I did a map!

I have been playing with R’s capacity to produce interactive maps and (after much trial-and-error) have finally come up with something that shows an interesting pattern.  The data plotted below are the species richness of dragonflies and damselflies from the British Dragonfly Society‘s database in West Yorkshire over the last 20 years.  The data are summarised to 1km grid squares on the British National Grid.  Below is a screenshot because WordPress doesn’t like iframes, but click it to go to the full map.

Capture

The scale is a bit odd to emphasise the range of the data, and there are many neater ways to do this.  In particular, R gives the option to render in interactive 3D using OpenGL, create actual interactive maps using Shiny, and use the Leaflet jscript packages.  There are more details on the plotGoogleMaps package that I used for this little map here.  The code is below:

Dragonfly.grid <- read.table("Dragonfly data.txt",header=TRUE)
attach(Dragonfly.grid)
Dragonfly.grid[,2]<-Dragonfly.grid[,2]*100
Dragonfly.grid[,3]<-Dragonfly.grid[,3]*100
library(RColorBrewer)
coordinates(Dragonfly.grid)<-c('Easting','Northing')
Dragonfly.grid<-as(Dragonfly.grid,'SpatialPixelsDataFrame')
proj4string(Dragonfly.grid) <- CRS('+proj=tmerc +lat_0=49 +lon_0=-2 +k=0.9996012717 +x_0=400000 +y_0=-100000 +ellps=airy +datum=OSGB36 +units=m +no_defs')
m=plotGoogleMaps(Dragonfly.grid,zcol='Species',at=c(0,2,3,4,6,8,12,21),colPalette= rev(rainbow(7,start=0,end=4/6)))

Created by Pretty R at inside-R.org

PhD opportunities in ecology and evolution

As part of the new NERC Doctoral Training Program at the University of Leeds, I have two PhD projects to advertise that are now (as of 15th November 2013) open to applicants:

1: DragonFlight: Linking the mechanics and energetics of flight to conservation status and responses to climate change in dragonflies

dragonfly-177338_1280The DragonFlight project builds on my earlier interests in dragonfly dispersal (1), macroecology (2), and flight morphology (3).  There has quite a bit of work done on the flight of dragonflies, but much of this has taken place in the laboratory and has not considered what goes on in the field.  Similarly, there has been quite a lot of landscape-scale work done in the form of mark-recapture studies or analyses of historical records (including my own), but none of this has really tested for the traits that underlie flight ability.  This project will link detailed biomechanical measurements of dragonfly flight to our knowledge of responses to climate change (i.e. range shifts) or conservation status.

2: Teaching old beetles new tricks: applying novel genetic techniques to re-establish a classic ecological model system, Tribolium

I’m really excited about this project.  Andrew Peel, a colleague at Leeds, has been working on the evolution of beetles (and animals in general) for a while and uses Tribolium as a model system.  I have been interested in the ecology of this system for some time and this project represents us banging our brains together. In particular, there are lots of nice ways that we can incorporate Andrew’s contemporary genomic techniques (e.g. RNAi) to test for genetic drivers of ecological phenomena.  The species is also an important pest species of stored grain, making any advances potentially applicable to pest control.

Note that both of these are “competitively funded”, which means that there are more projects than we can fund.  We interview candidates for all projects and then award the best candidates the projects that they applied for.  There are more details on the website, including how to apply.  Deadline is 24th January 2014.


References:
(1) Hassall C, Thompson DJ (2012) Study design and mark recapture estimates of dispersal: a case study with the endangered damselfly Coenagrion mercuriale. Journal of Insect Conservation, 16, 111-120.
(2) Hassall C, Thompson DJ (2010) Accounting for recorder effort in the detection of range shifts from historical data. Methods in Ecology and Evolution, 1, 343-350.
(3) Hassall C, Thompson DJ, Harvey IF (2008) Latitudinal variation in morphology in two sympatric damselfly species with contrasting range dynamics (Odonata: Coenagrionidae). European Journal of Entomology, 105, 939-944.

PubMed Commons is a huge leap forward

For me, PubMed Commons came out of nowhere.  I was aware of some innovations in publishing (check out journals like Cryosphere for examples of progress in academic publishing) but to have a huge group like PubMed involved in pro-actively pushing boundaries is a real game-changer. Here’s why it’s so important: academic publishing as it currently exists is broken. We have been using a model for publishing that is built around a century-old method for the dissemination of information.  This involves (i) the submission of articles to an editor, (ii) the selection of a small number (usually 2-3) of referees to review the paper and make sure it is adequate, and (iii) a judgement made by the editor and the referees as to whether or not the paper should be accepted.  At that point, the paper is either published (in which case it becomes a matter of record) or rejected (in which case it is never heard of unless published elsewhere).  What this means is that ENORMOUS amounts of scientific information is never seen, and that information that is released in given a sometimes-cursory review by a small number of people who may not be experts in the area.  The internet should already have changed that in a number of ways:Read More »

