SExI-FS

Spatially Explicit Individual-based Forest Simulator

User Guide and Software

Version 2.1.0

Degi Harja and Gregoire Vincént

World Agroforestry Centre (ICRAF) and

Institut de Recherche pour le Développement (IRD)
2008
Correct citation
Harja, D. and Vincént, G. 2008. Spatially Explicit Individual-based Forest Simulator - User Guide
and Software. World Agroforestry Centre (ICRAF) and Institut de Recherche pour le
Développement (IRD).

Disclaimer and Copyright

The activities related to the work reported in this document were implemented with the
support of World Agroforestry Centre (ICRAF), Institut de Recherche pour le Développement
(IRD) and Common Fund for Commodities (CFC). The opinions expressed herein are those of the
authors and do not necessarily reflect the views of ICRAF, IRD and CFC.

2008

World Agroforestry Centre

ICRAF Southeast Asia Regional Office
Jl. CIFOR, Situ Gede, Sindang Barang, Bogor 16115
PO Box 161, Bogor 16001, Indonesia
Tel: +62 251 625415; fax: +62 251 625416;
Email: icraf-indonesia@cgiar.org
http://www.worldagroforestrycentre.org/sea

ISBN: 979-3198-39-2

Design & layout by: Josef Arinto and Vidya Fitrian

Tree sketch by: Jasnari
Acknowledgements

A number of organizations and individuals provided assistance to make this work

successful. The authors would like to thank Dr. Laxman Joshi, Dr. Gede Wibawa,
Elok Ponco Mulyoutami, Janudianto, Diah Wulandari, Aniq Fadhillah, Josef Arinto,
Vidya Fitrian; IPB Computer Science students and consultant, Tiza Asterinadewi,
Arum Madarum, Ifnu Bima Fatkhan, Riza Nugraha; ICRAF site office staff, Ratna
Akiefnawati, Jasnari, Ilahang, Budi Cangkurawok, Endri Martini; IT support,
Usman Muchlish and Ahmad Taufik.
The Smallholder Rubber Agroforestry System Project

The Smallholder Rubber Agroforestry System (SRAS) Project in Indonesia and

Thailand (2004-2008) is funded by the Common Fund for Commodities (CFC) and
supervised by the International Rubber Study Group (IRSG). The project purpose is
to increase smallholder rubber productivity and to contribute to overall
sustainability of natural rubber production. The project aims to improve
productivity through integrating high yielding clonal rubber in smallholder
agroforestry systems; reduce production costs during the immature growth phase
of rubber plants; provide more affordable alternatives to small-scale rubber farmers
other than monoculture; and to maintain biodiversity and environmental
sustainability. At the final stage of the project, appropriate rubber technology for
farmers, lessons and recommendations from the project activities are being
documented and distributed to rubber-producing countries in Asia and Africa.

The project is led by the World Agroforestry Centre (ICRAF) in collaboration with
the Indonesian Rubber Research Institute (Indonesia), Prince of Songkla University
(Thailand), Centre de Coopération Internationale en Recherche Agronomique pour
le Développement (CIRAD, France), University of Helsinki (Finland) and Kasetsart
University (Thailand).

The Spatially Explicit Individual-based Forest Simulator (SExI-FS) software was

developed under various projects in collaboration between World Agroforestry
Centre (ICRAF) and Institut de Recherche pour le Développement (IRD).
The current version of the model is adapted for smallholder rubber-based
agroforestry system under the SRAS project.

This manual includes the latest version of the software.

Content

1. General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1. Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2. The SExI-FS Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3. The Minimum Requirement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1. Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2. Running SExI-FS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3 User's Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.1. Create New Simulation Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2. Project Setting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.3. Species Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.4. Evaluate Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.5. Tree Planting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.6. Construct Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.7. Running the Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4 Simulation Output. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.1. Vertical Projection Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.2. 3D Visualization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
4.3. Tree Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.1. Model Description and Main Algorithms . . . . . . . . . . . . . . . . . . . . . . . . 39
5.2. STReTCH Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
6 Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.1. Allometric Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.2. Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
6.3. Growth Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
 SExI-FS User Guide
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1. General Information

1.1. Overview
The SExI forest simulator focuses on tree-tree interactions in a mixed multi-species
agroforest. The high level of structural complexity of such traditional agroforestry
systems defies classical forestry approaches when it comes to optimizing
management practices. To cope with this complexity, farmers have adopted a tree-
by-tree management approach, which is closer to gardening than to any usual
tropical forestry or estate crop management model. Individual tree care and regular
tending takes the form of seedlings transplanting, selective cleaning and felling,
adjusted harvesting intensity.

Farmers' approach appears to be in line with two basic tenets of biology: first,
individuals are all different with behavior and physiology that result from a unique
combination of genetic and environmental influence, and second, interactions are
inherently local. Based on the same premises a computer model was developed to
explore different management scenarios.

The model uses an object-oriented approach where each tree is represented by an

instance of a generic class of tree. The simulated object trees, mimicking real trees,
interact through modifying their neighbors' environment. These modifications are
mediated through two major resources: space and light. A 3D representation of a
one-hectare plot of forest serves as the grounds for the simulation of this
competition.

The major objective of such a model is to get a coherent dynamic representation of a

complex system, where complexity refers here to the assemblage of locally
interacting individuals with different properties more than to the complexity of the
elementary processes involved. The model provides insight on what are the critical
processes and parameters of the dynamic of the system. It should also allow
exploring prospective management scenarios, help assessing the relevance of
present management techniques etc.

Model sensitivity tests confirm the importance of the parameters related to tree
geometry. This directly stems from the fact that competition is simulated by means
of spatial interactions, so that anything that alters either the shape, the size, or the
relative position of the trees have direct impact on the outcome of the competition
and therefore on the growth dynamic. These elementary influences are usually
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2
straightforward but their effect at different times and scales are difficult to predict
without simulating because of the numerous feedback loops at work and the non-
linear dynamics of the system.

To illustrate this, let's examine very simple cases. By simulating growth in a mono-
specific stand of regularly spaced trees planted at increasing densities, we observe
the following response. Planting at medium density translates into growth in height
of the trees in the center of the plot being superior to that of border trees, which is a
response to the increasingly limited access to light of the trees in the center of the
plot. When planting density is increased further though, growth in height of the
trees in the center of the plot becomes less than their neighbors: the level of
competition is so high that these trees get overtopped and suppressed by border
trees in more favorable position with respect to access to light.

Another simple test shows that ability to respond to low light availability by
enhanced growth in height (a response, which occurs at the expense of growth in
diameter) appears to be advantageous under specific conditions and
disadvantageous under others. If all species in the mixture share the same ability
and the same sensitivity to light level then this potential competitive advantage
turns out to be disadvantageous both for individual tree growth and for overall plot
productivity. But when trees with different sensitivity to light level or different
ability to alter their allocation of growth between height and diameter occur in a
mixture then this capacity proves to be an effective competitive advantage for
individual species. By accelerating the establishment of a multi-strata structure it
also increases the overall productivity of the plot through better allocation of spatial
resources.

Similarly, rather counter intuitively, an increased growth rate for a given crown size
appears to be an advantage for a species under certain circumstances but not all:
under very crowded conditions large crowns (showing low efficiency in terms of
light and space utilization) can show competitive advantage by suffering less from
crown encroachment and shading out competitor more efficiently. These are but a
few examples of the insight such generic models can bring.

More direct applications of the model include comparing alternative scenarios in

terms of financial return for instance involving rotational versus permanent
agroforests, etc.
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1.2. The SExI-FS Software
SExI-FS software is available on the Internet. It can be downloaded freely from
http://www.worldagroforestry.org/sea/Products/AFModels/SExI.

SExI-FS is targeted to be platform independent. It's developed using Java

Programming Language. It will be able to run on any platform that supports Java
Virtual Machine (JVM). The information about Java Programming Languages and
Java Virtual Machine can be accessed through http://java.sun.com.

1.3. The Minimum Requirement

The minimum requirements to run the 3D visualization of SExI-FS are:

1. 60MB Hard disk space (Included JVM)

2. VGA card with 3D graphics accelerator.

3. 128MB of RAM

4. PII 600MHz or equivalent

The minimum requirements to run SExI-FS without 3D Visualization are:

1. 60MB Hard disk space

2. 32MB of RAM

3. Pentium PC 133Mhz
 SExI-FS User Guide
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2. Getting Started

There are two installation packages, with built-up Java Virtual Machine (JVM) and
without. If you don't have a Java virtual machine installed on your computer, be
sure to get the package that includes one.

2.1 Installation
The installation steps are as follow:

Step 1. Introduction
It's displays general information about the software. Press the Next button to
continue.

Figure 1. Introduction

Step 2. Choose install folder

Write down the installation folder or press Choose button to show the folder
selection dialog. Press the Next button to continue (Figure 2).

Step 3. Choose shortcut folder

Write down the shortcut folder or use the other available options. Press the Next
button to continue (Figure 3).
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Figure 2. Choose install folder

Figure 3. Choose shortcut folder

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Step 4. Pre-Installation summary
This shows the summary of the installation setting. Press Install button to start the
installation.

Figure 4 Pre-installation summary

Step 5. Install complete

Done, you can start using the software

Figure 5 Install complete

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2.2 Running SExI-FS
Double click the SExI-FS shortcut on your computer. By default it will be under
Start > Programs > SExI-FS on Microsoft Windows.
The application will start with the main window as showed in Figure 6. It consists
of Projects windows (left), Welcome windows (center) and Properties windows
(right).

Figure 6 Main Window

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3. User Manual

3.1 Create New Simulation Project

You can create new projects either via the File menu on the Menu Bar (Figure 7a), or
directly by clicking the New project options in Welcome window.

Figure 7a. File menu

Figure 7b. Save Configuration

If you select the New project menu trough the File menu bar, it will show the same
options (Figure 8). You can create a new project either by using default
configuration or a pre-defined XML configuration file. The XML configuration file
can be created by saving a modified project as a configuration file (see Figure 7b),
thus the file can be modified externaly using XML or text editor. If default project
option is chosen, the plot size input dialog will show up (Figure 9). Set the
simulation Plot Size and click ok.

Figure 9. Plot size input for default project

Figure 8. New simulation project options

New project options tree will be showed on the Projects window (Figure 10).
 SExI-FS User Guide
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Figure 10. New project on main window

3.2 Project Setting

Each project group consists of selectable section items for setting up the general
environment, species and plantation plot (Figure 11). Highlighting each project
sections will show their property options on the Properties window (Figure 12). If
the Properties window is closed, you can double click the Section items to display it
again.

Figure 11. Project tree items

Figure 12. Project properties

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Highlight the root project section. The main project property will show in the
Properties windows. Define the project name and description.

You can't run the simulation before you plant trees on the plot (or add some pioneer
species component). You can use default setting and jump to Tree Plot section to
start planting the trees. Or define your preferred setting for this simulation project.

3.2.1 Environment Setting

Under the Environment tab values of some general parameters used in the
Regeneration module and the Belowground competition module are set. The
random seed is for the user to control the random generator used here.

Figure 13. Environment Setting

3.2.1.1 Regeneration
! Natural Mortality
Set this setting to true for enabling natural mortality

! Natural Recruitment
Set this setting to true for enabling natural regeneration
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! Empty Cell Preference
Controls the regularity of spacing of juveniles (0 completely random, 1 most even)

! Max Density
Maximum density (trees per ha). Recruitment ceases once max density is reached.

! Elaborate Light Map

Set this to true to use the more detailed light
calculation to compute available light at ground
level.
By default the light calculation for each grid cell
on the light map uses Simple Vertical Light
Calculation. The plot is divided into a grid of
cells (default size 5 by 5 m). For each cell at each
time step a coarse index of light availability is
computed based on overhead light of target cell
and 8 immediate neighbors (a single vertical
direction originating from center of cell is
explored for each cell). The average of canopy
Figure 14. Light map sample
openness on each grid cell is used in the
recruitment process to assess suitability of light
regime.
The elaborate light map uses the hemispherical photograph method, which can
capture a more realistic light penetration to the ground. This option will require
more computation time but is necessary for proper simulation of the recruitment
process.

