Preparing for fieldwork

By which I mean, preparing for my fieldwork.. other people’s fieldwork has already begun. I’m helping!

Fieldwork in a field

I’m assisting with open field personality trials of chickadees captured for Megan’s work. This involves setting up cameras, then introducing a bird to a cage and recording the birds movements for 10 minutes (to see how long it took for the bird to contact all four corners of the cage), introducing a novel object to the cage (to see how long it took the bird to approach it)  then extracting the bird. This is the tricky bit.

I’m also preparing for my own fieldwork, prototyping new designs of RFID feeders:

Early experiment with new tubes, new anti-squirrel cages

The idea is that the opaque tube so that birds can’t necessarily tell if a feeder is empty or not. At the same time I’ve been setting up more RFID boards and building more antennae.

First I solder coils to plugs.

Then I half fill glass tubes with resin. This was mainly an exercise in stopping my hands sticking to the tubes! I then embedded the coil into the resin and then filled the remaining space with more resin.








Finally we attach these antennae to the feeding ports using more resin.

In other news, I’ve been partaking in another Canadian activity, I’ve been to my first ice hockey game! Oh, apparently the word “ice” is superfluous. Anyway, I went to the season opener, the Ottawa Senators vs the Toronto Blue Jays. It was very exciting!








Both sides scored 3, the Blue Jays goals all by the same person (apparently it was also his debut game too). Eventually it went to something like extra time, where Ottawa finally won. Definitely a very cool experience!


Chickadees are hard to take photos of



I think I’ve been in Canada almost two months now. It’s hard to say as the initial turmoil of moving to a new country slowly changes into everyday routine. This generally involves getting up, trying to do some science until some time in the evening and drinking far too much tea.

I’ve met my study species properly now. A few weekends ago we went for a walk at a place called Muddy Lake (currently frozen and definitely not muddy). When walking along the paths you will generally be followed by a cloud of chickadees, who live in hope that you will be one of the many people that feed them. They whiz around your head, dancing from branch to branch, waiting for the food to be provided. If you DO have food, they will quite cheerfully eat out of your hand.


Despite their tameness taking a photo of them in a more natural setting is challenging, due to their dislike of sitting still for more than a second.


As well as having met my study species properly, I’ve also been working to get to grips with both social network analysis and the study of personality in animals. I had a passing interest in both of these topics before, but now I’m having to rapidly learn about how these analyses are done.


Chickadees are highly social and tend to move about in small flocks. We have information about which birds were with which other birds at feeders.This is generated by special feeders which can identify individual birds fitted with RFID readers.

Picture1An RFID feeder, photo by Teri Jones

We also have information about how certain birds reacted to personality tests as well as which birds are dominant and which are subordinate. There are quite a few interesting questions we could answer by bringing these datasets together. Wrangling the various files together is and working out how to analyse them is the main thing I’m currently dealing with. This involves spending a lot of time shuffling data about in R. I’m also trying to automate and improve some of the workflow for generating this type of data.

We’ve  had a few quite heavy snowfalls. This was my building the day after a particularly severe one:


and this was the window to our office on the same day as the sun was steadily blotted out:


A few weeks ago I gave a departmental seminar on my ENTIRE PHD. This involved talking for longer than I ever had before, which made it very easy to lose track of time. I was extremely afraid of speaking for too long and boring everyone to death.

Picture2So many slides!

I felt it went quite well. My main mistake was towards the end. I glanced at a clock (the WRONG clock) as it turned out and was convinced I’d gone overtime. I sped up for the last few slides (which is unfortunate as they are the most interesting) and then apologised at the end for speaking for so long. As it turned out, I’d looked at the wrong clock and came in under time. At least it left lots of time for the many questions, which hopefully indicate that people are interested in what I spent about four years of life doing.

I have been finding time to try and do some more CANADIAN things. For example, I’ve now tried Poutine which according to Wikipedia is Canada’s national food. It’s basically chips, cheese and gravy. I think that undersells it, it’s warm, tasty, cheesy, potatoey goo.


I also ambled up to Winterlude (a winter festival thing held in Ottawa), where the international ice sculpture championship:IMG_0759OWL


This included a demonstration of ice carving, which is apparently mostly done with powertools now!


I clearly need to find some more CANADIAN things to do. Someone mentioned something called Nanaimo bars..


More virtual birds

I have returned to my simulated rafts of shags. As well as general code refinements, I have also completely overhauled the way they dive and surface.

The dive rules have been in place for a while. They are as follows:


1. The virtual bird will dive wherever and whenever it wants, without paying any attention to what other birds are doing. Given that my hypothesis is that birds are using the diving behaviour of others to make their own diving decisions, this is the null model.

2. Birds are more likely to dive if another bird dived or surfaced recently. How likely they are to dive depends on how close the other bird was in space and time.

3. Similar to 2. but birds only have a limited cone of vision. They will not be away of a dive going on behind them for example.


