Potential Height Growth and Diameter Increment - 2014

Development of potential height growth and diameter
increment models for the parameterisation of an

individual tree growth model for Pinus elliottii
plantations in South Africa

Thesis presented in fulfilment of the requirements for the degree of
Master of Science in Forestry at the Faculty AgriSciences at Stellenbosch University
Supervisor: Prof Thomas Seifert
Co-supervisor: Prof Hans Pretzsch

Department of Forest and ood Science
Facult! of AgriSciences

April "#$%

&!

'erard (c)ard *indner
ii

Declaration

+! su&mitting this thesis electronicall!, - declare that the entiret! of the wor) contained
therein is m! own, original wor), that - am the sole author thereof .save to the e/tent
e/plicitl! otherwise stated0, that reproduction and pu&lication thereof &! Stellen&osch
1niversit! will not infringe an! third part! rights and that - have not previousl! in its entiret!
or in part su&mitted it for o&taining an! 2ualification3

Date: "4 Fe&ruar! "#$%

Cop!right 5 "#$% Stellen&osch 1niversit!
All rights reserved3

Stellenbosch University http://scholar.sun.ac.za
iii

Acknowledgements
First of all - would li)e to than) Prof3 Thomas Seifert for his support, mentorship, guidance
and valua&le input into this thesis3 The &alance &etween support and research freedom
allowed great personal self-development and greatl! improved m! s)ills and competencies
in Forest Science research and 'rowth and 6ield Science3
- would li)e to than) Prof3 Hans Pretzsch for initialising the pro7ect and his valua&le guidance
and support, especiall! during m! time in 'erman!3 -n this regard - would also li)e to than)
8r3 9alf 8oshammer who managed m! time in 'erman!, gave me practical guidance and
offered his support throughout3
Particular than)s also go to postgraduate colleagues who helped me along the wa! and Dr3
Stephan Seifert for his help with 9 programming applications and some valua&le code,
which was of great help to the stud!3
- would li)e to than) :omatiland Forests .:*F0, 6or) Tim&ers, 8ountain to ;cean Forestr!
.now Cape Pine0 and all of the particular people involved for their willingness to provide
data3 Further than)s go to the 8ensuration and 8odelling 9esearch Consortium .889C0 <
particularl! 8r3 He!ns :otze and 8r3 Trevor 8orle!, for pointing me in the right direction
for o&taining data for the stud!3
Personal than)s go to m! &rothers, +rian and +erndt *indner for their constant support and
discussions= +rian in particular for editing, programming and conceptual discussions3 Than)s
also to (smarie Scholtz for her love and support and also for insights and support into some
technical issues as well3 - am grateful to m! friends and famil!, particularl! m! parents, who
patientl! supported and encouraged me throughout the stud!3 8! appreciation is also
e/tended to m! colleagues at the Department of Forestr! and ood Science who made the
e/perience a most enriching one3
This stud! was partl! financed &! the >ational 9esearch Foundation .>9F0 within the scope
of the 'reen *andscapes Pro7ect3 -n particular - am grateful to the Department of Agriculture
Forestr! and Fisheries .DAFF0 for supporting me financiall! from undergraduate through to
postgraduate level3

