Modelling of Ecosystems
by Tools from Computer Science
Summer School at Czech University of Life Sciences, Prague,
16-20 September, 2013
Winfried Kurth
University of Göttingen, Department Ecoinformatics, Biometrics
and Forest Growth
Introduction to different modelling concepts (part 2)
Classification of models in plant and
ecosystem sciences
process models
physiology
Classification of models in plant and
ecosystem sciences
process models
physiology
...you remember the first Wise man:
Classification of models in plant and
ecosystem sciences
process models
physiology
Classification of models in plant and
ecosystem sciences
process models
physiology
... see also the model
BALANCE on Thursday
Classification of models in plant and
ecosystem sciences
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
structural models
morphology
the second Wise man:
process models
physiology
Classification of models in plant and
ecosystem sciences
structural models
morphology
process models
physiology
Structural models
capturing 3-d architecture of organisms
Motivation for structural models of trees
• ecosystem research:
forests as intensively structured life communities
relevant issues:
impact of tree architecture
- on carbon uptake and processing
- on water balance / drought stress robustness
interpretation of patterns of crown damage
simulation: competition, manipulations by foresters
Motivation for structural models of trees
• basic research:
- tree crowns (+ root systems) = complex structures
information compression?
- botanical knowledge basis
briding the gap:
practical view in botany/forestry – ecosystem models
- linking of models
• demonstration
visualization of future development
virtual landscapes as support tools for planning and
decision
Motivation for structural models of trees
• special requirements for modelling of
- light in a stand
- mechanics
- water flux in a tree
- competition
• bridge between process models and
botanical observations
• common basis for diverse processes in/at the tree
(enhancing the consistency between different models)
Origins, schools, motivations of plant modelling
• French school
(Hallé et al.: botany; CIRAD - AMAP Montpellier)
tropical forests; agronomy
The French school of tree architectural studies
Hallé, Oldeman and Tomlinson 1978: Tropical Trees and Forests
23 „architectural models“ (basic patterns of crown architecture)
computer-based simulation system AMAP:
„Atelier de Modélisation de l‘Architecture des Plantes“
Origin: work by Philippe de Reffye on coffee plants around
1976
first AMAP version (basis of the contemporary commercial
software REALnat, Bionatics): makes use of the 23
architectural models from Hallé et al.
early team members:
Ph. de Reffye, R. Lecoustre, M.
Jaeger, E. Costes, P. Dinouard,
F. Blaise, J.-F. Barczi, H. Rey, D.
Barthélémy, Y. Caraglio
agronomists, computer
scientists, botanists,
mathematicians
Origins, schools, motivations of plant modelling
• French school
(Hallé et al.: botany; CIRAD - AMAP Montpellier)
tropical forests; agronomy
• theoretical biologists (primarily in Great Britain)
• theoretical computer science
L-Systems: grammar of shape generation
mathematization
• computer graphics
Virtual Reality
efficiency of algorithms
Early and later computer graphics results
Origins, schools, motivations of plant modelling
(continued)
• forest ecologists and forest practitioners
- single-tree oriented growth models
- heterogeneous stands
- processes  morphological appearance
- ecosystem research
• bioclimatologists und biophysicists
- heterogeneity: nonlinear light response of photosynthesis
- tree mechanics, tree hydraulics
• entomologists
interaction herbivores – plant structure (agriculture)
CPAI Brisbane
Structural models
3 levels:
1. static description of structure
plant at a fixed date (e.g., at 16 September 2013)
Structural models
3 levels:
1. static description of structure
plant at a fixed date (e.g., at 16 September 2013)
2. dynamic description of structure, non-sensitive
description of development (ontogenesis) of a plant:
time series of 3-dimensional structures
Structural models
3 levels:
1. static description of structure
plant at a fixed date (e.g., at 16 September 2013)
2. dynamic description of structure, non-sensitive
description of development (ontogenesis) of a plant:
time series of 3-dimensional structures
3. dynamics, taking causal impacts / conditions into account
(sensitive models)
 different paths of development
 logical conditions for the decision between them
(simplest case: stochastic)
empirical basis: semi-automatic or automatic
