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.


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


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.


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.


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.



Links round-up: 04/03/2016

The Demography Beyond the Population Special Feature to come out of last years workshops is now available. This Special Feature spans across all six BES journals.

Using SQL with R can make working with large datasets much easier. Here is a tutorial on integrating PostgreSQL with R.

Rich Fitzjohn and Daniel Falster discuss how they built their ‘plant’ R package.

We have set up a Facebook group in an attempt to make the BES Quantitative Ecology SIG community more interactive and to encourage communication between our members. Please join up and post discussion to the group!


Applied Spatial Ecology Workshop at Penn State University, USA. 27-28 September 2016.

Grants are available for the course Introduction to Network Analysis in Life Sciences, 24-28 October 2016 at Transmitting Science, Barcelona, Spain.


Postdoctoral researcher in statistical ecology at Swedish University of Agricultural Sciences

Two postdoctoral positions in theoretical ecology at the Centre for Biodiversity Theory and Modelling, Moulis, France.

Research scientist in applied statistics at Marine Research Institute in Bergen, Norway

Postdoctoral fellow in numerical palaeoecology and quantitative ecology at University of Bergen, Norway

Links round-up: 12/02/2016

There have been a few new R packages (and associated papers) that look useful for ecologists recently:

For those currently looking for funding for post-doc fellowships, Adam Hayward and Dieter Lukas have put together details of funding sources and some related advice.


Registration is now open for the BES Macroecology SIG 2016 Annual Meeting. 7 – 8 July 2016, Oxford.

EcoSummit 2016 – Ecological Sustainability: Engineering Change. 29 August – 1 September 2016, Montpellier, France. Deadline for abstract submission is 15 February.



PR Statistics have a few upcoming courses including Time Series Models for Ecologists and Climatologists and Introduction to Python for biologists.


Postdoc at University of Stirling: working within WP1 of Hydroscape – Connectivity, stressors & responses within and across landscapes.

Statistical/mathematical programmer at Quantics Biostatistics, Edinburgh.

Postdoc at University of Sheffield: Modelling soil ecology for the SoilBioHedge project.


Links round-up: 22/01/2016

There is a huge diversity of phylogenetic metrics in use in ecology; the sPhy working group have reviewed and classified these metrics. The output is a guide to choosing the correct phylogenetic metric based on the research question. Tucker et al. 2016: A guide to phylogenetic metrics for conservation, community ecology and macroecology.

There have been some useful posts about performing Bayesian statistical analyses in R on the R-bloggers network recently: Bayesian regression with STAN: normal regressionKéry and Schaub’s Bayesian population analysis translated to STAN; and R users will now inevitably become Bayesians (a guide to the brms and rstanarm packages).


Applications for the BES Summer School are now open – more info here. They are also looking for PhD students to be mentors – application here.


Introduction to R (5th-9th September 2016) and Model-based statistical inference in ecological and evolutionary biogeography (28th November – 2nd December 2016) at Transmitting Science, Barcelona, Spain.

Spatial analysis of ecological data using R, 11th-17th April 2016, Isle of Cumbrae, Scotland.

Advancing in statistical modelling using R, 2nd-6th May 2016, Malham Tarn Field Centre, North Yorkshire.


Postdoc research associate at the University of Hull: Phylogenetic comparative analyses of vertebrate invasion success

Postdoc research associate at the University of Bristol: development and evaluation of representations of marine ecological diversity in an Earth system model

Associate Professor in Bioinformatics at University of Auckland, New Zealand

Associate Professor in Environmental Management at University of Nottingham

Links round-up: 08/01/2016


The Zöon package is now available on CRAN. This package allows users to create and run fully reproducible SDM workflows.

The macroeco python package is for analysis of empirical macroecological patterns and comparison to theoretical predictions. Accompanying paper here.

Some interesting online tutorials have caught my eye recently: a complete tutorial on time series modelling in R; Ethan White’s Programming for Biologists course materials; a quickstart guide to building an R package from the methods blog; how to use R as a GIS.

Plus, it’s this time of year again:
Propose a Thematic Topic Session for the 2016 Annual Meeting
11 – 14 December 2016, ACC, Liverpool, UK . More information and details of how to apply can be found here. Deadline: 09:00 (GMT) Monday, February 15 2016


Species distribution models: concepts, methods, applications and challenges. Évora, Portugal.  4th – 10th July 2016.

Two courses on Bayesian integrated population modelling using BUGS and JAGS: Utah State University, Logan 25th – 29th July 2016 and Patuxent Wildlife Research Center, Laurel/Maryland, USA 1st-5th August 2016.

Distance sampling workshops. University of St Andrews, 16th – 19th August 2016.

An introduction to statistical methods in epidemiology using R. Transmitting Science, Barcelona, 20th to 22nd June 2016.


Two PhD positions at Queen Mary University of London with Axel Rossberg: competition and coexistence in complex ecological communities and spatially explicit theoretical community ecology.

Tenure-track assistant professor of macroecology at CMEC, Copenhagen.

Post doctoral research assistant in agri-environmental science at ZSL Institute of Zoology, London.

Lecturer/senior lecturer in biodiversity and ecology at University College London.

Links round-up: 28/11/2015

The geoknife R package allows for reproducible processing and subsetting of gridded spatial data. Some example use cases can be found in the accompanying paper.

ggtree is an R package that extends the ggplot2 package to allow for visualisation of phylogenetic trees.

Emilio M. Bruna has argued that tropical biology (and ecology more broadly) could learn from psychology and aim to reproduce the results of classic studies. He has made suggestions of classic papers he thinks should be reproduced. The aim seems to be to bring together a working group; those interested should contact him.


Joint BES and CCI Annual Symposium
Making a Difference in Conservation: Improving the Links Between Ecological Research, Policy and Practice. April 11 – 13 2016, Cambridge


NIMBioS Tutorial: Game theoretic modelling of evolution in structured populations. April 25-27, 2016, Tennessee


PhD at University of Reading: Modelling functional connectivity of butterflies across landscapes using population and genetic data

Lecturer/Senior Lecturer at Imperial College, London: quantitative ecology or evolution

Postdoc at University of Edinburgh: Development and analysis of agent-based simulation models and Bayesian hierarchical statistical models of poacher and patrol behaviour. Search for vacancy ref 034750.