‘Size’ and ‘Shape’ in the Measurement of Multivariate Proximity

Ordination and clustering methods are widely applied to ecological data that are non-negative (like species abundances or biomasses). These methods rely on a measure of multivariate proximity that quantifies differences between the sampling units (e.g. individuals, stations, time points), leading to results such as:

  1. Ordinations of the units, where interpoint distances optimally display the measured differences
  2. Clustering the units into homogeneous clusters
  3. Assessing differences between pre-specified groups of units (e.g. regions, periods, treatment–control groups)

In this video, Michael Greenacre introduces his new article, ‘‘Size’ and ‘Shape’ in the Measurement of Multivariate Proximity’, published in Methods in Ecology and Evolution, May 2017. In the context of species abundances, for example, he explains how much a chosen proximity measure captures the difference in “size” between two samples, i.e. difference in overall abundances, and differences in “shape”, i.e. differences in compositions or relative abundances.  He shows that the popular Bray-Curtis dissimilarity inevitably includes a part of the “size” difference in its measurement of multivariate proximity.

This video is based on the article ‘‘Size’ and ‘shape’ in the measurement of multivariate proximity‘ by Michael Greenacre.

A new tool based on microbial interactions to analyze bipartite networks

Below is a press release about the Methods paper ‘BiMat: a MATLAB package to facilitate the analysis of bipartite networks‘ taken from the Pompeu Fabra University.

The Georgia Institute of Technology has created, together with the Pompeu Fabra University and the University of Canterbury, a new open-access and open-source tool for the study of bipartite networks

The team led by Joshua S. Weitz, Associate Professor at the School of Biology from the Georgia Institute of Technology, has developed BiMat: an open source MATLAB® package for the study of the structure of bipartite ecological networks inspired by real problems in microbiology and with broader applications. Cesar O. Flores, researcher at the School of Physics of the same institute, describes this new tool in an article published in the journal Methods in Ecology and Evolution. Sergi Valverde, Visiting Professor at the Complex Systems Lab from the Pompeu Fabra University, and Timothée Poisot, from the School of Biological Sciences of the University of Canterbury, are involved in the project. Continue reading

Understanding and Presenting YOUR Data

A Beginner’s Guide to Data Exploration and Visualisation with R
by Elena N. Ieno and Alain F. Zuur

A Beginner's Guide to Data ExplorationIn 2010 Alain Zuur, Elena Ieno and Chris Elphick published a paper in Methods in Ecology and Evolution entitled ‘A protocol for data exploration to avoid common statistical problems‘ (Volume 1, Issue 1). Little did they know at the time that this paper would become one of the journal’s all-time top downloaded and top cited papers, with a total of 22,472 downloads between 2010 and 2014.

Based on this success they decided to extend the material in the paper into a book.

Zuur and his colleagues at Highland Statistics ltd. give about 25 five-day statistics courses per year. Their typical audience consists of biological scientists at the post-graduate and post-doctoral levels. Early on in each course they have the following conversation with the participants:

Speaker: “Do you review submitted manuscripts for journals?”
Audience: “Yes.”
Speaker: “Do you like the statistical part of these manuscripts?”
Audience: “No!”
Speaker: “Do you understand the statistical part?”
Audience: “Not always.”

What if there were ways you could make reviewing your paper easier and more enjoyable for reviewers? What if making your manuscript easier to understand and nicer to read would increase the likelihood of your work being published?

A Beginner’s Guide to Data Exploration and Visualisation with R explains how you can do exactly that! Alain Zuur and Elena Ieno use ecological datasets to discuss the data exploration and visualisation tools you can use to make your paper simpler for readers and reviewers to understand. The authors also explain how to visualise the results of statistical models, an important aspect of scientific papers. Continue reading

Visualising MEE online

How time flies! Methods in Ecology and Evolution published its very first online extra one year ago today. In recognition of this, we’ve put together the following infographic which draws on the various web extras we’ve done since then.
Methods in Ecology and Evolution word cloud
Words are sized according to their relative frequency in the Methods RSS feed, containing blog posts, videos and podcasts. Click to enlarge!

More than the printed page

One of the big motivating factors in setting up Methods in Ecology and Evolution was the recognition that there are lots of ways to present research (without losing sight of the importance of peer review, rigour, and quality assurance).

However in terms of uptake and usage, the problem with the conventional paper is that it is not necessarily tailored to conveying research in a quick and convenient manner. For ‘methods’ papers a big problem is that users need to understand how new approaches and tools work in practice and even to see examples of the method in action. The printed paper or pdf is not always the best way to do this.

Some publications are trying out different ways of presenting research. For example the Journal of Visualized Experiments is placing the emphasis on video presentation of research. There are some examples from Evolution and Ecology. For example, here is some research on visual sensitivity in lizards:

http://www.jove.com/index/details.stp?ID=127

And here is something on applied ecology:

http://www.jove.com/index/details.stp?ID=227

(you need to register to see the whole thing, but the clip should give a good introduction).

More generally I think that in writing methods papers we could do a lot more to ‘sell’ our methods. For instance, more ‘tutorial’-style supplements to papers, there being a mechanism for authors and readers to talk to each other, and for users to share their experience.  By viewing these elements as a key part of the publication process everyone will benefit: authors will attract more readers, and users will find it easier to use new techniques.

Finally, and a bit more tongue in cheek this video includes an amusing take on the conventional publication process and the way that scientists conduct their debates via the literature (plus more!):

http://www.thedailyshow.com/watch/wed-august-5-2009/human-s-closest-relative