COURSES

-> About this Resource
Scope *______
Map *____

-> Preliminary Courses
Contents & Objectives *__________________
Map *____
-> Botany
Contents & Objectives *__________________
Map *____
-> Axis Typology Patterns
Typology basis *___________
Pictograms *_________
Sexuality & development *___________________
Growth *______
Branching rhythms *______________
Branching delays *_____________
Branching positional *________________
Branching arrangement *__________________
Axis orientation *_____________
Architectural models *________________
-> Architectural Unit
About Arc. Models *______________
Models limitations *______________
Architectural Units *______________
Reiteration *_________
Sequence of development *___________________
Morphogenetic gradients *___________________
Physiological age *_____________
-> An Example
Wild Cherry (young) *_______________
Wild Cherry (adult) *______________
Wild Cherry (mature) *________________
Quiz *____
Case study Quiz *_____________
Supplementary resources *____________________

-> Eco-Physiology
Contents & Objectives *__________________
Map *____
-> Growth Factors
Factors affecting Growth *___________________
Endogenous Processes *_________________
Environmental Factors *_________________
Thermal Time *___________
-> Light interaction
P.A.R. *_____
Light absorption *_____________
Photosynthesis *___________
Respiration *_________
Maintenance respiration *__________________
L.U.E. Model *__________
Density effect *___________
Density effect on crop *__________________
-> Biomass
Biomass Pool *__________
Biomass Partitioning *_______________
Crop models *__________
A Crop model example *__________________
Quiz *____
Supplementary resources *___________________

-> Applied Mathematics
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Map *____
-> Probabilities
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Discrete Random Variable *___________________
Expected value, Variance *___________________
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-> Useful Laws
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Binomial Law *__________
Geometric Law *____________
Negative Binomial Law *_________________
-> Dynamic systems
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Useful functions *____________
Beta density *__________
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Negative Exponential *________________
Systems functions *______________
Discrete dynamic systems *___________________
Parameter Identification *__________________
Parameter estimation *________________
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-> GreenLab courses
GreenLab presentation *__________________
-> Overview
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Growth and components *___________________
Plant architecture *_______________
Biomass production *________________
Modelling - FSPM *______________
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-> Principles
Presentation & Objectives *____________________
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-> About modelling
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Organs: tree components *___________________
Factors affecting growth *___________________
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GreenLab inherits from *__________________
GreenLab positioning *_________________
The growth cycle *______________
Inside the growth cycle *___________________
Implementations *______________
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-> Development
Presentation & Objectives *____________________
Map *____
Modelling Scheme *______________
Tree traversal modes *________________
-> Stochastic modelling
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-> Development
Growth Rhythm *____________
Damped growth *____________
Viability *______
Rhythmic axis *___________
Branching *________
Stochastic automaton *_________________
-> Organogenesis equations
Principles *_______
Organ cohorts *___________
Organ numbering *_____________
Substructure factorization *____________________
Stochastic case *____________
-> Structure construction
Construction modes *_______________
Construction basis *______________
Axis of development *________________
Stochastic reconstruction *___________________
Implicit construction *________________
Explicit construction *________________
3D construction *____________
Supplementary resources *____________________
-> Production-Expansion
Presentation & Objectives *____________________
Map *____
-> EcoPhysiology reminders
Relevant concepts *______________
Temperature *__________
Light interception *______________
Photosynthesis *___________
Biomass common pool *_________________
Density *______
-> Principals
Growth cycle *__________
Refining PbMs *___________
Organ cohorts *___________
GreenLab vs PbM & FSPM *___________________
-> GreenLab's equations
Summary *_______
Production equation *_______________
Plant demand *__________
Organ dimensions *______________
A dynamic system view *__________________
Equation terms *____________
Full Model *________
Model behaviour *______________
Supplementary resources *____________________
-> Applications
Presentation & Objectives *____________________
Map *____
-> Measurements
Agronomic traits *_____________
Mesurable/hidden param. *___________________
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-> Fitting structure
Principles *_______
-> Development
Simple development *_______________
Damped growth *____________
Rhythmic growth *_____________
Rhythmic growth samples *___________________
Mortality *_______
Branching *________
-> Crown analysis
Analysis principles *______________
Equations *________
Example / Exercise *_______________
-> Case study
Plant Architecture *______________
Development simulation *__________________
Introducing Biomass *_______________
Biomass partitioning *_______________
Equilibrium state *_____________
Supplementary resources *____________________

-> Tools (software)
Presentation & Objectives *_____________________
Map *____
Fitting, Stats *___________
Simulation *_________
Online tools *__________

GreenLab Course

Development

Structure construction


Axes of development lists define the basis of structure construction in the GreenLab model.

Axis of Development representation

    The axis of development state list can be easily represented as a part of an axis, with a simplified geometry.

      Attributes can be reported for each awakened state.

      So far, we have encoded the physiological age of the axillary in the previous examples.

      But other characters are worth encoding such as:
        - branching delay
        - other organs (leaves, sexuality), etc.

      In our representation examples, the underlying geometry is simple.

      For instance, in our examples, all states are represented by a rectangular cell, with a unit length, and a width reversely propotional to the ontogenetic age.
      Axillaries are shown with an insertion angle of 90 degrees, and 60 degrees for leaves.
      Cell colours reflect the status: grey if virtual (no phytomer, corresponding to a rest), blue if phytomer physiological age is 1, green for 2, red for 3, red for 4, etc.

        Axes of development representation
        An example of axis of development representation (Drawings M. Jaeger, CIRAD)
          This rhythmic growth example shows three physiological ages for a temperate species
          From left to right:
          Physiological age 1 axis of development. Cells in blue stand for phytomers, while grey stand for a rest cycle.
          Physiological age 1 with its axillaries. Note the branching delays, allowing synchronisation for the next growth cycle.
          Physiological age 2 axis of development. Cells in green stand for phytomers.
          Physiological age 2 with its axillaries.
          Physiological age 3 axis of development. Cells in red stand for phytomers.

Structure reconstruction

    The set of axes of development allows implicit and explicit structure reconstruction.

    Axis development
      The successive states describing a specific axis in the plant structure can be retrieved from its corresponding axis of development (same physiological age). It is in fact a simple copy, with an offset corresponding to the ontogenetic age.
      This copy ends at the shorter term derived from:
      - plant age,
      - a transition to a higher physiological age,
      - a termination specified in the axis of development (determinate growth, or death)

    Axis branching
      The branching process is a similar operation, except that the corresponding axis of development is defined by the physiological age of the axillary (and not the bearer's age)


    Reconstruction representation

      Using the simple axis of development representation framework, it is easy to build flat (2D) structure schemes.

      In such representation, branching angles are set at 60 or 45 degrees for better visibility.

      The rest periods (in grey) are interesting to visualize, defining the chrono mode view, showing the structure framework from a chronological point of view.
      While skipping the grey cells, i.e. skipping the rests, offers a more realistic view, representing only the phytomers, underlying the structure's "real" topology, defining the topo mode view.

      These modes are illustrated below.

        Axes of development reconstruction
        An example of structure reconstruction (Drawings M. Jaeger, CIRAD)
          This example is a reconstruction derived from the axes presented above.
          Left: the 3 axes of development.
          Middle: representation of the structure reconstruction in chrono mode.
          Right: representation of the structure reconstruction in topo mode, skipping the rests.

      Note that in this example, the structure is explicitly reconstructed.
      The three axis of development are partially copied to define the overall structure.