iv

Abstract
-ndividual tree models, as opposed to stand models, have the potential to greatl! improve sensitivit!
of forest growth models to changing conditions such as silvicultural amendments, irregular stand
structures, etc3 -t was the purpose of this stud! to e/tend two su&-components of a (uropean
individual tree growth model to introduce individual tree growth modelling concepts in South Africa
using Pinus elliottii as a stud! species3 Two main o&7ectives were esta&lished: 8odelling the
potential height of stands across different site 2ualities and modelling diameter increment using a
potential modifier approach with a com&ination of competition indices that change in importance
according to the edaphic conditions of the site3
Potential height modelling used three steps in order to achieve this o&7ective3 The first was to
compare site inde/ models &ased on different model fitting techni2ues, namel! nonlinear least
s2uares, generalised nonlinear least s2uares and nonlinear mi/ed effects models3 The nonlinear
mi/ed effects model proved to &e superior in terms of achieving the principles of regression
assumptions and model fit for the data range o&served3 The second step was to fit potential height
using nonlinear 2uantile regression on o&served spacing trial height measurements3 This proved to
&e a ro&ust techni2ue a&le to capture potentials according to the defined Chapman-9ichards model
structure3 The final step was to use the predicted site inde/ as a site classification varia&le in order to
predict potential height3 hile some small deviation occurred, potential height seems to &e well
correlated to site inde/ and validation on selected sites suggested that site inde/ can &e used to
model potential height until a more sophisticated site classification model is used for future
improvement of the model3
Diameter increment modelling followed si/ ma7or steps in order to appl! the full parameterisation
methodolog! of an age-independent diameter increment model dependent on tree diameter and
competition3 Diameter increment potentials were fit using site inde/ as a predictor of the potential
height curves3 8ultiple competition indices were tested on two sites to o&tain a com&ination of two
indices, which can capture overtopping and local crowding effects3 Principle components anal!sis
and variance inflation factors calculation were applied to test for collinearit! &etween indices3
Suita&le com&inations were tested resulting in a com&ination of the ::* and *ocal +asal Area
competition indices3 Changing importance of the two indices were o&served on the two sites tested
indicating a shift in the mode of competition according to a water gradient3
These were com&ined in a deterministic potential modifier model, which mimic)ed competitive
stages over age= however the validation showed a s)ewed distri&ution, which was not sensitive to
stand densit! gradients3 A stochastic model was constructed to model variance from o&served
residual plots using linear 2uantile regression to determine &ounds for a truncated normal
distri&ution which generates random deviates for a predicted increment3 The stochastic element
significantl! improved the performance and sensitivit! of the model, however the model was still
not sensitive enough at ver! high and ver! low spacing densities3 All in all two )e! models for an
adaptation of an individual tree growth simulator to South African conditions were successfull!
demonstrated3 The two main o&7ectives were achieved= however some indicated improvements
could &e made, especiall! for the competition indices where the sensitivit! of competition to
changing resource limitation according to site and temporal scales needs to &e further investigated3
v

Furthermore, the full set of models for simulating individual tree growth still needs to &e applied3
;verall, as a methodological approach, the stud! outlined pro&lems and future improvements,
introduced new concepts and can serve as a guideline for future parameterisation of an individual
tree growth model3