3.2.1.2 Belowground
! Belowground Competition
Enable Belowground competition option to simulate below ground competition
between neighboring trees. The parameters for root influential zone are explained
in section 3.3.7

! Imperata
Set this to true for enabling the Imperata (obnoxious weed) competition.

! Enable Soil Fertility

Set this to true for enabling the Soil Fertility map.
Soil fertility is set manually for each cell of a grid covering the plot or read from a
text file. Missing data are interpolated using bilinear 3 dimensional interpolation
(Press, et al. 1992).
 SExI-FS User Guide
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Fertility values vary between 0 and 1; a fertility of one meaning there is no soil
fertility related limitation.

! Fertility Based On Root Zone

If true, the fertility experienced by a tree will be computed as the average of cells
fertility value of cells within the tree root influential zone. Otherwise, the fertility
information will be taken at the exact cell location of the tree.

! Plot Fertility Index

This is an index of soil fertility of the plot (between 0 and 1)

! Soil Fertility Cell Width

The fertility map cell width (m)

! Soil Fertility Cell Height

The fertility map cell height (m)

! Fertility Map
Click on the input field to open the fertility map editor

3.2.2 Light Capture Setting

There are three categories of parameters to be documented in order to set-up the
light capture module: light model, spatial environment, and light interception
options (Figure 15).

Figure 15. Light Capture Setting

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Figure 16. Horizon Projection of Beams Vector Figure 17. Vertical Projection of Beams Vector
(here the number of inclination = 6) (here the number of azimuth = 8)

a. Light Model

Light Model settings control the level of detail used for exploring the sky vault, i.e.
the number of light beams and their weighting. The number of inclinations and
azimuths defines the number of beams. The parameters of the light model are:

! Number of Azimuth
Azimuth is the horizontal component of a direction (compass direction),
measured around the horizon from the North point, toward the East, i.e.
Clockwise.

! Number of Inclinations
Inclination is the angular distance of the orbital plane from the plane of reference
(usually planet's equator or the ecliptic).

! Lowest Zenithal Angle

Lowest Zenithal Angle defines the lowest angle considered for light calculation
(in radian).

! Interaction Distance
The interaction area is limited by the Distance of Interaction setting. The trees
outside the radius of interaction distance and are not included in light
attenuation calculation for target tree.

! Inclination weighted model

There are three models you can choose from:
1. SOC (Standard Overcast Sky)
This model weights each direction according to surface of sky vault fraction
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moreover assuming a decrease in light intensity from zenith to horizon, using
the formula:
Light ( )
x, α
=
1
[
x∗
1+
2∗ ]
sin (
)
α
3
2. UOC (Uniform Overcast Sky)
This model weights each direction according to the relative surface of the sky
vault explored by each beam.

3. Homogeneous
This option gives equal weight to each direction sampled.

! Default Light Capture Position

These are the position within a tree where the light (hemiphot) is captured and
used as light info for the subject tree. The available position options are:
1. Tree apex
2. Crown center
3. Crown base
4. Crown one third
5. Tree base

b. Spatial environment

! Torus Space
If selected then the plot is assumed to be toric, in such case the plot has no
borders as the trees from one side of the plot act as neighbors for the trees on the
opposite side. If not selected then the plot is limited by the border. (Note that the
area outside the border is considered as an open area).
In geometry, a torus (pl. tori) is a doughnut-shaped surface of revolution generated by
revolving a circle about an axis coplanar with the circle. The sphere is a special case of the
torus obtained when the axis of rotation is a diameter of the circle. If the axis of rotation
does not intersect the circle, the torus has a hole in the middle and resembles a ring
doughnut, a hula hoop or an inflated tire. The other case, when the axis of rotation is a
chord of the circle, produces a sort of squashed sphere resembling a round cushion. Torus
was the Latin word for a cushion of this shape.

! Topography
If topography is selected, the plot will using the topography data (if any), else the
plot is assumed to be flat.
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c. Interception

! Crown Permeability
If Crown Permeability checkbox is selected, the crown is considered as partially
transparent (transparency is also referred to as crown porosity in the following).
If Crown Permeability is not selected, it is assumed to be totally opaque.

! Trunk Interception
If Trunk Interception checkbox is selected, the trunk is considered to intercept
the light. If Trunk Interception is not selected, it's neglected.

3.2.3 Fertility Map Setting

Soil fertility is set manually for each cell of a grid covering the plot. Missing data are
interpolated using bilinear 3 dimensional interpolation (Press et al., 1992). Fertility
values vary between 0 and 1; a fertility of one meaning there is no soil fertility
related limitation.

Figure 18. Fertility map setting

To show the fertility map, highlight the Fertility Map project item on Projects
windows, check the Enable Soil Fertility checkbox on Properties window and click
the Fertility Map button below the table (Figure 18).

You can modify the fertility by either changing the fertility value on the table, or by
clicking the cells of the fertility map. Change the fertility index value below the map,
and then click on the map. The legend color shows the gradation of index value
between 0 and 1 (you can also click the legend color for changing the fertility index
value).
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The fertility map can be saved and used for other simulation project.

3.2.4 Topography Setting

A particular topographic settings can be specified. But enabling this option will
disable the torus space model. The area outside the border will be considered as an
empty space.

Figure 19. Topography setting

To add the topography information, you can insert one by one the altitude data to
the table. Or load the file that consists of altitude data. The file can be as tabulated
data format with one line of header. Each line of data should consist of three values:
X, Y and Altitude. The unit is meter (m). The example of the format data is as follow:

X Y Altitude
0 0 25
0 5 20.693
0 10 18.255
0 15 17.062
0 20 16.492

The altitude at any location on the plot will be interpolated using bilinear 3
dimensional interpolation (Press et al., 1992) based on the available topography
information.

The topography can be check using 3D visualization by clicking the View button
below the table. The data can still be modified, and click Refresh button to update
the visualization.
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The 3D Visualization object can be dragged using to view the other angle. The
toolbar below the 3D panel can be used to changes the projection (Perspective or
Parallel), zooming (the slider) and view the exact object side (combo box).

Bilinear interpolation (Press et al., 1992) is used to determine exact altitude of tree
base when trees are positioned on an existing topography map

(
x1 , y1 , z1 )
P1 = (
x2 , y2 , z2 )
P2 =
(
x3 , y3 , z3 )
P3 = (
x4 , y4 , z4 )
P4 =
(
xt , yt , zt )
Pt =

Pt is tree location and P1, P2, P3, P4 are topography data. Then:
(
zt =a)
1−(b )(
1− z1 + b)
a 1−z2 + (
abz3 +a)
1−bz4

xt −
x1 yt −
y2
a= b= where x1 ≤
xt ≤
x 2 , y2 ≤
yt ≤
y3
x2 −
x1 y3 −
y2

3.2.5 Scenario Setting

The scenario module is viewed as a flowchart model (Figure 20 Scenario setting).
The flow will be executed on each iteration for all the trees. The charts are editable.
The available Processes include only Cut Tree and Yield Harvest (future version
may include more Processes in the scenario). The Condition chart controls the flow
condition based on the tree variable.
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Figure 20. Scenario setting

3.3 Species Settings

To add a species to the project, highlight the Species Component section on Projects
window (Figure 21). The first time add a species, the Properties window will show
an empty species list (Figure 22). Click add button ( ) to add species component to
the list. Or you can load the previous saved species list by pressing load button ( ).

Figure 22. Species component properties

Figure 21. Species component section

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Once you have added some species
component to the list, highlight one of the
species item on the Projects window or double
click the one on Properties window (both will
have the same list of species). The properties
window will show the parameters of the
species selected (Figure 23).

You can directly modify the parameters

according to your preferences.

Label and description are identification for the

species. And the color is used for visualization
purposes only (legend). It is not meant to
simulate the real color of the tree species .

Other parameters are grouped according to

their function as explained right.

Figure 23. Species parameters

3.3.1 Basic Characteristics

Here are the general characteristics of a species:

! Initial DBH
The initial diameter for newly recruited trees (default is 1 cm dbh)

! Crown Porosity
A measure of crown transparency, here the crown is considered as partially
transparent (0-1)

! Survival Probability
The annual survival probability value of a completely suppressed plant
 SExI-FS User Guide
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(no growth) In addition, a systematic mortality is assumed once 5% of reference
tree crown size has been reached. See Documentation chapter for more details.

! Mortality Modifier
Mortality Modifier modulates the shape of survival probability curve as growth
rate is reduced (higher m values imply higher mortality rates at identical
growth rate). Default value is 15. See Documentation chapter for more details.

! 2nd Mortality Probability

nd
2 Mortality Probability is the probability that a tree dies from a neighbouring
tree fall (0-1) if it lies in the sector affected by tree fall. Default value is 50% (see
Documentation chapter for further computational details).

! Adult Size
The DBH at which a tree species reaches sexual maturity (determines start of
recruitment for non pioneer species).

3.3.2 DBH Function

The evolution of DBH over time (t) is modeled by a classical Chapman Richards
function:

dbh = e−
dbh_max * 1 − ()
k *t c

Approximating DBH annual increment with the first derivative of DBH with respect
to time (t) one can express dbh increment as a function of current dbh as follows:
 −1


dbh_init 
c 
dbh_inc = 
dbh_init * c * k
 
 −
1


dbh_max  
 
(See Documentation chapter for detail)

The parameter of c and k can be obtained from Non-linear regression of DBH -

DBH_increment plot (Calibration Procedures on Chapter 6).

3.3.3 Height Allometry

A reference allometric function relates tree height to tree dbh :

* dbh β
height =
α h

Height A is parameter name for α

(alpha) and Height B is parameter name for β
(beta).
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Where Height Max Absolute is species maximum possible height.

3.3.4 Crown Allometry

The crown width is linearly related to tree dbh by the following function:

Crown Width = A+ B*DBH

The parameters Crown Width A and Crown Width B refer to A and B in the above
formula (See Documentation chapter for detail).

3.3.5 Light Sensitivity

The parameters here define the light stress factor of the tree growth.

! Minimum Light Level

The minimum light level for a tree to grows.

! Optimum Light Level

The optimum light level for a tree to grows.

The curve below shows the light stress factor derived from the parameters:

(CP is Crown Position, an index, a measure of light ratio receipt by a tree)

! Flexi is a parameter which measures the ratio of height growth rates under the
most contrasted light conditions (between 0 and 1)

! Sensi is a measure of how sensitive the species is to shading, sensi > 1 (e.g. 2)
typical of a shade avoiding species and sensi < 1 (e.g. 0.5) of a shade tolerant
species
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23
3.3.6 Regeneration
! Beta Shape 1
Beta distribution function parameter 1

! Beta Shape 2
Beta distribution function parameter 2

! Immigration rate θ
θ (theta) is the relative weight of a species frequency in regional community
versus its frequency in the local community. It is used to compute the effective
contribution to local recruitment of any given species.

! Relative Abundance
The relative abundance of the species in the meta-community (regional flora).
See documentation chapter for more details.

3.3.7 Belowground
! Root Influential Zone Modifier
Species specific factor of root influential zone from default 20*DBH meters

! Index Of Root Anchoring

calculated as Dv2/dbh2 where dbh is tree diameter at breast height (1.3 m
height) and Dv is the diameters of all vertical roots (van Noordwijk 1999;
Akinnifesi et al., 2004)

! Index Of Root Binding of Soil

calculated as Dh2/dbh2, where Dh is the diameters of all horizontal roots (Van
Noordwijk 1999; Akinnifesi et al., 2004)

! Imperata Competition Factor

Modifier factor for Imperata competitions

The Index of Root Anchoring and Binding is a new added module. Currently these
parameters are used for the 3D visualization purpose only (Figure 24). Future
implementation will include this root module for belowground competition and soil
stabilization model.
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24

Figure 24. Roots visualization

3.4 Evaluate Species

The species setting behavior can be tested using Evaluate option. Right click the
species item on the Project tree windows and select Evaluate menu.

