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..


Snowy owls, snowmobile trails and beaver tails

So I think I’ve been in Canada for nearly two weeks now. I am gradually learning things.

For example, when someone talks about getting beaver tails, they actually mean some sort of delicious pastry:


I also learned how to write some basic video analysis stuff in python, and that a single chickadee in a controlled environment is an easier thing to track than multiple shags on the ocean:vlcsnap-2016-01-23-23h49m11s193I learnt that they deliberately thicken the ice here:


This is so the canal (which I walk along on the way to the office) can be turned into a massive ice skating rink. It opened for the first time today. I saw many people gliding effortlessly along, as well as some children being dragged along on sleds, which looks more my speed.  Since I got here I have occasionally been asked if I skate, to which I give a rueful laugh. I don’t think me and skates would really mix.

Another thing I learned is that batteries drain very quickly in the cold weather. Today myself and the grad students in my research group went to see if our lab vehicle still worked after sitting in a garage for a month or so. The answer was, it didn’t.


Battery is flat.

However once a man from the Canadian AA turned up and jump started it, the car had to be driven somewhere to charge the battery. So I got to go on jaunt to one of the field sites where chickadees are studied, alongside a snowmobile trail. This was great as I was keen to get out of the city and see some Canadian countryside, and see some chickadees in the wild.


We found many chickadees, but also a bald eagle!



Shortly after seeing this I left the trail to go and look at a heap of rusty farm machinery buried in the snow. When I came back to the path, I knew something was afoot. It was then that I learnt that Canadian ambushes are exceptionally polite, as I was warned I might want to put my binoculars away:

12615379_10208372060120941_7821439240601366873_oArg! (Photo by Teri Jones)

It was then decided that we would head back toward Ottawa and try and find some snowy owls that had been reported in the area. On the way we would stop for “Timbits”. I did not know who Tim was, or the answers to any related questions. I found out:


It seems that Timbits are a big box full of the centres of various doughnuts! These tided us by as we headed toward where we might find snowy owls.

We stopped at the edge of a field in the general area where the owls had been seen. We all climbed out of the car and had a general scan of the trees and hedgerows. Nothing. We got back in the car to try a different spot. This was rather similar to my previous experience of attempting to see specific birds, so I wasn’t overly hopeful about finding a snowy owl in an expanse of snowy fields.

Then Shannon who had been looking out of the moving car with her binoculars (I am fairly certain doing this would make me carsick) suddenly spotted something on an electricity pylon in the middle of a field. We parked as close as we could to have a look. The post was quite a distance from the road, but through our binoculars we could clearly see a snowy owl! I had never even seen an owl in daylight, let alone that clearly.

I tried to get a picture but even at maximum zoom it wasn’t enormously clear.


Still, the view through the binoculars was great. We stood and watched the owl for a bit, before deciding to head back down the road to try and find the female that was also supposed to be about. Once again I was sceptical. I think I’d just said finished muttering something along those lines when I suddenly has to ask:

“What’s that on the post?”


There, on a post right next to the road was another snowy owl. We parked up right next to it, getting a much better view than before. I decided I had to try and take a photo.

It was at this point was once again reminded that batteries drain incredibly fast in the cold. Like the car earlier, my camera refused to start up. I fumbled with the various spare batteries. None of them worked. This was absolutely typical but luckily the owl was fairly accomodating. Eventually through luck and the strategic warming up the batteries, my camera finally fired up:


Tomorrow: statistics course!

Gemeinsame Nahrungssuche bei Krähenscharben

headerOr, my new paper:

Social foraging European shags: GPS tracking reveals birds from neighbouring colonies have shared foraging grounds

has been published.

From the German translation of my title and abstract I have learnt that the German for shag is Krähenscharben. This paper based on my first year of fieldwork and data from the FAME project is now available from Journal of Ornithology! The paper looks at the movement and behaviour of shags foraging in the Isles of Scilly using high resolution GPS data, showing that most individuals forage in the same areas within the islands.

After the tale of woe that was my first year of fieldwork, it’s nice to see the data collected finally producing something tangible. The paper also uses some of my rafting dataset , which I hope to release a more detailed study of at some point in the future.

There is a full text version on Researchgate at some point in the future.

As stated at the bottom of the article, many people helped with this: A big thankyou to Richard Bufton, David Evans, Liz Mackley and the volunteers who assisted with data collection. Thanks to Vicky Heaney for population data and advice! Finally thanks to everyone at the Isles of Scilly wildlife trust for their invaluable assistance and for permission to work on the islands!

EDIT: Link to journal now fixed and full text now available on researchgate.

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!)

Behaving in Newcastle


Recently I and many other from the Bioscience department here in Cornwall, attended the annual summer meeting of ASAB (The association for the study of Animal behaviour) in Newcastle. I’d been to a few ASAB meetings before, but never one on this scale. Every tier of this building was full of posters, every room was used for talks, all related to animal behaviour.

We made an epic 9 hour road trip from Falmouth to get there, fighting our way through traffic jams and accidents and the Cornish tourist season to get to the north.

This sort of conference is a great way to share your results with others, get inspiration and ideas and to meet people interested in the same topics as you are. It’s always nice to meet people at the same stage of their research career and to chat about the work you’re all doing.

“Networking” (read: talking to people and going to the pub) is therefore an important part of these events. Here is a demonstration of such networking.


I’d never been to Newcastle before and found it to be a pretty nice city. The most bizarre thing about it was that it was absolutely covered in Kittiwakes. As in, the seabird. Which I had previously only encountered on bird islands. Nesting on buildings by the river and on the bridges.

Apparently the locals find the a nuisance. Personally I never got bored of hearing kittiwakes yelling in the streets, though it was rather surreal.

We also went for a meal at the St. James’ park football stadium, but as the room we were in could have been any function room in any building ever, I unfortunately can’t give much in the way of interest. We didn’t even manage a pitch invasion. The meal was rather small, but there was an awful lot of wine, which I think rather helped with the céilidh and dance (I refuse to use the word disco!) after.


As well as the talks and poster sessions, there were a few extra activities, like this play/lecture about Nikolaas Timbergen by a Dutch theatre group. Here we see a rather angry gull chick (sock puppet) helping to recreate the famous red spot experiments.

I was here to do more than just talk to other science-types, drink beer and watch funny plays about famous ethologists. I presented a poster, based on the GPS tracking data we’d gathered in the first year (click for a larger version)


The poster session went well, with me wearing my voice out from talking to people. The one free glass of wine we were given helped for a while, but after a couple of hours of speaking quite fast and enthusiastically while wildly waving my arms around (no doubt to illustrate some point about how shags raft and dive) I became quite hoarse.  Some more beer at BrewDog helped with this condition.


All in all, a pretty successful conference, though I was glad to catch up on my sleep!

Big thanks to Lolotte Faraut for the photos!