Translating between Matlab and R

I mentioned in a previous post that I’d write a guide about translating Matlab code to work in R, so that others can avoid the same mistakes I made. This should also function as an R users guide to learning Matlab syntax and vice versa. I hope some people find it useful!

Full article below.

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Then and now

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So I have had something published! It’s a literature review discussing how information can contribute to the formation and maintenance of animal colonies. For comparison, on the left is a literature review I wrote in my third year of my undergraduate degree, about four years ago. As was the case with me doing a project on shags in the isles of Scilly in my second year, this piece of work now seems strangely prescient.

You can find my review here on Biological Reviews.

This actually appeared on the internet last Thursday, but I had no idea of this until someone I’d cited contacted me about it. This work was first submitted for publication in June last year (though it was one of the first things I started writing back when I initially began my PhD). A couple of iterations later (and not at the dates given on the website!) here we are.

I think their presentation is definitely better than my attempt at doing columns.

Telling the difference

One of the questions I get asked the most is:

“How do you tell the difference between a cormorant and a shag?”

Now, assuming they want a serious answer and not a punchline, there are several things we can look for. Here is a picture of a cormorant and a shag standing next to each other:

There are immediately some obvious differences.

  • Cormorants are much bigger than shags.
  • Cormorants have a heavier, thicker beak.
  • Shags have far less yellow and white skin where the beak meets the face.
  • There is a different in colouration when the feathers catch the sun. Shags tend to look green, while cormorants look blue. (Funnily enough the welsh for shag is fulfran werdd which translates literally as “Green Cormorant”)
  • In this picture, the shags have crests which makes them very easy to identify. Unfortunately, these are only present during the breeding season and not present at all on younger birds.

This is a picture of a young shag:

This was taken at around the same time as the image above. As you can see no crest and no green colouring. There are still some things that we can use to distinguish this from a cormorant:

Where the beak meets the head, there is less yellow skin than would be found on a cormorant.

The shape of the head is also different, as can be seen in this photo, the front of the head slopes steeply, while the back of the head slopes gently as can be seen in this picture of a cormorant colony.

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Now this is all very well when you see a bird standing on a rock, giving you a clear view but what do you do when the bird is on the water, usually at the bottom of a cliff?

Handily there is an easy way you watch the birds dive. Cormorants will slip smoothly under the water while shags will kick their legs into the air as they dive.

So in summary the easiest things to look for when trying to tell the difference are:

  • The shape of the head and beak
  • The amount of yellow skin on the face
  • The diving action

Hope this helps!

More new articles

Just a heads up that two new articles added to the article section of the main site, both  summaries of recently released marine  science results:

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  • Hanging out with the Right dolphins

A study of how early socialising can have significant effects on the later life of bottlenose dolphins in Shark Bay, Australia.

Funnily enough the day after I wrote this (these articles sometimes take a while to get published on the main site) Celine Frere who has worked on the shark-bay dolphins for some time and recently started work at our university, gave a talk on “Incorporating social interactions into our understanding of evolution”. Which was rather a fun coincidence.

I have a few friends in the department who work on social networks. If this article interests you, I recommend checking out their blogs: Flock Mentality and The Irish Brent Goose Project for various goose based social network things.

  • Leopard seals look after their teeth

A description of the rather unique dual feeding strategy of the Leopard seals.

You can find these artciles under the article section the main website at fourth element.

I’m playing with the idea of directly linking to articles from these blog posts, but unfortunately this would just open the one article in a new tab without any of the surrounding website.How the article section on the site will be organised as more articles are added is also something to think about. If anyone has any feedback or suggestions into how any aspect of the site is run please e-mail me or comment and I’ll pass it on to the Fourth Element webmaster.

 Image courtesy of Wikicommons

The main page

This is just a quick look at the current contents of the article section of the main page.

There are currently three articles in the articles section:

  • Diving Adaptations

This longish article describes the various diving adaptations exhibited in air-breathing divers in British coastal waters, including humans! Humans have more adaptations than you might think. As well as humans several other species of mammal and bird are detailed.

The other two articles are short summaries of interesting marine science papers:

  • When you cannot see, flee.

Details how increased sediment and decreasing marine visibility is leading to changes in risk taking behaviours in fish.

  • Seabirds smell for a reason

Is a summary of interesting methods being used to look at how seabird smells can identify individuals.

Check all these out under the article section the main website at fourth element and expect more soon!

The first post.

Welcome to the official blog of the Shag Project! The first post of a blog is important to establish what this is all about.. so without further ado:

  • What is the Shag Project?

The shag project is a collaboration between myself and Fourth Element. My research is investigating the diving and foraging behaviour of the European shag, one of the UK’s most efficient diving birds. Fourth Element is a diving company with a keen interest in science and the environment. They will be providing support, tech and expertise for the research.

I’ll be updating this blog and our official website with stories of my adventures, articles about marine science and general science things that interest me.

One of my upcoming adventures is that I’m going to be learning to dive. This is going to be completely new to me, and I’ll be writing about my experiences here. Hopefully this will provide new techniques into how I study diving birds.

  • Who are you and what are you doing?

My name is Julian Evans and I am starting the second year of my Phd. As mentioned above I am studying the diving and foraging behaviour of European shags. I am particularly interested in how social information at the colony or on the water could affect a birds diving behaviour and strategy.

  • Why study shags?

Shags are one of the UK’s most efficient diving birds. These birds can be seen on rocky outcrops all around the British coastline or sometimes swiftly disappearing under the water. They are remarkable underwater hunters, pursuing and catching their prey in extremely challenging conditions.

Out in the Scillies, shags form absolutely enormous foraging rafts, diving and fishing together. How and why these rafts form is a mystery. What benefit do they give? Do they speed up the process of finding prey? Are the shags using other birds as is indicators of the presence or absence of fish under the water? Do they change the length of depths of their dives when in groups?

The honest answer is that we don’t know, and this is why they are an interesting species to study. Over the next two years I hope to use a variety of methods to attempt to provide answers. Methods may include things high tech as attaching small cameras to the birds to capture video and still images of a bird’s eye view of diving and fishing, to simply collecting huge amounts of behavioural data.

  • So what have you done so far?

In my first field season I attempted to examine broad foraging behaviours of the birds. Things such as:

– Are certain sites favoured consistently or is prey randomly distributed?

– Do birds from different colonies favour different sites?

– How do birds search for prey patches?

– Where do rafts form, do they form in certain places and times?

We used a combination of GPS tagging and observation to answer these questions. To find out how this went check out the field diary at the main website. (It’s a tale of woe)

Also on the main website are some articles I’ve written and a gallery of photos from the first field season.

More on the way soon!