#BES2016 Quantitative Ecology SIG events

With just a few days until BES2016 kicks off in Liverpool, here’s a handy guide to the events we have organised for the conference:

Best Practice for Code Archiving

Sunday 11th December 12:00 – 17:00

Interested in how to distribute and archive code? Join Methods in Ecology and Evolution Editor Rob Freckleton, along with several experts with backgrounds in programming and ecology to provide practical discussion of writing and sharing code for your research. All levels of expertise are welcome, especially those just starting out.

The workshop will be introduced by Natalie Cooper who will explain why reproducible code is important and give an overview of the rest of the workshop. We will then have three breakout sessions giving participants practical training in best practice for using code in ecology research. We will focus on quality, functionality, robustness and usability. Breakout groups will be led by code experts Mike Croucher, Laura Graham and Tamora James.

Finally, participants will have the opportunity to input into the development of new guidelines for archiving code for publication, which are currently being developed by the BES journal Methods in Ecology and Evolution. Journal Editor Rob Freckleton will introduce the new guidelines and lead a discussion on how they can best serve the community.

 

Lunch will be available from midday and tea and coffee will be provided.

 

Wikithon: Quantitative Ecology Documentation (QED)

Tuesday 13th December 1:15 – 2:45

Dominic Bennett, Institute of Zoology, London

We’ll be running a WIKITHON workshop at this year’s BES annual meeting conference for our wiki, Quantitative Ecology Documentation. The aim of the wiki is to help foster communication between ecologists on all things computational and quantitative in ecology, a “how I did this in R” pinboard of links, code and empathetic encouragements. Documents on the wiki can be very simple, “best ways to read data into R” very complex, “how to develop your own IBMs”, or even very original, “best ways to relax after extended and frustrating coding sessions”. At the workshop we’ll be demonstrating the new wiki and providing training on how to edit and create new pages. Then, the wikithon will commence! Attendees can write their pages based on a list of suggestions, or you can come up with your own ideas. (Oh plus…. the workshop may be featuring the, highly acclaimed, wikipedia music!)

 

Macroecology and Quantitative SIG joint mixer

Tuesday 13th December: Meet in the registration area at 18:20 or at the Pump House at 18:30

This year there will be a joint social between the quantitative and macroecology groups. We will be meeting at 18:20 in the reception and making our way over as a group. If you’re coming later, the Pump House is 5 mins walk from the conference centre; it can’t be missed! It’s the redbrick building with the large Victorian chimney. Activities include: informal networking, alcohol consumption, awkward standing around plus the possibility of laughter (N.B. please provide your own jokes/gags/amusing anecdotes). Oh, by the way, drinks are on us!

 

Additionally, committee member Robert Salguero-Gómez (University of Sheffield), is running a workshop on Monday 12th DecemberMacro-ecology through the lens of comparative demography.

A handy guide to How to survive the BES Annual Meeting has been provided by Markus Eichhorn. Enjoy!

 

Links round-up: 09/09/2016

We now have a new logo! In the spirit of openness, Nick Golding has shared the code he used to create these logos: network image and triangulation image

Methods in Ecology and Evolution brought out a Statistical Ecology Virtual Issue to go along with this summer’s International Statistical Ecology Conference.

There is now a package to interface with the > 1000 geoalgorithms from QGIS within R: RQGIS. Jamie Afflerbach has written a more general spatial analysis in R tutorial.

QAEco have written about their favourite R packages to use for ecological data analysis – let them know your favourite packages in the comments.

Events

Last day to register for the BES Macroecology SIG’s Early Career Event (NB, will be very general and not just for macroecologists, or even ecologists), 16th September 2016, London.

Challenges and Opportunities of analysing ecological citizen science data, 10th October 2016, Cambridge.

Courses

Applied Bayesian modelling for ecologists and epidemiologists. 24-29 October 2016. PR Statistics, Loch Lomond, Scotland.

Geometric morphometrics in R. 23-27 January 2017. Transmitting Science, Barcelona, Spain.

Data analysis in ecology. Online 5 week course provided by University of Oxford from 2nd November 2016.

Jobs

Postdoc at Ghent University, Belgium: Scaling up functional biodiversity research.

Postdoc and PhD positions available in the Pinsky Lab at Rutgers University, New Jersey: Metapopulation dynamics and population genomics.

Several Assistant Professor positions at University of Zurich, Switzerland.

Two PhD positions in the Pearse Lab, Utah State University: (1) ecological and/or evolutionary modelling, (2) plant ecology and fieldwork.

Call for Catalyst Postdocs at sDiv, Leipzig, Germany is now open.

Spatial Scientist and GIS analyst positions available in the Land Use and Ecosystem Services Science Group at Forest Research, Roslin, Scotland.

Links round-up: 17/06/2016

Events

People, politics and the planet: any questions? A debate on UK environmental policy in the aftermath of the EU referendum. 21st July 2016 at Royal Geographical Society (with IBG), London.

Registration and abstract submission is now live for the BES 2016 Annual Meeting. 11-14th December 2016, Liverpool.

Courses

Bayesian integrated population modelling using BUGS and JAGS. 12-16th December 2016 at Swiss Ornithological Institute.