“Camouflage on the edge” – a new paper on concealing colouration

In 2012, the US Government cancelled a $5 billion camouflage project under which it had already supplied uniforms to soldiers in Afghanistan.  The pattern of camouflage, called the “universal camouflage pattern” (UCP) was supposed to allow soldiers to blend in equally well in forests, deserts, and urban environments but had been deployed but never properly tested to ensure that it provided proper protection.  When this testing was finally carried out, it demonstrated that the camouflage performed poorly, and was actually putting soldiers at unnecessary risk.  It got so bad that US Army soldiers were trading their uniforms with locals so that they could wear something with appropriate colouration.  What this goes to show is how poorly we understand the mechanisms underlying camouflage, even while we spend enormous amounts of money attempting to exploit the phenomenon.  A new paper that my colleagues (based at Carleton University) and I published today in the Royal Society journal Biology Letters adds a key piece to the camouflage puzzle by illustrating for the first time the mechanism behind “disruptive colouration“.  The paper can be viewed for free at the journal homepage, as can all Biology Letters articles, until 30th November 2013 – go browse, it’s a fascinating journal with short, varied, interesting papers.

Read More »

Using R to look at engagement with Twitter at scientific conferences

Beh13 presentationI have been busy attending conferences recently (one of many excuses for not updating the blog) and I thought I would mention one significant difference between these conferences and those that I have attended previously.  At Behaviour 2013 (Newcastle, 4-8 Aug 2013 – that’s me talking about mimicry on the right), I tried live-tweeting for the first time.  Then at Intecol 2013 (London, 18-23 Aug 2013) almost all questions during the plenary talks were taken solely by Twitter.  This meant that I had a lot more experience of Twitter in an academic forum that I had had before, and I found it to be an immensely positive experience!  Not only did people come up and say “hi” because they recognised my name from Twitter (new networking opportunities), but I passively participated in multiple parallel sessions where usually I would only have had access to the session within which I was physically present (there were 16 parallel sessions at any one time at Intecol!).Read More »

Species with a chemical defence (but not a chemical offence) live longer

Dendrobatid frogs are the classic “aposematic” species: they advertise their toxins with bright colours

I wanted to spend a post talking about a new paper that was published recently (3 May 2013) with some colleagues from Carleton University.  It is easy to see the value of tasting bad: predators try to eat you, feel sick, then leave you alone.  Even better if you have bright colours or a strong smell (called “aposematic signals”) to go along with it – that way predators can learn to avoid your colours without having to taste you a second time.  In fact, they don’t have to taste you at all if other animals of your species also have the bad taste and the bright colours.  In theory, this chemical defence should reduce deaths due to predation which means that the prey live longer.Read More »

BREAKING NEWS: Correactology can no longer cure cancer!!

From http://www.someecards.com/workplace-cards/its-the-small-victoriesPresumably as the result of in-depth clinical trials (how else would they know that their treatments can cure so many severe and varied diseases and conditions?) the experts at the Correactology Centres (which I have discussed before) have removed “cancer” from the list of “ailments” that Correactology can treat.  A quick scan from an archived version of their “Ailments Treated” page from 4th November 2007 shows 127 ailments, but that list on the current version of the page is only 126.  In case you are wondering whether I am serious, I want to be absolutely clear that a PubMed search for “Correactology” produces zero results.  The removal of cancer from the list was an edit to the website, rather than a contribution to scientific research.  There have been no trials.  There are no datasets.  There are anecdotes and testimonials that score very low on the evidence pyramid.  Nevertheless, Correactologists take money from patients, claiming to be able to treat all kinds of diseases.  I will leave you to browse their (wish) list at your leisure, but I wanted to highlight a couple that are particularly unpleasant:Read More »

Leeds Big Data Week (big data for conservation biology)

I’m excited to be a part of Big Data Week this year. For those of you who aren’t familiar with the phenomenon of big data, IBM has a pretty good definition.  In essence, we are collecting huge amounts of data by virtue of living in a technologically advanced world, and those data are collected rapidly in a diverse range of formats. The challenge now is what to do with all of it! Big Data Week, which is running from 22-28 April 2013, is an international movement that was established in 2011 to connect businesses, data scientists, and technology groups to explore novel social, political, technological and commercial applications of big data.  Leeds Data Thing is my local big data group, formed in 2013 to provide a venue for the discussion of local big data applications.  They are putting on a range of events for BDW 2013, and I have volunteered to give a short presentation at one of those events.

Read More »