The species setting can be modified here and tested by growing a tree in an isolated
environment or using a static defined hemiphot. The defined hemiphot is act as
hemiphot captured by the tree as it grow. On the real simulation this hemiphot will
changes dynamically as the surrounding environment. This static hemiphot is used
to see the plasticity response of the species.

To edit the hemiphot, click the Legend bar below or fill in manually the light field,
then click on the Hemiphot canvas. You can save the hemiphot for further use.

To start testing the species, click on the Evaluate button, and fill in the number of
iteration, click Ok. The growth process of the tree will show on 3D visualization.
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25

Figure 25. Evaluate species

Figure 26. Evaluate species using hemiphot modification

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3.5 Tree Planting
Once you have set-up the species component for your simulation, you need to plant
trees. Highlight the Tree Plot component in the Project window, the Properties
window will show an empty tree table (Figure 27). To start planting trees, you
should move to Tree Planting tab, or you can click the button click here to plant
trees inside the empty tree table.

Figure 27. Tree table tab Figure 28. Tree planting tab

Planting trees can start with creating the template trees (Figure 28). The spatial
arrangement along which trees are planted is either random, manually specified for
each tree or created by repeating a user defined regular planting pattern.

3.5.1 Manual Planting

To plant the trees manually, press the Manual
button on Tree Planting tab (Figure 28).
The manual planting dialog will show up
(Figure 29). Select the tree species and click Plant
Template.
Figure 29. Manual planting dialog
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27
The tree plot will show up (it remains hidden until then), and you start to plant the
trees by clicking on the plot. A tree will be planted on the location you click (Figure
30). To stop the planting model, right click the mouse. And to plant other tree
species, repeat the above procedure.

Figure 30. Manual planting plot

After creating the plantation template, click the Apply Template Trees! button,
below the template table (Figure 28). The template trees will be cleared and the real
trees are added to the plot.

3.5.2 Randomize Planting

To use the randomized template for tree planting,
press the Random button on Tree Planting tab
(Figure 28). The random planting dialog will show
up (Figure 31). Select the species and set the number
of trees to be planted. You can specify the random
seed, for controlling the random generator. Click
Plant Template. Figure 31. Random planting dialog
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28
To add more trees, repeat the above procedure. Click the Apply Template Trees!
button below the template table (Figure 28) to finish the plantation. The template
trees will be cleared and the real trees are added to the plot.

3.5.3 Pattern Planting

To plant the template trees using pattern, press the Pattern button on the Tree
Planting tab (Figure 28). The pattern planting dialog will show up (Figure 32). Select
the Species and set the size of the pattern. Click on the pattern plot to place the tree
template as pattern. The plot will show a preview of the current pattern (Figure 33).

Figure 32. Single species planting pattern Figure 33. Single species planting pattern preview

You can create pattern with more than a single tree species (Figure 34). The plot
preview will immediately show-up (Figure 35).

27

Figure 34. Multiple species planting pattern Figure 35. Multiple species planting pattern preview
 SExI-FS User Guide
29
The tree pattern location and species can still be edited trough the tree table on the
right of the plot pattern. After creating the pattern click Plant Template button to
create the template trees. And click the Apply Template Trees! button to finish the
plantation.

3.6 Construct Tree

Users are able to reconstruct an established plot into SExI-FS. The geometry
structure is as follow:

1. X: the x position of the tree base (m)

2. Y: the y position of the tree base (m)
3. Species: the species label, if the label is match with the one in the species list
then it will be linked, otherwise new species definition will be created
4. DBH: the diameter at breast height of the tree (m)
5. Height: the height of the tree (m)
6. CR Depth: crown depth (m),
7. CR Curve: crown curve (m),
8. CR Radius: crown radius in vertical projection, can be more then one value
separated by semicolon (m),
9. Rotation: a rotation of the vertical projection of the crown geometry (degree).
10. CP: crown position index (0-1)
11. CF: crown form index (0-1)

Figure 36 shows the parameters description of the tree geometry. The definition of
crown radius is shown by the vertical projection of the crown. If there are only one
radius information (r1, the leftmost) the vertical projection will be a circular shape,
but if there are more then one radius information, the vertical projection will look
like on following the graph in Figure 36 (the rightmost graph use 5 radius
information). The horizontal and vertical projection information of the tree geometry
is then converted into 3D shape object.

Figure 36. Horizontal and vertical projection of tree geometry

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30
The geometry information of the trees can be inserted manually using the table
interface shown in Figure 37. The table is also able to load a text data file (tab
separated) with the format shown below:
iid x y spesies dbh height cr_depth cr_curve cr_radius rot cp cf
1 16.5 38.25 alpukat 0.10668 9.5 6.2 4.5 1.8;2 0 0.6 0.4
2 19.7 39.5 alpukat 0.17834 17 12 8 3;3.5 0 0.6 0.6
3 38.1 37.8 durian 0.05732 5 1.5 1 1;1;3;4 0 0.8 0.3

Figure 37. Construct trees

3.7 Running the Simulation

To start running the simulation, highlight the Project Root section on Project
window. The Properties window will show the project properties and the Run
button (Figure 12). Click the “Run” button, and enter the number of iterations, click
Ok. The simulation will run for the specified number of iterations (years). While the
simulation is running, you can see the progress bar that indicates progress of
simulation.

Figure 38. Running simulation

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4. Simulation Output

You can explore the simulation output by either inspecting the tree plotting in Two
Dimension (2D) and Three Dimension (3D) graphic or plotting the tree data on
statistical chart.

4.1 Vertical Projection Plot

The vertical projection plot is showing a 2D view of tree crowns vertical projection
(Figure 39). You can monitor the dynamic growth of the tree and its crown through
this plot. The plot management also can be done through this plot.

Figure 39. Vertical projection plot

4.1.1 Plot Options

Right click on the plot area, you will find menus for configuring the plot.

Zoom In : Magnify the plot

Zoom Out : Zooming out the plot

Hemiphot : Show hemispherical photograph

model for the selected location

Paint : Vertical projection paint model

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Outline : Outline paint model

Opaque : Opaque paint model

Transparent : Transparent paint model

Shaded : Shaded paint model

Show Info : Show information label of each tree

on the plot (Species, ID, DBH, etc)

Overlay : Overlay the layer plot

Light Map : Overlay the light map layer

Root Map : Overlay the root map layer Figure 40. Plot menu

Figure 41 shows the hemiphot for some location selected on the plot and Figure 42 is
the overlay of light map. Figure 43 Show info of tree (tree ID) overlay with root
map.

Figure 42. Light map

Figure 41. Hemiphot

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33

Figure 43. Show info of tree (tree ID) overlay with root map

Figure 44 Paint type for the tree, clockwise from top-left, outline, opaque,
transparent, and shaded. Shows various paint type for vertical projection of the
crown

Figure 38. Running simulation

Figure 44. Paint type for the tree, clockwise from top-left, outline, opaque,
transparent, and shaded
 SExI-FS User Guide
34

Figure 45. Tree selection menu

Cut Tree(s) : Cutting/removing the selected tree(s) from the plot. This can
be assumed as a manual plot management. You may cut the
trees for logging purpose or others. Figure 45 show the
simulation plot after 10 years of simulation using default
parameters. You can select and cut the trees, and run the
simulation again for a number of iteration.

Tree Hemiphot : Show hemispherical photograph model as viewed by the

selected tree

Show 3D : View the 3D visualization of the trees

4.2 3D Visualization
You can explore the tree in 3D Graphics. Make sure that you have minimum
requirement for viewing the 3D graphics (see section 1.3 Minimum Requirement).
Select the trees and right click, then select the Show 3D option. The 3D visualization
will show up (Figure 46). You show the 3D visualization without selecting the trees
to show the whole plot.
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35

Figure 47. Virtual Control

Figure 46. 3D visualization

The 3D view options are as follow:

Crown : View the crown

Branches : View the branches

Leaves : View the artificial leaves visualization

Wireframe : Show in wireframe mode

Solid : Show in solid mode

Textured : Show the textured object

Morphing : Show a smooth change between animation steps

You can control the angle view of the 3D visualization using the virtual control
shown on Figure 47. Or you can directly use your mouse to rotate the 3D object on
3D window.

In this 3D visualization you can play the animation by pressing the Play ( ) button.
The animation shows the changes of trees from step to step of iteration.
 SExI-FS User Guide
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4.3 Tree Data
Tree data output can be viewed through the Menu bar or Project popup menu. It
shows all the tree data history (Figure 48). Next you can either download the data to
be processed with some statistical software or directly view the plot and distribution
using the available chart tools.

Figure 48. Tree data

There are three types of charts that can be used to analyze the data, Bar Chart, Line
Chart and Scatter Plot.

4.3.1 Bar chart

Select the variable on the left panel and move it to the x and axis panel on the right.
By default the y axis is the number of trees based on the x variable class. You can
also group the data by moving some of the variable to Group variable list. The
“Bounds” setting is the number of x axis class.
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37

Figure 49. Bar Chart

4.3.2 Line chart

On the line chart you can define the X and Y variable from the available variable list.
And define the calculation method (Mode) in case the Y value is more the one per C
category. The calculation method available is average, sum and count.

Figure 50. Line chart

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4.3.2 Scatter plot
The X and Y axis can be set for by variable from the variable list.

Figure 51. Scatter plot

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5. Documentation

5.1 Model description and main algorithms

5.1.1 Main loop
The loop is run on a yearly time step. It starts with an initialization step, the initial
trees are recorded into the module as individual objects. Next the trees crown
attributes (Crown Form Index (CF) and Crown Position Index (CP)) are updated.
Crown Form is an index of how well developed a crown is and Crown Position is an
index of light availability. Simulation data is then recorded after this step.
Tree growth is then computed (diameter, height and crown volume increment).
At each step in time, for each tree a survival test is made. Finally at stand level a
recruitment test is conducted.

Figure 52. Main of SExI simulator

5.1.2 DBH Increment and growth reducers

DBH as a function of time (t) follows a Chapman Richards function:

dbh = e−
dbh_max * 1 − ()
k *t cC
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40
And approximating DBH annual increment with the first derivative of DBH with
respect to time (t) one can express dbh increment as a function of current dbh as
follows:
 −1


 dbh  c 
dbh_inc = 
dbh * c * k 
 
 −
1


dbh_max  
 

One can note that maximum increment is then

c−
1
 1
dbh_inc_ma x = dbh_max * k * 
1- 
 c
which is attained when
c
1 
dbh = 1−
dbh _ max*  
c 
Default initial diameter is one cm.

Figure 53. DBH Increment Function

Potential DBH increment as defined above is reduced by the effect of aboveground

and belowground competition. Thus the actual DBH increment is:

dbh_inc_act = dbh_inc * growth_reducer

Growth reducers considered in this model are:

a. Light Stress (Crown Position Index)
b. Crown Form Index
c. Local fertility index
d. Tree Production Effect (competition for carbon allocation between growth and
production of resin, latex, or fruit)
e. Belowground competition (based on local crowding)
f. Other possible growth reducers could relate to other ecological constraints
such as pest pressure, diseases, etc. (not yet implemented)
 SExI-FS User Guide
41
a. Light Stress

Light stress is related to light capture (i.e. crown position index value) in a species
specific way :
1.0

0.8
Growth Reduction Factor

0.6

0.4
Growth Reduction Factor

0.2
Shade Tolerant
Intermediate
Light Demanding
Min Opt
0.0
0.0 0.2 0.4 0.6 0.8 1.0

Light Index (CP)

Figure 54. Typical shape of the relation between light index and growth reduction
factor for different levels of shade tolerance (Min: Minimum level for growth to occur,
Opt: Optimum level for growth

CP stands for Crown Position, which is an index of access to light. The computation
of this index is explained in details in section 3.2.2 Light Capture Setting.

