ENA

Workshop, International Society for Ecological Modelling Global Conference 2016

May 7-8, 2016

Overarching Workshop Learning Objectives

Participants will be able to ...

  • Describe core features of network models and explain the advantages and disadvantages of this model type
  • Characterize the aims of network science and explain why they are relevant for ecologists
  • Identify multiple examples of network ecology
  • Analyze bipartite models with R
  • Identify the core components of Ecological Network Analysis (Ecosystems)
  • Use enaR to apply Ecological Network Analysis
  • Interpret selected Ecological Network Analysis results including Structural Analysis, Flow Analysis, Utility Analysis, and Control Analysis.

Note that all notes are password protected PDFs. The password will be distributed during the workshop.

schedule

Saturday, May 7
9 am Gather 
9:30 Welcome & Introductions Borrett & Lau
10-11 Introduction to Networks & Network Ecology (notes) Borrett
11- 11:30 Break  
11:30-12:25

Network Analysis with R - Getting started

We are assuming that all partipants have some familiarity with R. If you are newer to R, please work though the excellent tutorial by Ellner & Bolker -- Lab 1: Introduction to R for Ecological Modeling. We recommend doing the following exercises to test your understanding {2.1, 3.1, 5.1, 5.2, 5.3, 5.4, 8.2, 8.3, 8.4, 8.5, 8.6, 9.2}. Here are links to the requried data files: Chlorellagrowth.txt and Intro2.txt.

 Lau & Borrett
12:30 - 1:30 Lunch  
1:30 - 2:25 Bipartite Graphs in Ecology - Mutualistic Networks & Co-occurrence networks (notes) Lau
2:30-3:25 Introduction to Ecological Network Analysis (ENA) (notes) Borrett
3:30 - 4:00 Coffee Break  
4:00 - 4:55 Introduction to enaR (notes, Vignette, Borrett & Lau 2014) Lau
5:00-5:30 ENA Structural Analysis (notes, example-net-structure-1.r, solution) Borrett
     
Sunday, May 8
9 am Gather  
9:30 - 10 Review and Discuss issues from the previous day Borrett & Lau
10 - 10:30 ENA Structural Analysis (continued) Borrett
10:30-11:00 Break  
11:30 - 12:30 ENA Flow Analysis (notes) Borrett
12:30 - 1:30

Lunch

  
1:30 - 2 ENA Flow Analysis continued Borrett
2-2:30 Importing models into enaR (notes) Lau
skipped ENA Utility Analysis (reading)  
skipped ENA Control Analysis (reading)  
2:00 - 2:30 Coffee Break  
2:30 - 3:45 ENA Applications, Uncertainty Analysis, and Ecological Inference (notes, example(R)) Borrett & Lau
3:50-4 pm

Wrap Up

 Borrett

resources

readings

Primary

Network Ecology - General

Proulx et al. 2005. Network thinking in ecology and evolution. TREE

Borrett, S.R., R.R. Christian, R., R.E. Ulanowicz. 2012.  Network Ecology (Revised). In: A.H. El-Shaarawi and W.H. Piegorsch (Eds.). Encyclopedia of Environmetrics (2nd edition). John Wiley and Sons: Chinchester, pp. 1767-1772.

Dormann, C.F., Fründ, J., Blüthgen, N. and Gruber, B., 2009. Indices, graphs and null models: analyzing bipartite ecological networks. The Open Ecology Journal, 2:7-24.

Ecological Network Analysis

Fath and Patten 1999. Review of the Foundations of network environ analysis. Ecosystems

Ulanowicz, R.E. 2004. Quantitative methods for ecological network analysis. Computational Biology and Chemistry, 28:321-339.

Fath et al. 2007.  Ecological Network Analysis: Network Construction.  Ecol. Model.

Borrett and Lau. 2014. enaR: An R package for Ecosysetm Network Analysis.  Methods in Ecology and Evolution

Background

Barabasi 2012 Network Takeover. Science

Borrett et al. 2014. The rise of Network Ecology: Maps of the topic diversity and scientific collaboration. Ecol. Model.

Brandes et al 2013 What is Network Science? Network Science

Ch2 Sharing Anchors Community. In Clay Shirky (2008) Here Comes Everybody. Penguin Press.

 

 

enaR Software

Other useful software

Other Resources

Videos
Websites
Papers