vi

Opsomming
-n vergel!)ing met va)groeimodelle, het individuele-&oomgroeimodelle die potensiaal om die
sensitiwiteit van plantasiegroeimodelle vir veranderende omstandighede soos aanpassings in
&os)ultuur, onre?lmatige va)stru)ture, ensovoorts, drasties te ver&eter3 Die doel van hierdie studie
was om twee su&)omponente van @n (uropese individuele-&oomgroeimodel uit te &rei om
sodoende individuele-&oomgroei modellerings)onsepte in Suid-Afri)a &e)end te stel3 Pinus elliottii is
ge&rui) as studiespesie3 Twee hoofdoelstellings is &epaal3 (erstens, die modellering van hoogtegroei
potensiaal van opstande oor vers)eie vla))e van groeiple) )waliteit3 Tweedens, die modellering van
deursnee-aanwas deur ge&rui) te maa) van @n potensiaal matigings&enadering Apotential modifier
approachA met @n )om&inasie van )ompetisie-inde)se waarvan die &elangri)heid verander volgens
die edafiese toestande van die groeiple)3
Die hoogtepotensiaalmodellering &estaan uit drie stappe3 T!dens die eerste stap word groeiple)
&onniteitsmodelle vergel!) op grond van vers)illende modelpassingstegnie)e, naamli) nie-lineBre
minimum )wadrate, algemene nie-lineBre minimum )wadrate en nie-lineBre gemengde effe)
modelle3 *aasgenoemde het die &este gevaar in terme van die &eginsels van regressiemodelle asoo)
die mate waarin die model die waargeneemde data pas3 Tweedens is hoogtegroei potensiaal
gemodelleer deur nie-lineBre )wantielregressie op waargeneemde hoogtes van
spasi?ringse)sperimente toe te pas3 Die metode is ro&uust en in staat om potensiale volgens die
gedefinieerde Chapman 9ichards modelstru)tuur vas te vang3 *aastens is die voorspelde &onniteits
inde)s as @n groeiple) )lassifasie veranderli)e ge&rui) om sodoende die hoogtegroei potensiaal te
voorspel3 Alhoewel )lein afw!)ings voorge)om het, &l!) hoogtegroei potensiaal goed ge)orreleer te
wees met &onniteits inde)s3 1it validasie op gesele)teerde groieple))e &l!) dit dat &onniteits inde)s
ge&rui) )an word om hoogtegroei potensiaal te modelleer totdat @n meer gesofisti)eerde groeiple)
)lassifi)asiemodel &es)i)&aar is wat die model verder sal )an ve&eter3
Die volledige parametriseringsmetodie) van @n ouderdoms-onafhan)li)e deursnee-aanwas model
wat afhan)li) is van &oomdeursnee en )ompetisie &estaan uit ses hoof prosesse3 >ie-lineBre
)wantielregressie is ge&rui) om deursnee-aanwaspotensiale te pas vir vers)eie groeiple))e3 DiC is
ge)om&ineer met @n &onniteits inde)s om @n nuwe model te vorm waarmee hoogtegroeipotensiaal
)urwes voorpel )on word3 Daar is met veelvuldige )ompetisie-inde)se op twee groeiple))e
ge?)sperimenteer om @n )om&inasie van slegs twee inde)se te vind wat die effe)te van
oors)aduwing en plaasli)e verdringing )an vasvang, te vind3 Hoof )omponent analise APrinciple
components anal!sisD en variansie inflasie fa)tore &ere)ening Avariance inflation factors calculationD
is ge&rui) om vir )ollineariteit tussen die inde)se te toets3 'epaste inde)s)om&inasies is getoets3 @n
:om&inasie van die ::* en plaasli)e &asale oppervla)te A*ocal +asal AreaD )ompetisie-inde)se het
die &este resultate gelewer3 Die twee inde)se is as volg gesele)teer3 Eeranderings in die
&elangri)heid van el) van die inde)se is waargeneem op die twee toetspersele3 Dit dui op @n
vers)uiwing in die modus van )ompetisie afhangend van @n watergradi?nt3
Die twee inde)se is ge)om&ineer in @n deterministiese potensiaal matigings model wat die
)ompeterende stadiums oor ouderdom na&oots3 Ealidasie het egter @n s)ewe verdeling wat nie
sensitief vir opstandsdigtheidsgradi?nte is nie, gew!s3 @n Stogastiese model is ontwi))el om variansie
in die residuele grafie)e te modelleer3 *ineBre )wantielregressie is ge&rui) om grense vir @n
vii

afgestompte normaalverdeling wat ewe)ansige afw!)ings vir @n voorspelde aanwas te &epaal3 Die
stogastiese element het die prestasie van die deterministiese model mer)&aar ver&eter3 Selfs met
die stogastiese element, is die model egter steeds nie sensitief genoeg vir &aie ho? en &aie lae
opstandsdigthede nie3
Ter opsomming is twee modelle vir @n aanpassing van @n individuele-&oomgroeisimuleerder vir Suid-
Afri)aanse toestande su)sesvol gedemonstreer3 Die twee hoofdoelstellings is &erei)3 Daar is egter
steeds @n paar aangeduide ver&eterings wat aange&ring )an word3 Die sensitiwiteit van die
)ompetisie-inde)se op hulp&ron&eper)ings wat verander op grond van die ruimteli)e en temporale
s)ale moet veral verder &estudeer word3 Eerder moet die volle stel modelle wat &enodig word om
individuele-&oomgroei te modelleer nog toegepas word3 As @n metodologiese &enadering, het die
studie pro&leme uitgew!s en toe)omstige ver&eterings aangedui, nuwe )onsepte &e)endgestel en
)an dus dien as @n rigl!n vir toe)omstige parametrisering van individuele-&oomgroeimodelle3