Importing data into R Webinar. 22nd June 2016. Online, provided by RStudio.

Introduction to Bayesian hierarchical modelling using R. 23-16th August 2016, Loch Lomond, Glasgow.

Jobs

Senior Research Associate/Research Associate at Lancaster University. Computational environmental science (models in the cloud).

Postdoc at Centre for Macroecology, Evolution and Climate, Copenhagen. Community and ecosystem ecology.

 

Links round-up: 20/05/2016

Miller et al. have put together a review of the use of metrics and null models in community phylogenetics. They review a total of 278 metric/null model combinations and find that these are in fact 72 true unique combinations. They also find that the choice of null model is more influential over type I error rates than the choice of metric. The paper comes with an accompanying R package – metricTester – which allows for testing of method performance.

Lefcheck presents a new R package – piecewiseSEM – which is a structural equation modelling package designed with its uses in ecology, evoluation and systematics in mind. The paper contains two worked examples including code.

Events

Statistical Ecology Research Festival. 7th June, University of Kent, Canterbury.

IALE UK 2016 Conference: landscape characterisation – methods and applications in landscape ecology. 7-9th September, University of Reading.

Courses

Genetic data analysis using R. 16-20th August, Isle of Cumbrae, Scotland.

The use of phylogenies in the study of macroevolution. 19-23rd August,  Facilities of the CRIP at Els Hostalets de Pierola, Barcelona.

There’s also still time to sign up for our Data Management in R course on Monday (23rd May) at Charles Darwin House in London.

Jobs

Postdoctoral research assistant at University of Oxford. Human modified tropical forests.

Postdoc at CIBIO-UE, University of Évora. Modelling food web architectures under climate change.

Reader/Senior Lecturer/Lecturer at Queens University Belfast. Three positions: global change biology, agro-ecoinformatics and genetics and molecular biology.

Research Associate at CEH, Wallingford. Ecological modelling of pathogens threatening humans, animals, plants and ecosystems.

Data management in R course

There are still a few days left to sign up for our data management in R course. It’s next Monday (23rd May) at Charles Darwin House in London.

Sign up here!

This event is aimed towards participants with a basic knowledge of R who want to learn more about how to import and manage data within R. Participants will learn about a) how to get data into R (e.g. reading in from databases, other programmes and spatial data), b) how to manipulate single datasets (e.g. data formats, reshaping, sorting, outlier checks), c) how to work with multiple datasets (e.g. SQL in R) and d) methodologies for efficient data management in R (e.g. storing metadata, version control and workflows). Participants will need to bring their own laptops with an up to date version of R installed.

Links round-up: 08/04/2016

The Stan website now has a section detailing case studies – these are intended to reflect best practices in Bayesian methodology and Stan programming. Users can contribute their own case studies. On a related note, Hiroki ITÔ has translated some of the code from Kéry and Schaub’s Bayesian Population Analysis to Stan (chapters 3 – 9 so far, with the rest currently in the works).

Noam Ross has put together some crowdsourced resources on reproducible project organisation. Contains lots of useful links to further advice and discussion on project directory organisation.

SESYNC issue a call for proposals for collaborative & interdisciplinary team-based research projects.

Courses

Advances in DNA taxonomy, 8th – 11th August 2016, Loch Lomond, Scotland.

Jobs

PhD at Center for Macroecology, Evolution and Climate in Copenhagen. Using citizen science to examine behavior, resource use, biodiversity, and distributions of ants in Denmark.

Water resources model developer at James Hutton Institute, Aberdeen.

 

Links round-up: 18/03/2016

NEON have put up a wide range of tutorials for working with data in R. They include general data manipulation, spatial data analysis and working with time series data.

Viviana Ruiz-Gutierrez writes about the calibration model for reducing uncertainty in citizen science data. The model reduces uncertainty by accounting for both false positives and negatives, and is detailed here.

Want to give back to the ecological community while gaining experience of grant reviewing which looks great on your CV? The BES Review College is open for applications for the next round of grant reviews. Deadline 21st March.

Courses

The Quantitative Ecology SIG have organised two upcoming courses:

  1. Spatial data analysis in R. 20th April 2016 at the University of York
  2. Data management in R. 23rd May 2016 at Charles Darwin House, London

More information to follow on these.

Taming the BEAST: Bayesian evolutionary analysis by sampling trees. 26 June – 1 July 2016, Engelberg, Switzerland.

Advances in Spatial Analysis of Multivariate Ecological Data: Theory and Practice. 11 July 2016 – 15 July 2016, Loch Lomond.

Jobs

Research Associate in Epidemiology at University of Glasgow. Project: From observation to intervention: overcoming weak data with new approaches to complex biological problems.

Research Fellow in Spatial Modelling and Research Fellow in Applied Biogeography at University of Southampton. Project: Scaling Rules for Ecosystem Service Mapping.

Lecturer in Evolutionary Biology/Ecology/Conservation (4 positions) at University of East Anglia.

Postdoctoral Researcher in Statistical Ecology at Swedish University of Agricultural Sciences. Working with the Swedish Breeding Bird Survey data.

BES POST Fellowships for a three month funded placement in the Parliamentary Office and Science and Technology.