In short Crown Position is computed based on a virtual hemispherical photograph

that would be taken at tree crown base, the target tree crown itself being completely
transparent.

Figure 55. Hemispherical Photograph (left) compare with the model calculated (right) in
high-resolution method
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42

Figure 56. Low resolution Hemiphot, shows

a CP = 0.398 on range 0 1

b. Crown Form (CF)

Crown Form is an index based on the ratio of actual crown size to normal crown
size of a tree with same DBH. The crown size is defined by the surface area (or
alternatively the surface area of the convex envelop) of the crown. The difference
between actual and normal crown size may result from encroachment from
neighboring crowns, suboptimal light level or asymmetric development of the
crown. The asymmetric development of the crown is explained in the section
presenting the STRETCH module below:
crown _ surface _ actual
cf =
crown _ surface _ normal

Figure 57. An asymmetric development of crown shown on the model

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43
c. Belowground Crowding Index

Below ground competition is based on the following simple assumptions.

1. Root influential zone (IZ) of a tree is proportional to its size and symmetric in
shape (circular).
2. A crowding index is computed for any tree based on the overlap of neighbours'
IZ with target tree influential zone.
3. More competitive species have relatively larger IZ (i.e. higher resource capture
efficiency).
4. Overall below-ground crowding index effect on growth is site specific
(dependent on overall level of resources).

The relationship used to relate growth reduction to below-ground crowding index is

illustrated in the graph below, where s is the site index fertility value.

1
1
0.9

0.8
 BGCI 
ln( 0.5) ⋅
exp
f ( BGCI,
s) :
= 
 
0.7
s
Growth reducer

0.6
f ( BGCI,
1)
0.5
f ( BGCI,
2)
0.4

0.3

0.2

0.1
0.031 0
0 1 2 3 4 5
0 BGCI 5
Below Ground Crowding Index
Figure 58. Relationship used in SExi to compute growth reduction as a function of BGCI
 SExI-FS User Guide
44
d. Fertility

Local variation of soil fertility can also be simulated. A soil fertility map can be
entered manually for each cell of a grid covering the plot or read from a text file.
Missing data are interpolated using bilinear 3 dimensional interpolation (Press, et
al., 1992). Fertility values fall between 0 to 1, a fertility of one meaning there is no
local soil fertility related limitation (in addition to the overall fertility level defined
in the step above).

The fertility experienced by a tree will then depend on tree position in the plot.
Fertility index used for computing reduction in growth of a particular tree is simply
the average value over the cells included in the tree's influential zone. All cells
which center is included in the crown projection are used in mean fertility
calculation.

Figure 59. Fertility Map

e. Tree Production Effect

Tapping of rubber trees slows tree growth. Annual DBH increment decreases with
increasing tapping frequency. Research on rubber trees shows that after 200 days of
tapping, DBH increments decrease by about 50% (see review in Grist et al., 1998)
and data in (Vincent et al., Submitted for Agroforestry System). However the
decrease is not simply proportional (the simple fact that trees are tapped albeit
lightly seem to induced a strong decrease in dbh increment. The default function
used is:

GrowthReduction= 1/ (Exp((number_of_tapping_days_per_year/365)^0.5)
 SExI-FS User Guide
45
And is plotted below:
1

0.9

0.8

0.7
Growth reduction due to tapping

0.6

0.5

0.4

0.3

0.2

0.1

0
0 50 100 150 200 250 300 350
Tapping days per year

Figure 60. Growth reduction as function of number of tapping days (hevea default
calibration in SExI)

5.1.3 Height Increment

A reference allometric function relates tree height to tree dbh:
β
height =
α
h * dbh
h

Figure 61. Height -DBH function

Thus height increment, which is the function of DBH increment, is:

height _ inc =
α dbh _ incr ) β
h * [(dbh +
h
dbh β
− h
]

And the height increment corrected by the elongation factor is:

height _ inc _ elong =
height _ incr * c * break _ function
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46
Where c is the elongation factor:
c=
1+
flexi * (1 −
CP ) 1 / sensi
Where:

! flexi is a parameter which measures the ratio of height growth rates under the
most contrasted light gradients (0 and 1).

! CP is the crown position index (between 0 and 1).

! sensi is a measure of how responsive the species is to shading , sensi > 1 (e.g.
2) typical of a shade avoiding species and sensi < 1 (e.g. 0.5) of a shade tolerant
species.

and the break_function which is simply meant to ensure a smooth height growth
reduction when approaching asymptotic height is defined as follow:
h
k( −
1)
height _ break =
1−
e h max
where h is current height, hmax is asymptotic height and k curvature parameter
that is taken to be 20 for all species.

br( hc) 0.5

0 0
20 25 30 35
20 hc hMax

Figure 62. Height Break Function (hc=current height)

Enhanced height growth is achieved at the expense of dbh increment. Assuming

that total stem biomass scales isometrically with the product of stem cross sectional
area and tree height, the maximum possible height increment is then limited by
actual dbh increment.
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47
∆
h * dbh 2 +
2h * ∆
dbh * dbh +
2∆
dbh * ∆h * dbh +
h*∆
dbh 2 +
∆
dbh 2 * ∆
h
height _ inc _ max = 2
dbh

Note that max_height increment is independent of tree current slenderness!

Then actual height increment is:

Height_inc_actual = Min(height_inc_elong, height_inc_max)

Adjusting the actual dbh increment as the factor of slenderness:

! if height_inc_actual = height_inc_max then dbh_inc_actual = 0

! If height_inc_actual < height_inc_max then
Dbh_inc=

−(dbh 2 (h * s * +
∆
h) +
h*∆
dbh 2 +
2∆
dbh(h * dbh +
∆
h * dbh +
*∆
h))(h * s +
∆
hc) +
dbh * h * s +
dbh * ∆
hc
dbh _ inc =
−
h*s +
∆
h*c

Where s is the slenderness coefficient (current height/height of reference tree grown

in the open) dbh, ∆dbh, h, ∆h refer to dbh, dbh_inc, height and height_inc of
reference tree and hc and ∆hc stand for current height and height increment of
actual tree.

5.1.4 Crown Growth

A tree crown is represented as a deformable solid. Crown deformation can be global
in response to increased shading or local in response to radial anisotropy of incident
light or spatial constraint.

Local deformation is mediated via a set of vectors stemming from crown base and
subtending the crown envelope. Extension of the subtending vectors is affected by
local light and space availability as determined by species-specific parameters.

Crown deformation algorithm is detailed in the STReTCH module (Section 5.2)

below.

5.1.5 Latex Production

So far only latex yield of rubber and fruit production has been implemented. The
relationship between size (DBH) and maximum latex yield is considered to be linear
(Vincent
latexet=
al.,
a * 2000):
DBH + c
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48
Latex production is considered to decrease after a certain number of tapping
incisions due to bark consumption and diseases, etc.

By default, the decrease in latex production is set to start after 2000 days of tapping
(say + ten years of intensive tapping) and latex flow will completely dry up after
8000 days of tapping. Then prediction of actual latex production after corrected by
frequency of tapping (ƒ ):
 f −

2
2000  
latex _ act = 
latex * 1 −
  
and 0 if >8000 days
  6000  
 
Fruit production and timber production can be specified as a function of tree size
through the user interface.

5.1.6 Recruitment
Species defer in their preferred light environment for establishment. This light
preference is captured by a probability distribution function (which can be
estimated by the experimentally determined frequency distribution of saplings per
light classes).

A beta distribution is used which is defined as:

n-1 w-1
f(x) = G(n+w)/[G(n)G(w)] * x *(1-x) , with 0 < x < 1, n > 0, w > 0 ).
Some typical values for the two parameters are reported below and the
corresponding function plotted in the graph below where X refers to canopy
openness. Shade tolerant: shp1=2 shp2=10 (e.g. duku) RED
Light demanding: shp1=4 shp2=12 (e.g. damar, rubber) BLUE
Pioneer: shp1=12 shp2=8 (e.g. pulai) GREEN

3
Y

Figure 63. Hypothetical density probability functions

0 of sapling presence as a function of canopy openness
0.0 0.2 0.4 0.6 0.8 1.0
X
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49
The recruitment rate (number of saplings recruited per unit area per unit time) is a
function of the level of saturation of the plot carrying capacity. Carrying capacity is
itself considered to increase linearly from 0 to maximum carrying capacity as
canopy openness ranges from 0 to 1.

Contribution to the recruitment rate of the various species depend on the meta-
community composition (relative abundance in regional floristic pool) and local
community composition (relative abundance of adult trees per species in plot). Let è
be the relative weight of meta-community composition in recruitment. It may be
hypothesized that everything else being equal è will decrease with increasing size of
plot and with plot compactness (area/border).

The algorithm is based on a light map available at 1 m above ground level and a
map of distribution of the existing trees, and is outlined below.

Outline of recruitment algorithm:

Step 1. Light map segmentation

Sort light map elementary cells into 5 light classes. The segmentation uses intervals
equal to one fifth of the available light range. K-means clustering algorithm into
homogeneous light classes or quantile based segmentation could be used as an
alternative (not yet tested).

Step 2. Determining the number of recruits

For each light class, determine recruitment rate from a recruitment function
assuming that recruitment rate is a function of degree of saturation of the stand
carrying capacity (maximum sapling density) which is itself limited by light
availability; Median value of light class is used to estimate carrying capacity per
light class.

The default function used assumes that maximum density is proportional to the
available light or its proxy, canopy openness (CO). Default parameterisation uses
sets maximum density in high light (i.e. CO=1) to 5000 individuals per ha. It is
further assumed that sapling density will be 0 if CO=0. Recruitment rate is then
fixed as proportional to each light class density deficit (defined as max(0,(max
density - obs. density)). The suggested default value for recruitment rate is half of
the density deficit (and expressed as a number of recruits per unit area). In other
words it is assumed that the plot density would asymptotically reach its target
maximum density (with a rapid initial increment as 95% of maximum density
would be reached in just 4 time steps using the default parameterisation if the light
conditions would not change).
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50
Step 3. Identifying cells that will host the recruits.
Select cells to be colonized in current time step (if any).
For each light class the number of recruits is known and equal to the total area of
that light class x recruitment rate. The random allocation of those recruit to
particular cells is done according to a parameter α which reflects the relative bias
towards preferential establishment in empty cells (hence á controls spatial
regularity in recruitment) and may be set to 1 by default assuming that only empty
cells will be considered as potential location for new recruits. Conversely if α is set
to 0 all cells within a particular light class will be selected with the same probability.
Hence as overall density per light class governs the total recruitment rate this will
result in a spatially totally random distribution of seedlings within a light class
(provided that the draw is done on the whole set of cells for each individual). See
last section for details of the proposed algorithm (section 5.2.3 b and section 5.2.6).

Step 4. Determine to which species a recruit belongs

We now have identified the individual cells that will carry a recruit and the number
of recruits per cell. For each recruit, we then randomly draw the species to which it
belongs using the following procedure.

Let Fi be the relative weighted frequency of the species i, i.e. the relative “effective”
abundance of species contributing to regeneration inside the plot. By definition

∑
F =
i
1 i

Let Fi be the relative “effective” abundance of species contributing to regeneration

inside the plot. Fi is defined as

θi(
Fi _ metacom ) + (1 - θi)
(Fi _ local )
Fi =
∑(θ
i( Fi _ metacom ) + (1 - θ
i)( Fi _ local )
i

where 1 >= θ
i >= 0 can be viewed as a measure of a species' efficiency of dispersal

Suppose that there are M light classes and let Aij be the relative abundance of
species i in light class j. By definition
i, ∑
∀ Aij =
1
j

We further note Lj the relative frequency of recruits which fall into class j, hence
∑j
L =j 1 (which is determined in steps 2 and 3)
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51
We then compute the probability of recruiting a sapling of species i in a cell
belonging to light class j as Rij

Rij =
P( S =
i/L =
j) =
P (( S =
i) ∩
(L =
j )) / P(L =
j),

Noting that
P(( S =
i) ∩
(L =
j )) =
P( S =
i ) * P( L =
j/S =
i) =
Fi * Aij
we obtain
Fi * Aij
Rij =
Lj
Step 5. Fine location of individual saplings within cells
We have now defined for each cell the number of recruits and to which species they
belong. We then locate those randomly within their cell.

