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
[email protected]://people.uncw.edu/borretts/