viii

Table of Contents

Chapter $: -ntroduction and &ac)ground 3333333333333333333333333333333333333333333333333333333333333333333333333333 $-$
$3$ Pro&lem statement 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$
$3" +ac)ground and literature review 33333333333333333333333333333333333333333333333333333333333333333333333333333 $-"
$3"3$ Pinus elliottii plantations in South Africa 333333333333333333333333333333333333333333333333333333333333 $-"
$3"3" Forest growth modelling 333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-"
$3"3F Competition -ndices 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-%
$3"3% Competition s!mmetr! 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-%
$3"3G Eulnera&ilit! of forestr! to climate change 33333333333333333333333333333333333333333333333333333333 $-H
$3"34 Potential modifier approach 333333333333333333333333333333333333333333333333333333333333333333333333333333 $-H
$3"3H Silva 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$"
$3F ;&7ectives333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$F
$3F3$ Potential height model: 33333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$%
$3F3" Diameter increment model: 33333333333333333333333333333333333333333333333333333333333333333333333333333 $-$%
$3% The use of 9 in the stud! 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$%
Chapter ": Dataset description 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-$4
"3$ The correlated curve trend .CCT0 data 33333333333333333333333333333333333333333333333333333333333333333333 "-$4
"3" Triple S-CCT 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-"#
"3F >elder spacing trial 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-"#
"3% Permanent sample plots .PSP0 data 333333333333333333333333333333333333333333333333333333333333333333333333 "-"F
Chapter F: Site inde/ and potential height modelling 3333333333333333333333333333333333333333333333333333333 F-"G
F3$ -ntroduction 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"G
F3$3$ Site inde/ 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"G
F3$3" Potential height growth 33333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"G
F3$3F >onlinear regression assumptions 3333333333333333333333333333333333333333333333333333333333333333333 F-"G
F3$3% Chapter o&7ectives 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"4
F3" Step $: Site inde/ modelling333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"4
F3"3$ -dentification of dominant trees 3333333333333333333333333333333333333333333333333333333333333333333333 F-"H
F3"3" 8odel selection 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"I
F3"3F Dataset and trial Age 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"J
F3"3% Starting values: 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"J
i/

F3"3G >onlinear least s2uares 33333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-F#
F3"34 'eneralised nonlinear least s2uares 3333333333333333333333333333333333333333333333333333333333333333 F-F"
F3"3H >onlinear mi/ed effects model 333333333333333333333333333333333333333333333333333333333333333333333333 F-F"
F3"3I 8odel comparisons 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-FG
F3"3J >*8( final results .model selection0 3333333333333333333333333333333333333333333333333333333333333333 F-FH
F3F Step ": Potential height modelling 33333333333333333333333333333333333333333333333333333333333333333333333333333 %$
F3F3$ Description of the >*9K procedure 33333333333333333333333333333333333333333333333333333333333333333333 %$
F3% Step F: Prediction of potential height from Site -nde/ 333333333333333333333333333333333333333333333 F-%G
F3%3$ (ffect of stand densit! 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%G
F3%3" 9elationship &etween potential height and dominant height 333333333333333333333333333 F-%4
F3%3F Predictive e2uation 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%J
F3%3% Ealidation 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-G#
F3G Chapter conclusion 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-GG
Chapter %: 8odelling diameter increment in response to resource limitations and site
classification 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-G4
%3$ -ntroduction 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-G4
%3$3$ Dataset 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-GH
%3$3" Chapter outline 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-GH
%3" Step $: Site classification according water availa&ilit! and site inde/ 3333333333333333333333 %-GJ
%3F Step ": Determine the potential &ased on site conditions 333333333333333333333333333333333333333 %-4#
%3F3$ Comparison of sites 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-4#
%3% Step F: Fit various competition models 3333333333333333333333333333333333333333333333333333333333333333333 %-4F
%3%3$ Distance dependent competition indices 333333333333333333333333333333333333333333333333333333333 %-4F
%3%3" (dge effects 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-44
%3%3F Competition search radius .influence zone0 33333333333333333333333333333333333333333333333333333 %-44
%3%3% Performance of competition indices 3333333333333333333333333333333333333333333333333333333333333333 %-4J
%3G Step %: Selecting competition indices 333333333333333333333333333333333333333333333333333333333333333333333 %-H$
%3G3$ Earia&le selection 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-HF
%3G3" Principle component anal!sis 333333333333333333333333333333333333333333333333333333333333333333333333333 %-HG
%3G3F 9elative importance 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-HJ
%34 Step G: 1se C-Ls in a deterministic potential modifier e2uation 3333333333333333333333333333333 %-I"
%343$ ;&7ective $: -ncorporating the *+A competition inde/ 3333333333333333333333333333333333333 %-IF
/

