Network analysis for ecologists using R (NTWE01)
Delivered by Dr. Marco Scotti
This 5 day course will run from 6th – 10th March 2017 at Millport
field centre, Isle of Cumbrae, Scotland (please note that although the
field centre in on an island it is extremely easy and uncomplicated to
reach by public transport from both within and outside the UK)
The first graphical representation of a food web dates back to 1880,
with the pioneering works of Lorenzo Camerano. Since then, research on
ecological networks has further developed and ecology is one of the
fields that contributed the most to the growth of network science.
Nowadays, ecologists routinely apply network analysis with a diverse set
of objectives that range from studying the stability of ecological
communities to quantifying energy flows in ecosystems.
The course is intended to provide the participants theoretical knowledge
and practical skills for the study of food webs. First, lessons and
exercises will introduce basic principles of network theory. Second,
ecological examples will be focused on binary food webs, networks
depicting who eats whom in ecosystems. Algorithms quantifying either
global food web properties or single species features within the trophic
network will be introduced. Third, we will study how the architecture of
the food webs can be used to investigate robustness to biodiversity
loss, thus helping to predict cascading extinction events. Then,
ecosystem network analysis (ENA), a suite of matrix manipulation
routines for the study of energy/matter circulation in ecosystems, will
be presented. We will apply ENA to characterize the trophic structure of
food webs and quantify the amount of cycling in ecosystems. Finally, we
will learn how to visualize food web graphs to illustrate their features
in an intuitive and fancy way.
(PLEASE NOT THIS COURSE IS PRECEDED BY ‘STABLE ISOTOPE MIXING MODELS
USING SIAR, MIXSIAR AND SIBER’- A COMBINED COURSE PACKAGE IS AVAILABLE
Course content is as follows
Monday 6th – Classes from 09:00 to 17:00
Module 1: Introduction to graph theory and network science.
Basic terminology for learning the language of networks: from nodes and
links to degree distribution.
Three types of mathematical graphs and their properties: random
networks, small-world networks, and scale-free networks.
Tuesday 7th – Classes from 09:00 to 17:00
Module 2: The use of graph theory in ecology: (1) networks representing
various interactions in ecological communities (e.g., predator-prey and
plant-pollinator networks); (2) networks illustrating interactions at
different hierarchical levels (e.g., social networks at the population
level and species dispersal in the landscape graph).
Who eats whom in ecosystems and at which rate? Binary and weighted food
Quantitative descriptors of food web networks (e.g., fraction of basal,
intermediate and top species, connectance and link density).
Wednesday 8th – Classes from 09:00 to 17:00
Module 3: The structural properties of food web networks.
Biodiversity loss and food web network robustness. How to predict
secondary extinctions using the information embedded in the network
structure of the food webs.
The relevance of bipartite networks in ecology for the description of
various interaction types (e.g., plant-pollinator and plant-seed
Thursday 9th – Classes from 09:00 to 17:00
Module 4: Ecosystem network analysis (ENA): basic principles and
Input-output analysis: partial feeding and partial host matrices.
Possible ways to trace indirect effects in ecosystems.
Trophic considerations: the effective trophic position of species in
acyclic food webs.
Finn cycling index and the amount of cycling in ecosystems.
Friday 10th – Classes from 09:00 to 16:00
Module 5: Can network analysis help to better understand possible
consequences of global warming on ecological communities?
Network visualization with Cytoscape: how to change the layout of graphs
illustrating food web interactions (the Style interface to modify node,
link and network properties).
There will be a 15 minute morning coffee break, an hour for lunch, and
a15 minute afternoon coffee break. We keep the timing of these flexible
depending how the course advances. Breakfast is from 08:00-08:45 and
dinner is at 18:00 each day.
Please email any inquiries to [hidden email] or visit our
Please feel free to distribute this material anywhere you feel is
Upcoming courses - email for details [hidden email]
INTRODUCTION TO PYTHON FOR BIOLOGISTS (October)
LANDSCAPE GENETIC DATA ANALYSIS USING R (October)
PHYLOGENETIC DATA ANALYSIS USING R (October/November)
SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November)
ADVANCING IN STATISTICAL MODELLING USING R (December)
MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (January)
ADVANCED PYTHON FOR BIOLOGISTS (February)
STABLE ISOTOPE IXING MODELS USING SIAR, MIXSIAR AND SIBER (Feb/Mar)
INTRODUCTION TO GEOMETRIC MORPHOMETRICS USING R (June)
Dates still to be confirmed - email for details
INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS
BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS
GENETIC DATA ANALYSIS USING R
INTRODUCTION TO BIOINFORMATICS USING LINUX
INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING
Oliver Hooker PhD.
128 Brunswick Street
+44 (0) 7966500340
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