Modelling of Ecosystems by Tools from Computer Science Summer School at Czech University of Life Sciences, Prague, 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 process models physiology the second Wise man:

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

scale levels: P plant U growth unit I internode relations: < successor + branch / refinement MTG (= multiscaled tree graph) coding: multi-scale description

Turtle: goes according to commands imperative approach: „turtle geometry“

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 1 st + 2 nd level of description: morphological measurements mapping branches encoding GroIMP or other statistical data analysis growth grammar with parameters GroIMP or other time series of three-dimensional structures graphicsother simulation programmesstatistical d.a. static dynamic

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 structural models morphology process models physiology the third Wise man:

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“: statistics aggregated models structural models morphology process models physiology

Classification of models in plant and ecosystem sciences „model triangle“: statistics aggregated models structural models morphology process models physiology functional-structural plant models (FSPMs)

Classification of models in plant and ecosystem sciences „model triangle“: statistics aggregated models structural models morphology process models physiology functional-structural plant models (FSPMs)

Classification of models in plant and ecosystem sciences „model triangle“: Combination of botanical structures and functions (e.g., light interception, water flow) in a coherent, single model processes linked to morphological entities statistics aggregated models structural models morphology process models physiology functional-structural plant models (FSPMs)

Classification of models in plant and ecosystem sciences „model triangle“: 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 statistics aggregated models structural models morphology process models physiology functional-structural plant models (FSPMs)

Functional-structural plant models (FSPMs)

Overview of an exemplary (more complex) FSPM:

Acknowledgements  Gerhard Buck-Sorlin  Octave Etard  Reinhard Hemmerling  Michael Henke  Ole Kniemeyer  Yongzhi Ong and particularly  Katarína Streit for providing a lot of images... (for this and for the subsequent tutorials...)