%343" ;&7ective ": -ncorporating a water inde/ 333333333333333333333333333333333333333333333333333333333 %-I%
%343F 8odel &ehaviour 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-IG
%343% 8odel validation 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-IH
%3H Step 4: Create a stochastic model incorporating natural varia&ilit! 333333333333333333333333 %-II
%3H3$ -ncorporating natural variation 333333333333333333333333333333333333333333333333333333333333333333333333 %-II
%3I Chapter conclusion 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-JJ
Chapter G: Conclusion and recommendations 3333333333333333333333333333333333333333333333333333333333333333 G-$#"
G3$ Potential height modelling 333333333333333333333333333333333333333333333333333333333333333333333333333333333333 G-$#"
G3" Diameter increment modelling 33333333333333333333333333333333333333333333333333333333333333333333333333333 G-$#F
G3F Additions for model completion 333333333333333333333333333333333333333333333333333333333333333333333333333 G-$#F
G3% ;verall thoughts 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 G-$#%
Chapter 4: 9eferences 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 4-$#G
Chapter H: Appendices 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 H-$$$
Appendi/ A: >*8( random effects anova ta&le 3333333333333333333333333333333333333333333333333333333333 H-$$$
Appendi/ +: Eoronoi pol!gon increment relationship for the >elder and Tweefontein sites
respectivel! 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 H-$$F
Appendi/ C: ;&served and predicted D+H for the deterministic model 3333333333333333333333 H-$$G
Appendi/ D: Simulation steps for the deterministic model 33333333333333333333333333333333333333333 H-$$4
Appendi/ (: Simulation steps for the stochastic model 33333333333333333333333333333333333333333333333 H-$"#
Appendi/ F: Select e/amples of 9- Code 333333333333333333333333333333333333333333333333333333333333333333333 H-$"G

/i

Table of Figures
Figure $-$: H!pothesis on the relationship of plant size on growth rate in a given
stand with respect to the size s!mmetr! of competition3 Stands are usuall! in a
continuum &etween these e/tremes where light limitation result in size as!mmetric
relationships and size s!mmetric relationships where underground resource
limitations are prevalent3 S!mmetric competition occurs when competition is not
related to tree size .figure from Pretzsch and +i&er, "#$#03 333333333333333333333333333333333333 $-G
Figure $-": Figure illustrating two different t!pes of competition indices theoreticall!
more suited to overtopping and local crowding respectivel!3 333333333333333333333333333333333 $-4
Figure $-F: -llustration of the site factor model used in S-*EA, used as the precursor
to modelling potential height growth . Pretzsch et al3 "##"03 3333333333333333333333333333333333 $-J
Figure $-%: (ffect of competition on the modifier values of d&h and height3 From ()
and Du)e) $JI# 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$$
Figure $-G: Silva flow diagram and the potential height-age relation in S-*EA
predicted from site 2ualit!3 This curve is used for the simulation initialisation 33333 $-$F
Figure $-4: The diameter increment model function in S-*EA determined &! diameter
.D+H03 Predicted increment is then &ased on a modifier which ta)es competition into
account3 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$F
Figure "-$: Height measurements on the four CCT spacing trials showing a clear
stratification &etween sites 3333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-$I
Figure "-": Height measurements on the four CCT spacing trial indicating different
growth patterns and growth trends for different planting densities 333333333333333333333 "-$I
/ii

