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

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 »

A new MOOC from Leeds: “Fairness and Nature: When Worlds Collide”

Picture1It’s a pretty exciting time to be teaching in higher education.  There has been a wave of critical evaluation (mostly by the teachers themselves) which has led to a great deal of progress over the past couple of years.  This has led to a recognition that lecture-based courses are not the “be all and end all” of university teaching, and that there are better ways to do things.  Massively Open Online Courses (MOOCs for short) are playing quite a large role in redefining how university teachers engage with their students and how we think about delivering the student experience.

The new MOOC from the University of Leeds is called “Fairness and Nature: When Worlds Collide”, and is being run by Professor Jon Lovett in the School of Geography. Jon is a charismatic and passionate guy with a wide range of experiences in the interaction between people and the nature world, and it is these themes that are explored in the course.  If you want to find out more, head over to the FutureLearn site and sign up (it’s free!).  Here’s a taster:

There are some key characteristics of MOOCs that make them different from conventional university courses:

  • Variable length – MOOCs can be anything from 1 week to 12 weeks, with the breadth and depth of content varying accordingly.
  • Entirely online – with no need to rely on built infrastructure, MOOCs can (and, indeed, do!) cater for tens of thousands of students, rather than the usual hundred or so.
  • Flexible study – because of the online nature, students can participate whenever is convenient for them.  Sometimes this means that students drop-off entirely (completion rates are relatively low) but that isn’t really the point of MOOCs.  MOOCs are frequently designed to provide access to education for as many people as want it, and any learning is a bonus.
  • Flexible structure – the online platform allows a wide variety of multimedia, interactive, connected resources to form the backbone of a course.  These make for a very engaging learning experience.

All these factors combine to make a new and interested way of teaching and engaging a wider range of students, and I look forward to seeing where the MOOC movement goes.

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 »

A nice review of the demands of open science

The journal Psychological Inquiry has just made an issue on open access science open access.  I’ve flicked through a couple of articles and they look like a thoroughly interesting combination of pros, cons, and speculations.  In particular, the opening article states the needs of an open science movement very clearly in its abstract:

We call for six changes:

  1. full embrace of digital communication;
  2. open access to all published research;
  3. disentangling publication from evaluation;
  4. breaking the “one article, one journal” model with a grading system for evaluation and diversified dissemination outlets;
  5. publishing peer review; and
  6. allowing open, continuous peer review.

I think these six principles sum-up the needs of the research community quite well.  We are working in an out-of-date and horribly expensive system that is not benefitting scientists or those who use the science.  There has always been pushback against these kinds of measures (see the response in the same issue of Psychological Inquiry by the editor of a different journal), mostly along the lines of “it’s too hard” or “that won’t work”.  However, those sorts of arguments are undermined by a number of journals which are doing precisely these things extremely well.  I’ll mention Cryosphere as an example that I have had experience with.  A few small changes could go a very long way towards improving the system, and we cannot let the editors and publishers try to convince us that it cannot be done!

Three simple reasons why MOOCs are a good thing

A group of UK universities (mine included) have embarked upon a new initiative called “FutureLearn” which seeks to take the raw success of MOOC providers like Udacity, EdX and Coursera (almost exclusively North American) and build them into a diverse and viable teaching framework.  This is a really exciting opportunity for the UK universities involved, and I am looking forward to seeing how it turns out.  I also have a vested interest, as I am (as of a couple of weeks ago) chairing a Faculty committee on the integration of technology into student learning.  However, I have been reading a lot of material about MOOCs that has been less than positive and so I think it is probably worth pointing out some important benefits of MOOCs to help balance the debate: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.

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While we wait for the open access revolution, self-archive!

I’ve just had a paper published on open access in ecology and evolution, so I thought I would let you know what it’s all about.  I wrote a few weeks ago about how you can often post more of a scientific paper online without violating copyright than you might think.  I went through a couple of journals in which I had published articles, and tried to work out what I could self-archive.  The answer was usually “quite a lot”!  Then someone in the comments popped up and mentioned the SHERPA-ROMEO website, which allows you to search for the name of the journal in which your paper has been published and then shows you the policy on self-archiving.  Well, being the data-lover that I am I decided to check out the rest of the journals in ecology and evolutionary biology (all 165 that were listed on Thomson Reuters Journal Citation Reports).  The results were pretty interesting…

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How much of an academic paper can you post online? Most of it!!

Edit: As was pointed out in the comments, you can find self-archiving info for most journals at http://www.sherpa.ac.uk/romeo/ [h/t Laurent]

I have been a bit frustrated about scientific publishing, as you might have been able to tell if you read some of my earlier posts on open access in academia.  I posted earlier this week about Aaron Swartz and the legal predicament in which he found himself when he downloaded huge numbers of scientific papers.  I was frustrated at the lack of access that most people experience to academic publishing, but didn’t want to resort to breaking the law to remedy the situation.  However, a certain amount of that frustration could have been relieved had I just taken the time to figure out where the boundaries lie in the copyright documents that I sign when I publish papers.  I decided to have a look to see how many of my rights remain, and I was quite interested to find out that I can post a reasonable amount of information on the web without breaking any laws.  As ever, this isn’t legal advice.  However, there do seem to be a few generalities that others can use to guide the release of their publications depending upon the publisher that owns the journals within which their papers are published:Read More »

The (current) limits of open access and #PDFtribute

EDIT [18/1/13]: At almost exactly the same time as I was posting about how the revolution was coming, the revolution started.  Mathematicians are setting up community-run, open access journals independent of larger publishers.

I had never heard of Aaron Swartz before he died.  Swartz was 2 1/2 years younger than me and spent his life working on, with, and around the internet and its various limitations.  I have a lot of respect for what he accomplished, not only in terms of the technical progress that he was a part of, but also because of his philosophy about open access to information.  In the wake of his death, supporters took to Twitter to post free copies of their publications, whether or not the material was in the public domain.  This reflects Swartz’s actions in downloading millions of academic papers from the MIT network which precipitated the court case that he was fighting when he chose to end his life.Read More »