Parameters specific to the recruitment step

Species specific parameters:

! Relative species abundance in overall community

Each species in a scenario is attributed a weighting factor such that the ratio of
this weight to the sum of weights over all species is equal to the relative
abundance of that species in the metapopulation. By default a new species is
created with a weight of one.

! Species dispersal limitation

1- θreflects species dispersal limitation should be close to 0 for pioneer species
and may be close to 0 for strongly aggregated species.

Overall parameters

α
?
relative preference for empty cell (default alpha=1)
This is implemented in the following way. Cells are given a weight of

(1 - α 1
* occupied cell) where 1
occupied cell is 1 if cell is occupied and 0 if it is empty. If α
=0
then each cell is drawn randomly from the complete set of cells, if α =1 then each
cell is drawn randomly from the subset of empty cells (note that after each draw the
cells are re-weighted to reflect change in occupancy). Practically for 0< α <1, cells
are “placed on a line” in an arbitrary order from 0 to sum of cell weights. Cell i and
cell i+1 being separated by a distance equal to weight of cell i+1. Then a random
number between 0 and Sum of weights is drawn and the recruit is allocated to the
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52
cell whose associated interval contains the value obtained randomly (the cell
corresponding to the first graduation larger than the random number drawn).

?
maximum sapling density
The default value is set to 5000 per ha but may be changed according to local
data and developmental stage considered for the recruitment step.

The light map used in the recruitment module is computed for a 1x 1m grid using
the similar light calculations as for trees light index (i.e. the so called “detailed” light
map as opposed to the “simple” light map as described in the SLIM section).

5.1.7 Mortality
Survival probability is computed from two parameters: Min survival probability and
m. Min survival probability is the survival probability value of a completely
suppressed plant (no growth). m is a parameter affecting curvature of the
relationship between growth rate and survival probability.

This formulation is equivalent to a logistic model (which is strictly equivalent

mathematically speaking)

Log(sp/(1-sp))=ax+b equivalent to sp=1/(1+ exp(-ax-b))

By default x should rather be a measure of relative growth rate (instead of growth

rate relative to max growth rate given current size as this would incorporate
senescence). However note that this will most probably not by easy to calibrate for
all tree size and may have to be refined (one way would be to have size as a explicit
predictor in addition to relative growth rate).

Survival probability increases with the ratio between actual and maximum growth
rate r:
dbh _ inc
r=
dbh _ inc _ max

sp = (
(
min_ sp +
1− *(
min_ sp ) e−
1−m*r
)
)
Where m is mortality modifier.
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53
1
1

0.95

( r)
Su rvival probability

sp( 0.9 ,
15 ,
r) sp ( min ,r
m,):
= 

min +
(1 −
min) ⋅
1−e 

−
m⋅

sp( 0.8 ,
15 ,
r) 0.9

sp( 0.9 ,r
5,)

0.85

0.8 0.8
0 0.2 0.4 0.6 0.8 1
0 r 1
Growth rate
Growth rate relative
relqtivetotofree
freegrowing
growing

Figure 64. Relationship used in SExI to relate survival probability to growth rate relative to free growing tree
of similar size.

In addition, systematic mortality is assumed once tree crown size has reached 5% of
1
normal crown size .

By default annual survival probability is a function of current growth rate relative to

max growth rate given current size, i.e. it does not take into account senescence as
tree approaches maximum size. Senescence may be incorporated simply by using
growth rate relative to species absolute maximum growth rate (rather than growth
rate relative to max growth rate at current size). Alternatively tree size relative to
species maximum could be considered as an additional predictor.

The trees that don't survive enter the tree fall module.
The tree fall module deals with secondary damage due to tree fall. The direction of
fall is random. Any tree smaller that 0.9 times the height of the falling tree and
which is located in the area of potential damage is damaged. Area of potential
damage is a sector defined by the direction of tree fall and the crown width of fallen
tree and initial position of tree.

1
The latter might be replaced by a probability value function of CF that would look like 1-EXP (-(SRCF1*CF))
 SExI-FS User Guide
54

Figure 65. Diagram of tree fall sectoral damage

Potentially damaged trees less than half the size of the falling tree are either killed
(in a proportion equal to a parameter referred to as secondary mortality probability
parameters) or damaged. Tree damage here means a deterioration of crown form (ca
50% decrease of crown volume). This is achieved by shedding half of the VBs on one
side of the crown.

5.1.8 Reference Tree

Reference tree is a tree which grows in an optimum environment (isolated). The tree
is grown for a number of years, and its various features (dbh, height, crown size, etc)
are stored in an array. The relation between dbh and other dimensions of reference
tree is sometimes referred to as “normal” relation.

When computing reference dimension value for a particular dbh “local” Lagrange
interpolation method is used. The interpolated polynomial is calculated from the 3
closest value indexes. This procedure is meant to avoid large interpolation error on
curve shape by linear section interpolation. The fact that only 3 values are used for
interpolation should avoid Runge oscillations which can become problematic with
high degree polynomial interpolation (e.g.
Http://sonia_madani.club.fr/Cloaque/Arithmurgistan/Interpolation/lagrange.html).

5.2 STReTCH Module

5.2.1 Introduction Statement of objectives
Despite a wide range of development strategies - architectural models sensu (Hallé
et al., 1978) - all trees face the same fundamental constraints in terms of light capture
and notably need to strike a balance between investment in support structure and
assimilatory organs. The objective of the Stretch module is to propose a generic
 SExI-FS User Guide
55
model to represent crown shape flexibility in response to light and space limitations
independent of the detailed tree architecture.
We reckon that a proper crown model should in particular be able to allow for the
simulation of a number of “typical” development trajectories.

Responses expected to be covered by the crown model include:

! Flexible growth allocation either towards lateral crown expansion or towards

growth in height depending on the prevailing light environment. Ex: a sapling
growing slowly (with limited crown development) in the understorey until a
gap occurs in the canopy above it, the successive release in growth (“rush
towards the light”) and the subsequent vigorous lateral expansion of the tree
crown once the tree has reached the upper canopy (or possibly its death if the
canopy gap closes by lateral growth before the tree makes it to the top).

! The model should be able to reproduce the change in crown ratio (crown
depth/total tree height) as well as the change in height/dbh allometry
coefficients observed for trees under different planting densities.

! The model should also be able to simulate the asymmetric growth resulting
from row planting which allows an efficient occupation of space without
significant decrease in overall tree growth rate (cf. low sensitivity of rubber dbh
increment to planting pattern for a given planting density).

In the Stretch approach the crown is represented by a growing deformable solid.

This expanding polyhedron is defined by a set of vectors (later referred to as
“Virtual Branches”) all stemming from the crown base.
The growth rate of those Virtual Branches (VB) is a function of (local) light
conditions (local response) and their relative position (to capture the crown
elongation a species specific characteristic). The way in which VBs are affected by
(local) light conditions or constrained by their relative position within the crown is
species dependent.

5.2.2 Ecological basis Biological Principles

While overall growth - as captured by the dbh increment will decrease under sub-
optimal or supra optimal light levels, crown shape may also be affected by sub-
optimal or anisotropic light and in return affect overall growth performance. Two
major mechanisms may contribute to crown shape alteration under specific light
conditions.
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56
A. Local asymmetric competition between branches within a tree.
The so-called branch autonomy theory states that the local carbon balance between
production and demand for growth and respiration determines the fate of the
branch and notably whether it will be shed. However there is increasing evidence
that such a simple view is not tenable (Henriksson 2001, Sprugel 2002, Lacointe et
al., 2004). Notably it was shown that the light level at which a branch will be shed
depends on the relative light level (to the rest of the crown) rather than the absolute
level of light experienced. Even though dominant trees have more resources to
allocate, branches on suppressed trees are able to grow and produce new foliage at
solar irradiances where branches on dominant trees die. Thus branches are
sufficiently interdependent that a positive carbon budget by itself does not ensure
branch survival; branch position relative to other branches on the same tree is also
important (Sprugel et all, 2002). Furthermore, the increased growth of non-shaded
branches in trees where only two branches were shaded suggests that resources
were preferentially allocated to branches in more favourable positions (Henriksson
2001). Hence we expect that local deformation of a crown (for example the
opportunistic development of a part of the crown in response to local abundance of
light side gap, row planting etc will be better modeled as a combination of the
overall growth potential modulated by local gradients.

B. A whole tree active shade avoidance response under low light (notably lateral shading)
by which crown growth is reoriented towards height at the expense of lateral
growth and which is commonly observed under high tree population density or low
light levels. This response may result from a combination of biological mechanisms.
Relative or absolute increase of growth in height may also be a response of internal
competition of allocation of “growth potential” within the crown as a decreasing
gradient of light (or space) availability from apex to base is common. Hence the
distinction made here between global or local response is somewhat arbitrary and is
made for operational purposes. Vertical light gradient of increasing intensity
towards the top of the canopy is not only common under dense planting where
overhead light is abundant while lateral light is very much restricted but also in the
forest understory where a similar gradient (though probably less pronounced) may
prevail in many cases (Montgomery and Chazdon 2001). Hence new leaves are
produced where light resource is most abundant (a local response) which translates
into a global deformation of the crown: only the upper-most part of the crown
receives adequate light to maintain active growth and therefore elongation of crown
occurs.

The strategy of "compression" in the understorey and accelerated growth under gap
as described in (Sterck 1999) for example would indicate that for canopy species
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57
whose juveniles start to grow in the understorey, the relevant signal to trigger
accelerated growth in height might be the light gradient rather than the light level.
It has been shown that poplar trees can alter their growth rates under modified
red/far red ratio and noticeably increase their relative growth in height (Gilbert et
al., 1995). This may be a widespread response to shading (Ritchie 1997). Our
measurements of hundreds of trees belonging to a dozen species growing either in
dense plots while receiving overhead light or overtopped in the understory reveal
very similar overall h-dbh alteration (ICRAF unpublished). Hence overall light level
is the environmental cue used in SExI to model vertical stretching of tree.
A number of casual observations suggest that crown rise is accelerated by increased
light gradient (e.g. durian with low branches until it reaches the upper canopy and
emerges, shorter rubber trees with reasonable crown depth under dense stand of
rubber trees themselves having the crown reduced to the most extreme top of the
tree). This would illustrate a change in growth strategy (growth allocation pattern)
in response to gap opening for example. In the proposed implementation of the
model increased slenderness will force crown rise.

5.2.3 Crown shape modeling

a. Analytical framework

Crown development is decomposed into vertical extension and horizontal extension

of VBs (“Virtual Branches”), and light may affect each directional component
differently.

Growth of an individual VB will depend on:

1. Overall growth potential: Individual VB growth will depend on the overall

(potential) crown volume increment associated with dbh increment (which notably
depends on overall light limitation). The relationship between crown volume
increment and dbh increment is controlled by h-dbh and dbh-CW power
relationships2.

2. Species crown profile (default implementation is half ellipsoid): in order to

maintain the general shape of crown profile (ellipsoidal, conical, paraboloid of
revolution,etc) in the absence of deformation due to competition, the growth of any
VB is a function of its relative position in the crown.

