ECMTB & Progress

Another slightly overdue post!

I’ve been quite busy with my paper lately – I think I’ve got some good models, and I’m enjoying writing them up. I’ve also started marking some papers for the Scottish Mathematical Challenge – the 2011 questions can now be found here (the deadline has passed, but how many can you answer?).

I also found out over the weekend that my talk, “Macroparasites in Managed Systems: Using mathematical models to help reduce the Impact of Argulus foliaceus in UK Fisheries” has been accepted to ECMTB (European Conference on Mathematical and Theoretical Biology) in Poland at the end of June – exciting stuff!

Long time no post

Let’s be honest, my resolution to blog every week has been a bit of a flop so far. In my defence, I’ve been fairly busy – at the start of February I gave a presentation to the CS&M crowd; a couple of weeks ago I submitted an abstract to talk at ECMTB in June (should hear any day now), and today I took part in a group presentation with my fellow 4b92ers to show the lovely SBES crowd what we’ve been up to – a little intimidating, but good practise, and everyone was lovely (probably something to do with the home-made cookies and carrot cake). Another month or two and I’ll be presenting to PGTips, SGRS (perhaps), Cefas and finally my supervisors for my second year viva – the next few months are going to fly.

Other than that I’ve started teaching again (PDM9L4), and the rest has been fairly repetitive work – writing and running simulations. I did get round to making some contour plots in Mathematica yesterday – nothing tricky about these, but they are quite pretty:

The contours are parasite burden, x-stocking and y-catch effort, the plots are of increasing mortality rate per parasite per host, from left to right.

In other news I finally got round to using my magnificent giant cupcake mould on Sunday – whether I’ll use it again is up for debate (it uses a LOT of mix and took forever to cook), but isn’t it cute?

Mathematica Indexer

I’ve been meaning to install a Mathematica indexer for a while, after seeing it mentioned quite a while ago.

Today I finally got round to installing one – you can find it here. It’s basically a plug-in for Google desktop (or MSN), which allows you to search within Mathematica notebooks. Nothing too exciting, but it seems to do what it says on the tin – highly recommended if you’re spending too much time searching through notebooks manually.

Project Management, Black Swan and more paper writing

This week I’ve been carrying on with my paper, and starting to think about the presentation I’ll be giving at the start of February.

I also attended a Project Management seminar (run by fistral) on Wednesday, in the hope that it’d encourage me to get a bit more organised, as well as looking lovely on my CV! The seminar lasted one day, and taught us how to initiate projects, identify (and deal with) tasks that could delay the project, and how to balance the scope of a project against time and cost. The advice was straightforward, and it was easy to see how each of the issues raised could be applied to most projects; I’d recommend the course if you ever get the opportunity to attend. I got a lot more out of it than I expected to, and I’ll be going to the Advanced Project Management and Project Risk Management seminars later on in the year.

On Tuesday I went to an advance showing of Black Swan at the cinema – my one word review would have to be, “bonkers”. Probably the most exciting thing I’ve seen at the cinema in a while, so on that basis I’d recommend it. As my Dad said afterwards, “you couldn’t sleep through that racket”… high praise indeed.

Modelling plans

At the moment I’ve only really written models with logistic growth rates in the host population, which means that the population will have a fixed non-zero equilibrium in the absence of infection. In effect, this is equivalent to saying that fishery managers stock to a certain density.

Over the next few weeks I’ll be comparing the effects of reduced catch rates (caused by Argulus infection) and different stocking methods on the population size, intensity of infection and yield. I’ll be looking at the following types of stocking:

1. Constant
2. Replacement – putting back the amount of fish that have been caught
3. Compensatory – as 2, with a fixed percentage more to compensate for mortalities
4. Reactive – adding as many fish as necessary to maintain a rod average

The model I’ve been using so far suggests that reactive stocking is dangerous when dealing with an Argulus spp. infection since the parasite burden increases with the stocking rate, and the parasite is known to reduce catchability. This is actually a pretty common practise, so the findings could turn out to be pretty important.

Anyway, more on this next week, for now it’s time to start my weekend.

Next week I’ll be working on the above, as well as a presentation (or two?), a project management seminar, and some teaching seminars.

Mathematica – Manipulate

For the last few days I’ve been playing around with the Manipulate[] function in Mathematica. Basically I wanted to be able to show different combinations of models on the same plot, without having to comment out bits of code all the time.

The result is this:

It took a bit of fiddling to get it right – I started off with all the plot commands inside Manipulate, but it crashed any time I added more than one plot. Eventually it clicked that it would make more sense to create the plots first, and nest the Show[] command in Manipulate instead. You’ll notice that the unticked option is just a transparent version of the same plot – this is probably not very efficient, but it does stop the axes from moving around every time you check or uncheck a box.

Anyway, here’s the code:

tmax = 50;
h01 = Plot[t, {t, 0, tmax}, PlotRange -> All,    PlotStyle -> Transparent];h1 = Plot[t, {t, 0, tmax}, PlotRange -> All];h02 = Plot[2*t, {t, 0, tmax}, PlotRange -> All,    PlotStyle -> Transparent];h2 = Plot[2*t, {t, 0, tmax}, PlotRange -> All];h03 = Plot[3*t, {t, 0, tmax}, PlotRange -> All,    PlotStyle -> Transparent];h3 = Plot[3*t, {t, 0, tmax}, PlotRange -> All];h04 = Plot[4*t, {t, 0, tmax}, PlotRange -> All,    PlotStyle -> Transparent];h4 = Plot[4*t, {t, 0, tmax}, PlotRange -> All];

Manipulate[ Show[g1, g2, g3, g4, PlotRange -> All,   PlotLabel -> "Manipulate Example"], {{g1, h1, “h1″}, {h01,    h1}}, {{g2, h2, “h2″}, {h02, h2}}, {{g3, h3, “h3″}, {h03,    h3}}, {{g4, h4, “h4″}, {h04, h4}}, ControlType -> Checkbox]

Progress so far and things to do

I started my PhD in October 2009, so I’m a year and a bit in now. So far I’ve produced a literature review, which summarises the problems caused by Argulus foliaceus, a macroparasite commonly found in UK trout fisheries; the existing methods of control – namely Emamectin benzoate (delivered to trout in feed)  egg-laying boards (a method of physically removing parasite eggs from the water); and why we think they’re not working as well as they should.

I’ve also produced and analysed a baseline ODE model based on Anderson and May’s macroparasite model, which includes a reduced catch rate when the average parasite burden is high. This had some interesting results, in particular a refuge for the fish caused by the infection, which may explain certain phenomena seen in the field. I’m currently turning this into a paper, with the help of my supervisors.

In May 2010 I visited Cefas and got hold of some data on fisheries in the UK; there’s very little (if any) published information about the running of stillwater fisheries, so I hope to put rights to this in the near future.

So, a to-do list for the next few weeks is in order:

1. Make a pretty Mathematica demo for supervisor meeting this Tuesday
2. Write papers 1&2
3. Write my presentation for the departmental research day on Feb 4th
4. Make my website

New Year, New Start (…and possibly some other clichés)

Welcome to my new blog!

I started a blog last year, but only updated it about three times, and most of the entries were a little dull, if I’m honest.

This year I’m going to post my progress on Friday every week. It shouldn’t be that hard, right?! Hopefully my writing will improve and it’ll get more interesting with time.