ENA

Ecological Network Analsysis Workshop @ ISEM 2023, May, 2023

Workshop co-organized by Brian Fath and Stuart Borrett

Notes for Getting Started

Tutorial Learning Objectives

Participants will be able to ...

  • Describe core features of network models and explain the advantages of this model type
  • Identify the core components of Ecological Network Analysis (Ecosystems)
  • Use several software tools facilitate model construction and to apply Ecological Network Analysis

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

Course Agenda & Resources

1. Introduction to Networks, Ecological Network Analysis, and Network Environ Analysis

Networks I - Introduction

Networks II - Flows

Networks III - Utility
2. Network Construction Network Construction Notes
3. Ecological Network Analysis in R - Using enaR Using enaR notes

Exercise 1 - Getting Started with enaR

exercise1.r

Exercise 2 - Loading a model into R

exercise2.r, oyster.dat, MDMAR02.xlsx

Exercise 3 - Analyzing multiple models

 exercise3.r

Exercise 4 - Uncertainty Analysis

 example-uncertainty.R
4. Applications of Ecological Network Analysis Networks IV - Applications

resources

readings

Primary

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.

Borrett and Lau. 2014. enaR: An R package for Ecosystem Network Analysis.  Methods in Ecology and Evolution 5:1206-1213.

Borrett, S.R. Introduction to Networks & Network Ecology Lecture Notes, ENA Tutorial, International Society for Ecological Modelling 2016.

Borrett, S.R., Sheble, L., Moody, J. and Anway, E.C., 2018. Bibliometric review of ecological network analysis: 2010–2016. Ecological Modelling, 382, pp.63-82.

Background

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.

Scharler, U.M. and Borrett, S.R., 2021. Network construction, evaluation and documentation: A guideline. Environmental Modelling & Software, 140, p.105020.

General

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

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

Barabasi 2012 Network Takeover. Science

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

Borrett, SR, Fath, BD, and Kazanci, C. Proposed changes in the mathematical notation used for Ecosystem Network Analysis for clearer communication.  The International Society for Ecological Modelling Global Conference 2016, Towson, MD. (Poster Presentation)

Other useful software

Other Network Science Resources

Videos
Websites
Papers