2
Dbh-CW is entered by user as a bilinear relationship linear from 0 to 0.05 m dbh and then from 0.05 to max dbh but
is re-implemented as a power function to avoid discontinuity problems
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58
3. Vertical stretching resulting from reallocation of growth from lateral expansion to
height increase (a response to the light gradient) it is constrained by species specific
plasticity (flexi). Vertical stretching of crown is done by co-limiting its lateral
extension through associated limitation in dbh increment assuming that total stem
biomass scales isometrically with the product of stem cross sectional area and tree
height. Crown size is further reduced (shedding lower VBs) via the relationship
linking maximum crown volume to dbh established for free growing trees.

4. A local deformation factor. The impact of local light level (spatial heterogeneity of
the incoming light = light anisotropy) is modeled by modulating the horizontal
extension as a function of the relative (to average) illumination of light sector
associated to each VB. The degree of crown plasticity is assumed to be identical to
flexi and is hence species specific. Some additional species-specific parameter might
be necessary to refine species differences. This flexibility can be adjusted through the
amplitude of the sectoral light used to define the local light level (the larger the
sector the lesser the difference in light perceived by neighbouring VBs)

b. The Algorithm

Vertical stretching of crown

Compute vertical and horizontal growth component of VBs of reference tree based
on species specific shape and actual overall growth reducers.

Computation of stem height and dbh increments are described in section 2.3 Height
Increment. Those values are then used to compute crown stretching by computing.
VB increments based on crown profile.

Half ellipsoid profile

(vi_a) VB_incr_ver=cos (theta) * height_inc

(vii_a) VB_inc_hor= sin(theta) * CW_increment

theta is the angle of VB with vertical, and CW_increment is calculated in the

following way (i.e. replacing the experimental bilinear relationship between dbh and
CW with a power function to avoid discontinuity).

Step 1. Using the parameters of the estimated linear relation between CW and dbh
which holds for dbh>=5 cm, compute (x1,y1) (x2,y2) the coordinates of the points of
the curve CW=f(dbh) where:

X1= 0.05, y1=0.05*b+a, x2=dbhmax, y2=dbhmax*b+a

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59
Step 2. Compute the corresponding A and B parameter values of the power function
such that CW=A*dbh^B
−
log[ y1] +log[ y 2]
A=
−log[ x1] +
log[ x 2]
−
log[ x 2 ] log[ y1]+log[ x1] log[ y 2 ]
log[ x1]−
B=
e log[ x 2 ]

Step 3 Compute the crown width increment as the expected crown increment for the
normal tree given the current dbh hence

CW increment = A*((dbh+incr)^B-(dbh^B))

If the tip of a VB is inside a neighboring crown the horizontal component of growth

of that VB is set to 0 (but height increment is still applied to ensure decent crown
profile).

Conical profile
Assumptions identical to above (implicit assumption: dbh =dcbh)
To maintain conical profile we compute the expected displacement (absolute
increment) of all VBTips as a function of height growth and lateral extension of
crown base.

Let H be the crown depth length and L the expected (not necessarily equal to actual!)
crown radius at crown base for previous dbh (before current time step increment),
then expected VB length of angle with vertical is

l= (sin/L + cos /H)^-1

let L'=L + height increment and H'= expected crown radius at crown base for new
dbh (previous dbh + dbh_inc) then expected new length of VB with angle with
vertical is

l'=(sin/L' + cos/H')^-1

and the current increment in length of VB of angle is computed as l'-l

Where L= (a*dbh +b)/2

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Lateral deformation of crown

Based on the sky map and the light model adjust VB_inc_hor only for anisotropy of
incoming light. At this stage we assume that the number of VBs per tree is fixed and
set to the following:
Default number of VBs on vertical direction is 15 (6 degrees each), and 15 Vbs for
lateral direction (12 Degrees). Then the default number of azimuths of the sectoral
light map is set to 15 (same as the number of VBs for a given inclination. The
number of inclinations of the sectoral light map is set to 5 (equal to number of
inclination in the light model, medium precision). Orientations of VBs is
randomized by choosing the first VB randomly.

Note: Number of VBs and sectoral light resolution is not accessible to user

Sectoral map calculation algorithm outline

If
number of sectoral_Map azimuths is less than number of light_model
azimuths or number of sectoral_Map inclinations is less then number of
light_model inclinations
then
for each sector of sectoral light map, find all light model sectors which
intersect with the sector of sectoral light map. Then set the value for the
selected sector of sectoral light map as the average of intersected light model
sectors value.
Else
Set the sector value of sectoral light map to the value of the closest sector of
light model.

For each of the (15-1) * 15 VB directions (excluding vertical VBs) we compute an

index of efficient lighting for each direction and the average value of the index. Note
that this is done for all directions (whether there is or not a corresponding VB alive).

The ratio of this light level to the average light level is used to adjust the horizontal
component of growth for each growing VB.
Note that whether there are VBs missing or halted does not affect the deformation of
the remaining Vbs. Also note that the growth modifier may theoretically reach
values as high as the number of directions! This would happen in case all directions
but one have effective light of zero (completely opaque) in which case the growth
 SExI-FS User Guide
61
modifier for the only growing VB would be equal to the effective light of that
particular azimuth/average effective light = number of azimuths. Such extreme
cases are however not possible with the default parameterization due to built-in
correlation between the levels of light perceived by adjacent VBs (overlapping of
sectors). Finally extreme departure from the mean value are only likely to occur
when a large majority of VBs perceive very low light levels which is necessarily
associated to low CP and low overall growth and hence individual growth of VBs
should remain within reasonable boundaries.

Let G(i) be the standard growth rate (equal for all azimuth) computed in previous
step.
Let L(i) be the sectoral light associated to VBazimuth i.
The following algorithm is used to adjust G(i) to L(i).

Step 1
“Effective” light level L'(i) is first computed for each VB direction as:
If L(i) > optilum
then L'(i)= optilum
else L'(i)=L(i)

Step 2
For all VB present, not halted by collision, and receiving sufficient light (see section
5.2.4 on step 1 for details and notably additional condition that limits the total crown
surface that may be lost in one time step through shedding due to low light) G'(i),
the modified growth rate is computed as:
If L'(i)>AVG(L'(i))
G'(i)=G(i)*(1+flexi* (1-(AVG (L'(i)/L'(i)))^sensi))
IF L'(i)<AVG(L'(i))
G'(i)=Max(G(i)* (1-flexi* (1-(L'(i)/ AVG (L'(i)))^sensi)),0)

The above formulation is consistent with the way flexi and sensi are used to
implement whole tree response to shading. Flexi essentially controlling the
maximum departure from reference (here symmetric) growth, and sensi an index of
sensitivity to shading either local or global.
 SExI-FS User Guide
62

Figure 66. Percentage increase in VB extension in Figure 67. Percentage change (decrease) in growth
high light microsites as a function of sensitivity and rate of vertex as a function of light ratio (local light
light ratio (average light/local light). flexi=1 /average light) and sensitivity when local light is
less than average light. flexi=1

Finally if VB is inside neighboring crown (i.e. has intruded a neighbouring crown

G'(i) is set to zero (no growth through neighbor's crown envelope).

5.2.4 Branch shedding

Branch shedding always starts with lower most VB in any azimuth.

1. A first test for VB survival is made prior to VB growth. If VB sectoral light-level is

below a certain threshold then it is dropped. Threshold light level at which lower
most VBs are shed is set to be equal to minimum.

2. Once VB have grown the crown surface is checked against the expected crown
surface (cf allometric relation between dbh and crown volume in reference open
grown trees). In case current crown surface is above reference crown surface
additional selective branch shedding will occur until crown surface is reduced to
the maximum possible crown surface. VBs are dropped one by one starting with
the VB receiving the lowest light (comparing lower most vb along all azimuths).
As an alternative crown volume may be used instead of crown surface as a
measure of crown size. The procedure is similar to using crown surface as a
control. First, each VB is assigned a weight approximating its contribution to
crown volume. The elementary volume associated to a VB used to compute is
weight is the volume of the 2 tetrahedra defined by the three vertices defined by
the closest 3 neighbouring VBs. left, right and top neighbours, and the target VB
itself. The weight of a VB is then computed as the sum of the elementary volume
assigned to it to the sum of all such elementary volumes. When a particular VB is
dropped the total crown volume is reduced proportionally to the weight of the
shed VB.
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63
Notes:

If systematic crown rise of reference tree occurs, it should be specified through the
>
graphic user interface can.
NO significant crown overlapping is tolerated in the model except for possible in-
>
growth of a tree within a larger overhanging crown.
At present a species with low flexibility and high shade tolerance will show higher
crown boldness as it will retain its VBs longer and fail to reallocate growth
3
preferentially to well lit VBs. Differential "crown shyness" could further be controlled
by limiting the number of steps a VB may survive if prevented from extending
laterally. As a consequence species tolerant to low light may in fine be even more
tolerant to crown collision as they may be halted only temporarily and resume growth
once the other crown has shed its branches.
At each time step VBs are resampled (along a set of fixed directions) and VB tips new
>
position interpolated from previous VBs positions. If VBs are missing, the lower most
remaining VB is always located along the vector immediately below (larger angle with
vertical) the existing VB at the same distance from tree vertical axis. If all VBs along a
particular azimuth have been dropped a new VB is regenerated with length equal to
average length of all VBs of same inclination.

5.2.5 Collision detection

Collision determines halt of growth of VB. The collision between neighboring
crowns is detected if there is intersection between the horizontal vector joining VB
tip to tree crown vertical axis and any triangle defined as a result of triangulation of
VB tips location in 3D of neighboring trees.

Note that as a result of this implementation vertical growth rate of tree top apex is
not affected by collision. However the VB growing from inside another crown will
be halted if they come to intersect with containing crown envelope.

3
Note that crown shyness is used here to refer to the reaction of a tree crown colliding with another tree rather than
in the more restricted meaning it usually refers to ("individual subcrowns and crowns which grow clearly
separated from one another, with intervening vegetation-free borders; most common in single-specie and single-
cohort stands and in stands on windy sites"). Two primary hypotheses have been put forth to explain canopy
shyness - the first that wind-blown branches abrade each other at tree boundaries and damage buds, preventing
leafing, and the second that mutual shading at the boundaries of trees prevents growth (Putz et al., 1984) and see
Rudnicki et al., (2003). "Stand structure governs the crown collisions of lodgepole pine." Can. J. For. Res. 33(7): 1238-
1244..
 SExI-FS User Guide
64
5.2.6 Triangulation algorithm
A proprietary triangulation algorithm is used which takes advantage of the fact that
VBs are regularly spread and notably that on a given azimuth there can be no
missing VB between lower most VB and apex.

Let n be the number of azimuth and p the number of inclinations. The total number
of VBs (including apex) in a full crown (no missing VB) is then n*(p-1) + 1 and the
associated number of triangles is n*(2(p-2) + 1)=n* (2p-3).

Each time a non-vertical VB is dropped, so are two triangles as can be seen from the
algorithm below and illustrated in the figures.

The algorithm:

Let H(i,j) be a VBTs height at inclination index i and azimuth index j. (Assuming
that each VBTs has height and horizontal distance from axis).

i = 0 is the lowest VBT for each azimuth direction.

The following algorithm iterate the VBTs through the inclination index on the two
following series of VBTs per azimuth directions H(Ia, Jc) and H(Ib, Jc+1).

Step a:

For each increments of Ia and Ib, start from a=0 and b=0, find Min(H(i1, Jc), H(i2,
Jc+1)) , store the result as one of triangle element. If the lowest VBT is in J series then
a++ else b++ (increase one step).

Find next element Min(H(i1, Jc), H(i2, Jc+1)), store it (VBTs with the same index) as
the second element of triangle.

Step b:

If the two stored triangle element is on the same series of azimuth then the third
element should be the lowest element on opponent series.

Else increase the i of the lowest VBT series and find next Min(H(i1, Jc), H(i2, Jc+1)) as
the third element of triangle.

Store the last two elements of the previous triangle as the elements for the next
triangle.

If there is more than 1 VBT left in both series then Go to step b.

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65
Else put the last VBT as the third element, and Repeat from step a for the next j
(azimuth direction index; j++).

