightweight.  However, this is not beneficial if you want to sink, which cormorants do.  Thus, as they dive, scientists hypothesize cormorants rearrange their feathers allowing water to seep in, decreasing their buoyancy whereas most birds will arrange their feathers in such a way as to repel water.   When you look at the structure of the feathers themselves, cormorant feathers are actually different: the density of the barbs is actually where it’s thinnest in other birds.

A less than white looking American White Pelican. Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

A less than white looking American White Pelican. Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

After our visit to Bear Cut Preserve, we headed to the other side of the road to Miami Seaquarium Marina where we picked up more gulls and views of aquatic birds. The feather detail on the American White Pelican is also notable.  So colorful!  And the bill looks like the Pelican had a wonderful, messy encounter with a painter.

Preening Double-crested Cormorant.Photo taken on January 8, 2015  with a Nikon 3200 Sigma 500mm.

Preening Double-crested Cormorant.Photo taken on January 8, 2015 with a Nikon 3200 Sigma 500mm.

Preening cormorant.  Got to wet those feathers just right.

Regarding the second reason to return.  It wasn’t until much later in the trip, possibly the flight home when I got to the portion of Kenn Kaufman’s book discussing the birds of Florida’s Cape.  Clearly we needed to go further south and even out on the water for the best birds.  So some day we will definitely need to return to Florida for both the more western and more southern birds.  Onward, birds!

Florida Total: 76
Bill Baggs State Park, Cape Florida: 23
Bear Cut Preserve, Crandon Park: 18
Miami Seaquarium Marina: 8
New for Florida: 13
Lifers: 2

Paper: Ribak, G., Weihs, D. & Arad, Z. Water retention in the plumage of diving great cormorants Phalacrocorax carbo sinensis. J. Avian Biol. 36, 89–95 (2005).