D.E. Hines

enaR an package for Ecological Network Analysis

Acknowledgements

Core Sound, Fall ClosedOyster Reef Lake Lanier

U. Scharler & B.D. FathJ. Mejaski

Stuart R. BorrettUniversity of North Carolina Wilmington

Matt LauNorthern Arizona University

Shaoqing Chen

General Approach

http://affordable-tack.com

Nitrogen

Ecological Network Analysis

Wind in the Willows

Patterns reflectdevelopment constraints

and system function

Form Function

Ecological Network Analysis (ENA)Economic Input–Output Analysis

(Leontief)

Networks of energy–matter flows and storages– trace a single conservative currency

(e.g. nitrogen, carbon)– usually assume steady-state

“Macroscope” to investigate – organization & connectivity– direct & indirect interactions– Resilience & sustainability

ENA Applications: Examples

Alligators enhance frog populations- Indirect mutualisms

1999Trophic Ecology

2012

Strength of coupling between BGC processes- Nitrification + Denitrification- Nitrification + Anammox

Biogeochemistry

2012

Urban metabolism of Vienna- Carbon perspective- Energy production, Construction key

Urban Metabolism/Sustainability

Two Schools of ENAUlanowicz School Patten School

Environment Focus

Photo courtesy of C Thomas

Trophic Focus

Information Theory

Photo from http://www.cbl.umces.edu/~ulan/

University of Maryland University of Georgia

Network Environ Analysis

Distinct but interwoven development of ENAAscendency Concept

Environ ConceptPhenomenological Graph Diff Eqs

ENA SoftwareTools for Science & Innovation

NETWRK 4.2

Fortran Code, DOS executable

Ulanowicz & Kay 1991Environmental Softwarehttp://www.cbl.umces.edu/~ulan/ntwk/network.html

WANDAllesina & Bondavalli 2004Environ. Model. Softw.

Excel based, more user friendly

Ulanowicz School Patten School

EcopathChristensen & Pauly 1992Focus on model construction

NEA.mFath & Borrett 2006Environ. Model. Softw.

Matlab Function Collected NEA algorithms

http//people.uncw.edu/borretts/research.html

EcoNetKazanci 2007Ecol. Mod.

C++, Web ServerParticle Tracking Approach

http://eco.engr.uga.edu

No software covers both schools

Different availability, use, extensibility

Connect

Extensible

Software Design Objectives

Collect

Available

Tools for Science & Innovation

Algorithms from both Ulanowicz and Patten ENA Schools

Increase availability- Low cost software- Run on multiple OS (PC, Mac, Unix)

Users can - access original code- add new functionality

Additional network science tools- Social network analysis- ERGM

Connect

Extensible

enaR package for

Collect

Available

Tools for Science & Innovation

AlgorithmsPatten- structure, flow, storage, environs, control,

utilityUlanowicz- ascendency, mixed trophic impact, balanceR: a statistical programming environment- Wide use- Free, Open source- PC, Mac, Unix- CRANExisting Packages- network (Butts, 2008)

- sna (Butts, 2008)

- statnet (Handcock, 2008)

- iGraph- bioconductor

Illustrate some ena package functionality

Data Input: Model DataNode Names

F: Flows from i to j

Data Input: Model DataNode Names

F: Flows from i to j

Data Input: Model DataNode Names

F: Flows from i to j

z: Inputs

e: Exports

r: Respirations

y: Outputs (e + r)

Living: logical (T or F)

Data stored as a network object

pack() and unpack()

(Butts 2008)

Data Input: read.x

read.scor() read.wand()

Plain text file

NETWRK 4.2 - SCOR WAND

Collect

Visualization

> data(oyster)> plot(oyster)

Simple Plot Fancier Plot

Internal Fluxes

Connect

Flow Analysis Example

Column-to-Row Orientation

Simultaneously Analyze Multiple Models

> ns = lapply(model.list, get.ns)> barplot(ns$id)> barplot(ns$ASC.CAP)

model.list = list of Network Model data objects

get.ns() = ena function to calculate network statistics

Low n High n

50 trophic ecosystem models(Salas & Borrett 2011)

Extend

Indirect / Direct

Ascendency / Capacity

sna: CentralityConnect

Centrality – relative importance of node, many types

Core Sound, NC ecosystem Model (Deheer, 2012)

Centrality Calculations- degree()- betweenness()

gplot.target()

Future Work• Add Additional Algorithms– Lindeman’s Spine– Cycle Basis– Schramki’s control analysis revisions

• Connection to Ecopath– Shiela Heymans, Villy Chistensen

• What will you do with the package?

• How will you extend it?

Collect

Connect

Connect

ConnectExtensible

Summary

Collect Available

enaR: package for Ecological Network Analysis

UlanowiczPatten

FreePC, Mac, Unix

CRAN

Open SourceUsers can grow

Existing Packages- network- sna- bioconductor

borretts@uncw.eduhttp://people.uncw.edu/borretts/