Note: the algorithm below is used for triangulation of semi-irregular VBs location (previous
crown type algorithm). And it's quite robust.

Figure 68. Left figure shows the initial VBTs connection (subpart of a crown VBTs); right figure shows the VBTs
connection after a VBT shed at i=0 and j=1. the series of VBTs at j1 then re-indexed for i.

Figure 69 Connection after a VBT shed along the same line

5.2.7 Algorithm for crown volume computation

Volume of the crown is calculated as the sum of all connected tetrahedra, one face of
which is a triangle of the crown envelope (as a result of the triangulation described
above). Each triangle is then connected to the center of crown base (added to each
triangle as one other vertex to form a tetrahedron).
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66
Then tetrahedron volume is calculated using the formula below:
Let the tetrahedron be specified by its polyhedron vertices at (xi , yi , zi) where
i=1, ..., 4. Then the volume is given by:
x1 y1 z1 1
1 x2 y2 z2 1
V=
3! x3 y3 z3 1
x4 y4 z4 1

(http://mathworld.wolfram.com/Tetrahedron.html)

5.2.8 Crown deformation and the pipe model theory

We may need to explore further the application of the pipe model in order to link
more formally crown volume and dbh values.
To maintain consistency between overall crown volume and tree diameter we
further assume that leaf area and stem cross sectional area are linearly related. This
allometric relationship based on the functional relation between sapwood area and
leaf area, is expected to be robust (Morataya et al., 1999) and hold under the
following provisions:
a. Stem diameter is measured just below crown (instead of breast height).
b. Relationship is location specific (under different evaporative demand this relation
may be significantly altered).

Then LA is further broken down into crown volume and leaf area density (per unit
volume). Assuming LAD to remain stable across time and space within a particular
tree this implies that we can extend the allometric relation between stem diameter
and LA to stem diameter below crown and crown volume (or crown surface if we
consider that leaves are predominantly located on a thin layer on the outer most
side of the crown). This relation is used to enforce branch shedding under extreme
deformation (elongation) of tree in response to light gradient, i.e. as crown volume
is constrained the lower most branches are shed.

A tapering equation could be used to link dbh and diameter below crown so that the
assumption of linear relation between stem cross sectional area and leaf area would
be more robust. In first approximation a conical truncated shape may be used (based
on data collected by Hubert de Foresta in Krui for example) for the part between
diameter at breast height and diameter at crown base height (but see also, for a
discussion of the various approaches that may be used,
http://sres.anu.edu.au/associated/mensuration/shape.htm#equation).
 SExI-FS User Guide
67
In fact the model should be able to compute cross-sectional area of stem at any
height based on any kind of stem profile if such information is provided by user.
This could be implemented simply using numerical approximation to compute
deltadb-h and delta-h in the Stretch module.
 SExI-FS User Guide
69
6. Calibration Procedures

Below are some guidelines and examples on how to collect tree data to be used for
calibrating the SEXI-FS model, with emphasis on the STReTCH module (crown
deformation).

6.1 Allometric Data

The purpose is here to define relationship between various tree dimensions and how
those allometric relationships are affected by tree environment

6.1.1 Tree selection

Trees from the following three categories are purposefully sampled over the whole
range of diameter of interest (e.g. 5 to 50 cm dbh); all trees should have a CF score > 3.

The three categories considered are:

! Isolated trees
! Co-dominant trees in dense stands (usually pure stands) i.e. CP>=4
! Suppressed trees (CP<=2)
6.1.2 Tree parameters to be measured
! Tree height (h)
! Height of crown base (hcb)
! Height of maximum crown width max width
(hmcw).
h
! Height of maximum crown width
may coincide with height of crown hmcw
base. The height of maximum crown hcb Carl-Leiss
width (a shape parameter) is used Altimeter
to compute crown volume. Figure 70. Height measurement

! Crown width
Crown diameter is measured in two perpendicular directions. Crown projection
 SExI-FS User Guide
70
diameter is first measured along maximum crown width axis and then
perpendicularly to this first direction. The average is used for crown width
(Figure 71).
For the purpose of recording the whole stand into SExI-FS and get more accurate
prediction of crown width, the radius projection of crown can be measured with
more then 4 direction. Figure 72 shows how the eight radiuses are measured
while also keeping the relative direction angle info.

N
U 1
b 2
8
a
7 3

6 5 4

Figure 71. Crown width measurement Figure 72. Crown radius measurement

! Crown Position (CP)

The crown position index, which depends on the
relative position of the crown within the canopy,
reflects the light conditions prevailing at a
particular moment (Figure 73). Crown Position
scale is defined as follows (Alder and Synnott
1992):
5 = Emergent: Crown plan exposed vertically
and free from lateral competition at least within
the 90º inverted cone subtended by the crown
base.
4 = Full overhead light: Crown plan fully
exposed vertically but adjacent to other crowns
of equal or greater height within the 90º cone.
3 = Some overhead light: Crown partially
exposed vertically but partly vertically shaded
by other crowns.
2 = Some side light: Crown plan entirely
vertically shaded but exposed to some direct Figure 73. Dawkins crown position classification
(in Alder and Synnot 1992)
 SExI-FS User Guide
71
light due to a gap or edge of overhead canopy.
1 = No direct light: Crown plan entirely shaded vertically and laterally.

! Crown Form (CF)

The Crown Form index tries to capture the photosynthetic potential of a tree. It is
an architectural characteristic and will tend to reflect the development history of
the tree (Figure 74). Crown Form scale is defined as follows (Alder and Synnott
1992):
5 = Perfect. The best size and development generally seen, wide, circular in plan,
symmetrical.
4 = Good: Very near ideal, sylviculturally satisfactory, but with some slight defect
of symmetry or some dead branch tips.
3 = Tolerable. Just sylviculturally satisfactory, distinctly asymmetrical or thin, but
apparently capable of improvement if given more space.
2 = Poor: Distinctly unsatisfactory, with extensive dieback, strong asymmetry and
few branches but probably capable of surviving.
1 = Very Poor: Definitely degenerating or suppressed, or badly damaged, and
probably incapable of increasing its growth rate or responding to liberation.

Figure 74. Dawkins crown form classification (in Alder and Synnot 1992)

! Crown porosity (isolated, dominant, co-dominant trees)

Crown "porosity" to light is defined as the percentage of sky visible from below
the crown and is simply assessed using sub-vertical photographs towards the sky.
Best time to take good quality photographs is early morning or under heavily
overcast skies (no direct sunlight). Low branches can make pictures of the entire
crown difficult or impossible, as we can't move back far enough to capture the
whole crown. In that case it is recommended to beginners to take a series of
 SExI-FS User Guide
72
pictures of parts of the crown, in
a systematic pattern. Once
experienced, selection of a
representative part of crown in
the field is a more efficient way
of doing. In most cases selection A B
of a representative portion of
crown (which can be the entire
crown once it has been
delineated on the photograph
but is more commonly restricted
to half a crown excluding the
C D
tree trunk) will be done by
cropping part of the digitised Figure 75. Crown porosity of Pterospermum javanicum (A),
image on the computer. Shorea javanica Koord. et Valeton (B), Parkia speciosa Hassk. (C),
and Lansium domesticum Correa (D).

Once a representative portion of the crown has been selected and cropped the
picture is converted into black and white bitmap format in order to assess the
percentage of visible sky. Image thresholding (deciding which level of grey
defines the limit between black and white i.e. between tree parts and the sky) is
the critical step. Most image processing software offer facilities that allow instant
comparison between the original image and the classified image which provide
some control over the quality of the thresholding step.

Note: crown porosity cannot be measured on trees growing in the understorey. This may
be problematic as there are indications that tree porosity is responsive to tree growth
environment and may be significantly lower in shaded trees than trees fully exposed to
light.

6.1.3 Tree growth environment

When relating tree dimensions to its growth environment care should to be taken in
making sure that the current environment does reflect the growth environment of
the tree (which may have changed over time through self thinning, tree fall creating
gaps, differential growth rates in height affecting CP, etc).

Local density and local basal area are recorded by measuring the trees growing in
the vicinity of the target tree. A tree is recorded if its dbh is >= 5 cm.
 SExI-FS User Guide
73
A circular plot with radius rmax around the target tree is defined with:
rmax =max(r1,r2)

Where r1 is defined as the maximum crown width of target tree and r2 equals the
distance to the furthest tree in physical contact with target tree.
If rmax=r1 then local density is simply computed as total number of trees divided by
plot area (Pi*rmax^2) by and local basal area as the sum of all cross sectional areas of
individual trees divided by plot area.
If rmax=r2 then local the furthest tree (which defines the plot radius) is counted as
half inside and half outside the plot and hence given a weight of 0.5 both when
computing density and basal area.

Note: in case of regular planting (which for example may be the case for rubber plantation)
the elementary plot may be delineated as a rectangle (which is quicker in the field) including
all 8 “neighbouring” trees (two on the line and the three trees on each neighbouring planting
line). In that case the plot area is simply defined as 9 times average planting distance.

For all trees within a circular plot, the following three variables are recorded: tree
species, tree diameter, whether the tree neighbouring tree crown is in contact with
target tree crown is (Boolean).

6.2 Data processing

6.2.1 DBH-Crown diameter
DBH and crown diameter are related by 30
linear regression. Data from the various Duku
groups are pooled to establish this Durian
relationship. It is useful however to check Jengkol
Pulai
Crown width (m)

that groups do not differ significantly 20

Sengon
(biologically meaningfully rather than
statistically). If scaling appears not to be
isometric, log-log regression may be used
10
assuming a power relation between crown
width and stem diameter.

6.2.2 DBH-Crown surface

0
0 100 200 300
Assuming a half-ellipsoid approximation Girth (cm)
of the crown profile we then compute the
Figure 76. Girth-Crown diameter relations
approximate crown surface as
 SExI-FS User Guide
74
e = (1-(cr*cr)/(cd*cd))^0.5;
if(cd > cr) {
crown surface = PI*cd*cd + PI*cr*cr/e*ln((1+e)/(1-e));
} else {
crown surface = PI*cr*cr + PI*cd*cr/e*arcsin(e);
}

where cd stands for crown depth (total height height of crown base) and cr is crown
radius (half of crown width).
see http://mathforum.org/library/drmath/view/51743.html for derivation of the formula of
surface area of an ellipsoid.

Then estimated surface (or volume) is fitted to dbh; a loglinear fit is usually
satisfactory (as total leaf area is expected to scale linearly with stem cross sectional
area e.g. Morataya et al. 1999).

Again we expect this relationship to vary little between groups (which can be tested
by ANCOVA) and data for the various groups should be pooled for this adjustment
to increase robustness of parameters estimates.

Note: multilayer trees (sensu (Horn 1971) which are rare in our data sets) are likely to show
a more consistent linear fit between crown volume and dbh rather than crown surface. This
may be explored using the estimated volume of crown computed as 1/3*Pi*cwa *cwb*CD
(half ellipsoid), where cwa and cwb is crown width measured twice perpendicular (see tree
parameter measured on section 6.1.2).

6.2.3 Estimation procedure of the flexi parameter

Objectives
We are interested in assessing the change in the slope (derivative) of the height-dbh
relationship observed in trees of various species when grown either isolated or in
dense stands. In the SExI-FS model, this corresponds to the flexi parameter (precisely
the ratio of the derivatives is equal to flexi +1)

Data
We assume we have two tree population samples measured in contrasted conditions
(i.e. isolated or in dense stands). We further assume that the “dense stand” sub-
population may be considered representative of the most extreme conditions, i.e. we
capture most of the species possible range of growth conditions. In case the height-
dbh relationship of either of the two subpopulations shows a strong dispersion an
envelop curve analysis could be used (e.g. stochastic frontier functions may be used
 SExI-FS User Guide
75
instead of standard regression; see free software at:
http://www.uq.edu.au/economics/cepa/software.htm) but has not used in the
present study.