digitization
different possibilities:
• combination digital caliper - digital compass interface software
(Oppelt et al. 2000)
• electromagnetic digitizer
(Polhemus Fastrak, used e.g. by Sinoquet et al., Clermont-Ferrand)
• ultrasonic digitizer
• mechanical arms
• 3-d laser scanner
• processing of stereophotos
example: electromagnetic digitizer
tracking system „Polhemus Fastrak“
example: electromagnetic digitizer
tracking system „Polhemus Fastrak“, results
trees,
example: electromagnetic digitizer
tracking system „Polhemus Fastrak“, results
Mangrove trees
concerning description level 1:
static description of structure
two approaches:
(a) tables
each morphological unit of a plant = one row
dtd code = „descriptive tree data“, or MTG code
(b) imperative (command-driven):
„Turtle geometry“
virtual turtle „constructs“ the structure,
the description are the commands which control it
turtle geometry command language
Example for dtd coding
of a real branching
system:
MTG (= multiscaled tree graph) coding:
multi-scale description
scale levels:
P plant
U growth unit
I internode
MTG (= multiscaled tree graph) coding:
multi-scale description
scale levels:
P plant
U growth unit
I internode
relations:
< successor
+ branch
/ refinement
imperative approach: „turtle geometry“
Turtle:
goes according to commands
more complex structures can be generated this way
(see later...)
The second level of description:
Dynamic description of plant structures
• how do plants change during ontogenesis?
one of the first modelling attempts: AMAP
Modelling the activity of meristems
shape of tree = trajectory of its meristems
approach for modelling:
shape of tree = trajectory of meristems
• primary meristem
• branching
• secondary meristem
(to be added:
mechanic deformations, deformations with physiological causes,
damages, processes of senescence and mortality)
meristem-based modelling: Theory
Adrian D. Bell 1979:
3 basic processes
- formation of a shoot (growth)
- transition to resting state (and new activation)
- death
similarly de Reffye 1981:
3 meristem states
- dormance (sleeping)
- croissance (growth)
- mortalité (death)
state transitions with probabilities
 binomial distribution, Markov chains
combination 1st + 2nd level of description:
morphological
measurements
mapping branches
static
encoding
GroIMP or other
statistical data analysis
growth grammar with parameters
dynamic
GroIMP or other
time series of three-dimensional structures
graphics
other simulation programmes
statistical d.a.
Results:
Structural, dynamical
models of trees based
on botanical
measurements
Application example:
virtual laser scanner
Classification of models in plant and
ecosystem sciences (continued)
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
statistics
aggregated models
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
statistics
aggregated models
the third
Wise man:
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
statistics
aggregated models
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
„model triangle“:
structural models
morphology
statistics
aggregated models
process models
physiology
Classification of models in plant and
ecosystem sciences
„model triangle“:
statistics
aggregated models
functional-structural
plant models (FSPMs)
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
„model triangle“:
statistics
aggregated models
functional-structural
plant models (FSPMs)
structural models
morphology
process models
physiology
Classification of models in plant and
ecosystem sciences
„model triangle“:
statistics
aggregated models
functional-structural
plant models (FSPMs)
structural models
morphology
process models
physiology
• Combination of botanical structures and functions
(e.g., light interception, water flow) in a
coherent, single model
• processes linked to morphological entities
Classification of models in plant and
ecosystem sciences
„model triangle“:
statistics
aggregated models
functional-structural
plant models (FSPMs)
structural models
morphology
process models
physiology
• Structure: Arrangement of morphological entities
(modules) like shoots, leaves... in 3-d space,
connections between them („topology“), shape (geometry)
• effects of processes on the development of structures
Functional-structural plant models (FSPMs)
Overview of an exemplary (more complex) FSPM:
Acknowledgements
(for this and for the subsequent
tutorials...)
 Gerhard Buck-Sorlin
 Octave Etard
 Reinhard Hemmerling
 Michael Henke
 Ole Kniemeyer
 Yongzhi Ong
and particularly
 Katarína Streit
for providing a lot of images...
www.grogra.de