Previously I only had one rule for surfacing: birds would surface at a random time after they had dived, within a circle of a random radius centred around where they initially dived . The distance they were allowed to travel was constrained by how long they’d been underwater. They were also more likely to surface in proximity to other birds, so as to maintain the cohesion we see in real birds.

Just before ISBE, my supervisor suggested that actually we probably want to try out a variety of surface rules to try a few different scenarios. This required a complete rewrite of the simulation, but this was a good opportunity for me to merge all my various dive rules into one piece of code too. Though there was quite a bit of hair pulling involved, I eventually ended up with a simple unified function.

The surfacing rules birds can now obey are as follows:


1. Surface completely randomly in time and space. Virtual birds can reappear at any time within a circle of random radius centred around their dive, with the maximum radius depending on how long a bird was underwater. They don’t care if they are near another bird on the surface or not.

2. Same as rule 1, but birds are more likely to surface closer to another bird. The time they stay underwater is still random, which still controls the maximum possible distance they can travel underwater.

3. Similar to 2. with an important addition: A bird is more likely to surface in close proximity (in time and space) to a bird it dived in close proximity to (in time and space). This is to attempt to simulate birds following each other more closely underwater.

Of course. rewriting my code so that I can switch between which rules a simulation is using just by changing a number in my simulation uses was somewhat tricky, but eventually I hammered out all the bugs. Unifying all my code like this will make the selection of a best fitting model much simpler.

So New York is now a Place I have Been.

When I first started all this I was not expecting to go to New York.

I’d never travelled outside the UK a great deal. A couple of fieldtrips to Africa during my undergrad and masters courses were the furthest I’d ever been. Family holidays always involved camping someplace in the UK and I was not the sort of PhD student who went off to study exotic animals in far away places.  Calling my study species exotic is rather stretching the definition of the word.

As such, when my supervisor told me I should go to New York I was somewhat shocked.

It was at some point during my first year. We were discussing conferences. My supervisor told me that I should aim to present at ISBE during my third year.

I nodded wisely (Hah! My third year was at least an eon away, and as such would never arrive!)

“It’s in New York”

Once again I nodded wisely. (I knew New York existed, I had seen it on the telly. Nevertheless the idea of putting me, who found Falmouth in summer altogether too many people, in this glamorous metropolis seemed ridiculous)

“You should definitely aim to present” he reiterated.


The meeting concluded.

“Hah!”  I thought as I sat down at my desk again. “Present non-extant results in the far future in a semi-mythical city? What a silly notion”

When I looked up again and discovered a couple of years had passed, it was time to try and submit an abstract for ISBE. I felt my collective behaviour work was by far the most exciting thing I had going, though it was still something of a work in progress. However I did my best to write something that sounded good and sent it off and waited.


After the deadline I finally got an e-mail acknowledging my submission. At some point (after a decent period of worrying) I had confirmation that I had a talk.

So I went to New York.

IMG_0028New York: Closer to Falmouth than you might think.

It’s my first ever international conference, and the organisers had definitely pulled out all the stops to impress us. Here is me and my friend Anne (Who I did my masters course with and is absolutely the sort of PhD student who goes to far away places to study exotic species) at one of the poster sessions.

10314695_10154480191695268_7907632277241076551_nPhoto credit: Sheridan Willis (whom I also did my MSc with)

This was the view from the window:


However I couldn’t get too distracted by all of this. I had come here to do a talk. As I mentioned before it was to be the last talk of the day in my session. Turned out my session would also be in a room on the 10th floor of the building, specifically designed to roast behavioural ecologists. There was no view from these particular windows, only more heat.

I generally find it hard to judge how a talk has gone. I felt fairly happy with it afterwards, but the actual details were hazy. I did my best to answer some questions and then took the lift  elevator downstairs again.

And that was it. I’d spoken at an international conference and hopefully acquitted myself well. In New York. It is something I would never have imagined myself doing at the start of this project. I still have trouble imagining it now.

Also, guess where the next ISBE is!

BuTA-PIIUAAjJqR.jpg large


Virtual birds

A few months ago I gave a talk at the ASAB Easter conference in Sheffield about how I’m analysing the foraging rafts using collective behaviour. Of course, what with one thing and another, the work wasn’t as far along as I would have liked. After I got back from fieldwork and crunched the new data, I decided it was time to look at this work again.

One of the main reasons for pushing this work is that I am giving another talk on this at an international conference. In New York. In a few weeks. Do not let my restrained tones hide how terrified/excited I am about this.

The conference is ISBE, the Internation Society of Behavioural Ecologists. I applied for a talk back at the beginning of the year and several months later, here we are:



(Last talk of the day, hopefully some people will be awake)

I’d really better get some results together hadn’t I?

To recap what I had already done:

-Extracted positions of individual birds from video.

vlcsnap-00028-Tracked these individuals and then used these positions to create trajectories.