We use the data collected by ICRAF by mid 2004 for 6 species for which sample size
seems suitable (Lansium domesticum, Hevea brasiliensis, Durio zibethinus, Archidendron
jiringa, Alstonia angustiloba, Paraserianthes falcataria).

Methodology
Step 1: graphical analysis and data transformation
Assuming that the dbh-height relationship may be correctly described using the
following relationship: height=a*dbh^b, data are first log transformed and plotted
using linear smoother. We visually check that the log transformation is fine
(graphical analysis of residuals may help pinpoint possible problem such as
heteroscedascity or unwished pattern in the residuals).

Step 2: first parameter estimates

For most species it can be seen that the regression lines of the two sub-populations
are almost parallel and we therefore choose to analyse data using a GLM where sub-
population differ only in terms of their intercept (i.e. assuming homogeneous slope).
In one case (Paraserianthes) this assumption is clearly not met but this may be due the
data set used as a single very dense evene-aged plot was sampled.

From the model above we Table 1. Estimates of flexi parameter for 6 species used in
estimate three parameters SExI-FS model
for each species (a1, a2 and
b). Species group Log(a) a Sensi + 1
And the ratio of the Lansium isolated 0.582 1.78961408
derivatives are equal to the dense plot 0.932 2.53958327 1.42
ratios of the a1 and a2 Durio isolated 0.399 1.49033362
parameters if b are dense plot 0.799 2.2233165 1.49
identical leading to the Archidendron isolated 0.84 2.31636698
estimates for the different dense plot 1.41 4.0959554 1.77
species reported in Table 1. Hevea isolated 0.963 2.61954333
dense plot 1.275 3.57870141 1.37
Rerunning the equal model Sengon isolated 0.853 2.34667633
without those two outliers dense plot 1.441 4.22491862 1.80
yielded similar estimates Alstonia isolated -0.006 0.99401796
for sensi. (Marked with an dense plot 0.268 1.30734714 1.32
asterisk in table beside)
 SExI-FS User Guide
76
Note on crown deformation parameterisation: crown asymmetry resulting from
neighborhood competition is commonly observable and has been measured (Brisson 2001).
However we have not yet attempted to directly measure the parameter governing the ability
of a crown to adjust to lateral anisotropy of resources due to difficulties involved in
standardizing such measures. One favourable situation which may occur with planted
species would make use of crown deformation response of trees growing under different
planting patterns (i.e. inter-row, and on the row inter-tree distances). Rather, we make the
assumption that flexibility in tree height adjustment (ratio of k value in the height-dbh
relationship under contrasted vertical gradient) is a good proxy for the ability of a species to
adjust its crown expansion under lateral anisotropic distribution of light.

6.3 Growth Data

Permanent sample plot data are used to derive the following parameters

! Species potential growth function (site specific)

! Species sensitivity to shading
! Species sensitivity to tapping
! Species influential zone (determining BGCI)
6.3.1. Potential growth function
Standard procedures are used to analyse data from Permanent Sample Plot (see for
example Alder and Synnot 1992, Vincent et al 2001 for an introduction to such
methods). Predictors used in the GLM include size, crown indices (and tapping
regime). Rare species (< 10 individuals monitored) are grouped into a miscellaneous
grey species for the data analysis purpose. Once factors effect are estimated,
potential growth is computed after correcting for CF, CP, Tapping index (and
possibly BGCI/ Below Ground Crowding Index).
Corrected dbh increment is used to adjust the dbh_inc=f(dbh) using a Chapman
Richard function with standard non linear regression procedures.

Using precisely the method described above on PSP sample plot for rubber and
comparing the growth rate as a function of size obtained from Sembawa plantings,
we can observe that the patterns are not consistent. Essentially, data from PSP
provide an estimate of maximum potential growth which is strictly decreasing with
tree size whereas data from Sembawa density trial indicate that maximum growth
rate may be attained later in case of low density (6x6 planting pattern).
 SExI-FS User Guide
77
4 0.04
0.04

3 0.03
0.03

CR
DBH_INCR
COR

DBH_IN
2 0.02
0.02
SPACE
SPACE
1 0.01 3x3
0.01 3x4 3x3
4x4 3x4
5x5 4x4
0 0.00 6x6 5x5
0 10 20 30 40 50 0.00 0.05 0.10 0.15 0.20
0.00 6x6
0.00 0.05 DBH0.10 0.15 0.20
DBH
DBH
Figure 77. PSP standardised dbh increment data Figure 78.Density trial (annual dbh increment in m per year,
(computed for CF 5, CP 3 and no tapping) in cm per year plot average values, tapping starts around 0.15 cm dbh)

This strictly decreasing growth rate with size found in analysing the PSP data
(instead of the expected typical increase and decrease in growth rate) is probably at
least partly due to the fact that the monitoring starts at about the size when the
rubber reaches its maximum growth. Early growth (needed in the model if we want
to simulate growth starting at diameters less than 0.05 m) cannot be directly
estimated from PSP data but need to rely on additional measurements, this was
done by using data from other experimental plots where growth of seedling was
measured starting from planting.

Why should “maximum potential growth” decrease faster in PSP - even after
increments have been corrected for CF, CP and tapping - than what is observed in
low density plantation trials? There are at least two possible explanations. The first
one is that below ground competition (which we have not corrected for) is stronger
in PSP (mature agroforest) than in young plantations where it is minimal during the
earlier stages. A similar conclusion, i.e. that below ground competition most
probably limits early growth of rubber saplings grown in rubber agroforest was
reached after careful comparison of growth of rubber plants under artificial shading
and under live canopy (Vincent et al. in prep).

However, such an explanation is not entirely satisfactory as high below ground

competition should most likely translate into a sustained lower growth rate over the
whole period of early growth and cannot be unequivocally related to a shift in
maximum dbh growth rate. Another, possible explanation, is that the difference
observed between rubber agroforest and young plantation reflects the fact that dbh
 SExI-FS User Guide
78
increment in young trees growing under strong light gradient may be reduced as a
consequence of accelerated height growth which occurs under limited light and
which correlatively limits diameter increment. To test this hypothesis, we can test
for dbh*CP interaction using the same PSP data as above. It turns out that the
interaction between both predictors is statistically highly significant and that smaller
trees are indeed more sensitive than larger trees to sub-optimal CP scores.

Note that the above procedure may eventually yield robust estimates only for
abundant species. Hence it is preferable whenever possible to develop potential
growth curve by repeated measurement of isolated trees (or low density stands).

Experience also indicates that sensitivity to shading is poorly captured in PSP data
(often there is no clear species specific response) indicating that additional
information should be used to estimate/check Minilum and Optilum parameter
values (minimum and optimum light levels for growth). For lesser abundant species,
one option is to repeatedly measure purposefully sampled trees. Sample should
whenever possible include open grown trees (Crown Position=5). Sample should
only include trees with optimal or near optimal crown shape (CF>=4) and cover a
range of diameters. Trees should be sampled in similar edapho-climatic
environment. If a decent sample of trees is available across a range of CP classes
shade response (CP effect on growth) can be meaningfully estimated.

Alternative/complementary options include using scarce published literature and

local ecological knowledge about the species of interest. The latter may notably yield
useful ranking between species (both in term of growth rate and shade tolerance).

6.3.2. Below Ground Crowding Index (BGCI)

Usually BGCI is correlated to above ground indices (CP and CF) and in species rich
PSP it may be difficult to show statistically significant growth reduction which is not
yet captured by CP and CF indices. In some particular cases (e.g. limited number of
species and expected contrasted competitiveness for below ground resources such as
water) it may be possible to actually estimate BGCI from repeated measurements.

What we try to estimate (and which is supposedly different between species) in the
present case is the influential zone of each species. In other words we assume equal
sensitivity to resource shortage but differential resource capture efficiency
represented by a relatively larger or smaller influential zone. Thus, the basic idea is
to explore for the different species a range of species specific (and size dependent)
influential zones.
 SExI-FS User Guide
79
The general model to be fitted for each species is:

DBH_Inc=Pot_inc+CP+CF+tapping+BGCI

In the most general case, assuming that only CF is species independent fitting the
above model for a particular target species requires estimating 3 (pot inc) + 5 (CP as
categorical) + 1 (tapping) + n (lambda, species specific IZ scaling factor)= 8+ n
parameters. In addition CF (common to all species) needs to be estimated too.

Although this is certainly feasible it cannot be done using procedures available in

standard statistical packages but requires the development of a global optimization
algorithm (see Canham et al,. 2004 for such an example) which we have not done
yet.
 SExI-FS User Guide
81
References

Akinnifesi F K, Rowe E C, Livesley, Kwesiga F R, Van Lauwe B and Alegre J C. 2004. Tree
root architecture. In: Van Noordwijk M, Cadisch G and Ong C K (eds.) Below-ground
interactions in tropical agroecosystems. Concepts and models with multiple plant
components. CABI publishing, p 61-82.
Alder D, Synnott T J, 1992. Permanent sample plot techniques for mixed tropical forest.
Tropical Forestry Paper 25, Oxford Forestry Institute -Department of Plant Science,
Oxford.
Brisson J. 2001. Neighborhood competition and crown asymmetry in Acer saccharum. Can. J.
For. Res./Rev. Can. Rech. For. 31, 2151-2159.
Canham C D, LePage P T, Coates K D. 2004. A neighborhood analysis of canopy tree
competition: effects of shading versus crowding. Canadian Journal of Forest Research
Revue Canadienne De Recherche Forestiere 34(4): 778-787.
Gilbert R, Seavers G P, Jarvis P G, Smith H. 1995. Photomorphogenesis and canopy
dynamics. Phytochrome-mediated proximity perception accounts for the growth
dynamics of canopies of populus trihocarpa x deltoides 'Beaupré'. Plant, Cell and
Environment 18: 475-497.
Grist P, Menz K, Thomas. 1998. Modified BEAM Rubber Agroforestry Models: RRYIELD and
RRECON. Canberra, Australia, ACIAR.
Hallé F, Oldeman R A A, Tomlinson P B. 1978. Tropical trees and forests. An architectural
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Henriksson J. 2001. Differential shading of branches or whole trees: survival, growth, and
reproduction. Oecologia 126(4): 482-486.
Horn H S. 1971. The adaptive geometry of trees. Princeton University Press, Princeton.
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F A. 2004. Testing the branch autonomy theory: a 13C/14C double-labelling experiment
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Montgomery R A, Chazdon R L. 2001. Forest structure, canopy architecture, and light
transmittance in tropical wet forests. Ecology 82(10): 2707-2718.
Morataya R, Galloway G, Berninger F, Kanninen M. 1999. Foliage biomasssapwood area and
volume relationships of Tectona grandis L.f. and Gmelina arborea Roxb.: silvicultural
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Press W H, Teukolsky S A, Vetterling W T, Flannery B P. 1992. Numerical recipes in C (2nd
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Putz F E, Parker G G, Archibald R M. 1984. Mechanical Abrasion and Intercrown Spacing.
American Midland Naturalist 112:24-28.
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Ritchie G A. 1997. Evidence for red: far red signaling and photomorphogenic growth
response in Douglas-fir (Pseudotuga menzii) seedlings. Tree Physiology 17: 161-168.
Rudnicki M, Lieffers V J, Silins U. 2003. Stand structure governs the crown collisions of
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Sprugel D G. 2002. When branch autonomy fails: Milton's Law of resource availability and
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Sterck F J. 1999. Crown development in tropical rain forest trees in gaps and understorey.
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Appendix

This manual is also complement with CD which contains some file as listed below:

! Simulation (*.s)
A full simulation file included the tree and plot data.

! Simulation data (*.txt)

Statistical data output is saved on this format

! Simulation setting (*.xml)

Predefined simulation setting is save on this format

! Tree Species (*.trs)

Tree species file is save on this file type with XML content format

! Hemiphot (*.hem)
Hemiphot image is save on this file type with XML content format