– Ran these trajectories through a correction matrix, to account for any distortions the camera might introduce

– Created code to remove unrealistic tracks.

– Wrote further functions that I can use to manually delete and merge tracks.

– Extracted the dive and surface events


– Created various graphing functions, such as taking the corrected trajectories and plotting them back to their original positions to check my working.


What I have done in the last week (working frantically):

– Created a simulation based on zonal interaction models. Virtual birds that mooooooove.

– Wrote code that will compare the real data with my models, using things like radial density.

relpos– Added the ability for my virtual birds to DIVE.

– Modified simulation so the birds can react to these dive and surface events.

What am I doing now?

So the goal now is to produce results by choosing the simulation that best matches up with the data. In order to do this I need to choose the best “weight” for each of the things that might affect a birds movement (the effect of repulsion from other birds vs. the effect of attraction to other birds for example). I am currently exploring these weights manually, but eventually I need to run some code to optimise each of these weights for each piece of data.

I’d also like to add some more complicated diving rules (At the moment diving is totally random) where they will be influenced by other dives. I then need to come up with ways of checking this method of diving against the data, to determine how realistic this sort of behaviour is..

I fly out to New York in a few weeks. This is why I spend my weekends locked in the office.

Just to finish up here is a video from one of my early simulations with some random parameters. Those birds can’t seem to get away from each other fast enough! I suspect they might also need a bit more autonomous movement to stop them doing the crazy little dance when they can’t find other birds.



St. Agnes

I’ve been spending a few days on St. Agnes, sorting out a couple of MSc students, Anna and Lucy who arrived on Monday. After the storm on Saturday which managed to ground the undergraduates, I have to confess I was a little nervous about the impression the Isles of Scilly might make on them.

As it happened, it looked like this:



Well, that’s the Scillies for you!

After getting them set up on the campsite, the real work began. Lucy and Anna are carrying out very similar work to my study last year, but around St Agnes. This allows us to fill in some areas on our maps of rafting behaviour that I couldn’t observe from St Mary’s, but knew rafts formed. So on Monday afternoon we began to work out patrols around the perimeter of the island and decide on appropriate observation points on those patrol routes.

Then we had a barbecue. It’s tough in the field sometimes!

I stayed with my friend Bob, who I first met staying in the Woolpack in my first year of fieldwork, working on land-bird surveys. I believe he was supposed to stay for 6 months, but the Isles do have a habit of grabbing people.

The next day was once again stupidly sunny, but we couldn’t stop to enjoy it. There was more island to be walked and methodology to be learned. And I spotted our first rafts of the season, which Anna and Lucy proceeded to practice observing.


With some help..


Guys! Guys! Hey guys! Whaddya looking at?


Oooo, birds.

I returned to St Mary’s today and tomorrow must continue my own fieldwork. Though there was a brief reality check this morning, with some standard Scillies wind and drizzle, the sun came out again this afternoon. If this continues, I’m going to need a stronger sunscreen!


Post-op behaviour in Sheffield

I recently gave a talk at this year’s ASAB’s Easter meeting in Sheffield. This is a change from previous ASAB meetings where I’d presented a poster. The other difference was that I was also presenting without an appendix. A somewhat superficial change, but one that made preparing my presentation interesting.

I ended up in hospital on the Tuesday of the week before and went into surgery on the Wednesday. When I was discharged on Thursday, some people told me it was a bit mad to still want to head up to Sheffield on Sunday: “You know, normal people would take some recovery time “. I was also behind on the work I’d intended to do in preparation for the talk.

Nevertheless, me and my large collection of medication travelled to Sheffield. My talk was scheduled for the final morning of the conference, which gave me a bit more time to prepare. The first day of the conference was something of a workshop, with discussion on various issues in science. The second day was comprised of talks from students and plenary speakers followed by a poster session (with free drink), a meal and a ceilidh. Unfortunately I couldn’t dance or drink, which as my talk was the next day was possibly for the best.

On the last day, fuelled by various painkillers and antibiotics, I gave my talk.

I didn’t realise I looked so serious!


Unfortunately these pictures probably represent the driest looking slides of my presentation, but I suppose the equations and graphs make it look more… sciencey.


The main body of the rest of the presentation was talking about the analysis of rafting data using collective behaviour techniques.

These are the trajectories of individual birds within the raft (run through a transformation to control for any distortion introduced by the camera). These trajectories allow us to extract information about the relative positions and alignment of individuals within the raft:


Which I’ll use later in models of movement within the raft. I still intend to do a more thorough write-up on collective behaviour at some point, when these models are more complete.

After the talk the final question  I fielded (as I was walking back to my seat) was from the ASAB president, who enquired what kind of surgery I’d had.

The answer (for enquiring minds) is keyhole surgery, otherwise I certainly wouldn’t have made it up to Sheffield. I’m very glad I did though!


(Thanks to Jared for photos!)