Figure "-F: FD plot of height growth trends in the CCT spacing trials with a linear
average response curve indicating little change &etween ma/imum height growth
&etween different stand densities 333333333333333333333333333333333333333333333333333333333333333333333333 "-$J
Figure "-%: FD plot of diameter growth trends in the CCT spacing trials with a linear
average response curve indicating significant change &etween height growth
&etween different stand densities 333333333333333333333333333333333333333333333333333333333333333333333333 "-"#
Figure "-G: >elder trial designs &ased on different spacing geometries3 >elder .$J4"03
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-"$
Figure F-$: Flowchart of site inde/ modelling section of this chapter .Step"0 33333333 F-"H
Figure F-": Dominant height modelling e/ample for the 8ac 8ac "J4Gspha plot with
red dots representing the dominant trees, the red and &lac) dashed lines
representing the dominant and mean height curves respectivel! 3333333333333333333333333 F-"I
Figure F-F: (/ample of an >*S fit on the eza "J4G plot 33333333333333333333333333333333333333 F-F#
Figure F-%: 9egression diagnostics for the eza "J4G plot 33333333333333333333333333333333333 F-F$
Figure F-G: Scatter plot matri/ of the relationship &etween three parameters of the
Chapman 9ichards e2uation for a model fit, showing significant correlation &etween
the parameters3 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-FF
Figure F-4: 9esidual plots of an e/ample dataset using different modelling techni2ues
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-F4
Figure F-H: Fitted dominant height curves for the CCT trials 333333333333333333333333333333333333 %#
Figure F-I: Fitted potential height curves for the CCT dataset for different stems per
hectare3 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %"
/iii

Figure F-J: Potential height of the highest CCT trial value .8ac, spha M $"%0 plotted
over PSP data of a wide range of sites, the &lue line is the potential of the CCT plot,
the red line represents the mean height of the PSP dataset 333333333333333333333333333333333333 %F
Figure F-$#: Site -nde/ values on different stand densities for the CCT dataset33333 F-%4
Figure F-$$: (/ample of potential and dominant height-age curves for the eza trial
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%H
Figure F-$": Potential height plotted over dominant height for all of the the CCT
dataset plots 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%I
Figure F-$F: Final parameterised model of potential height-age using S- as a
predictor 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%J
Figure F-$%: Deviation from the o&served potential height-age compared to the
potential height predicted e2uation 333333333333333333333333333333333333333333333333333333333333333333333 F-G$
Figure F-$G: 8edian deviation in percentage of the o&served and predicted potential
height curves 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-G"
Figure F-$4: Potential height curves plotted over PSP data of different classes3 The
red lines represent the predicted potential height for the upper &ound of the S-
classes presented a&ove3 The top left image presents all of the data with $G, "#, "G
and F# S- predicted potentials 333333333333333333333333333333333333333333333333333333333333333333333333333333 F-GF
Figure F-$H: Fitted predicted potential height curves fitted on selected independent
PSP data 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-G%
Figure %-$: D+H -ncrement - D+H scatterplot on the 8ac 8ac CCT trial, showing
decreasing linear gradient over age 3333333333333333333333333333333333333333333333333333333333333333333333 %-G4
Figure %-": Flowchart of the chapter outline showing wor)ing steps of the
methodological approach used in the stud! 333333333333333333333333333333333333333333333333333333333 %-GI
/iv

Figure %-F: Fitted potential increment curves for the four sites considered for
increment potential estimation 3333333333333333333333333333333333333333333333333333333333333333333333333333 %-4$
Figure %-%: Potential increment over D+H curves parameterised from the CCT trial
data= the different curves represent different S- values 3333333333333333333333333333333333333333 %-4F
Figure %-G: Eoronoi pol!gons calculated for the >elder spacing trial as an e/ample 3 %-
44
Figure %-4: >egative Correlation of the *+A competition inde/ with diameter
increment at different measurement !ears .ages0 using different competition search
radii, the correlation was multiplied &! -$ for illustrative purposes3 3333333333333333333333 %-4H
Figure %-H: *inear regression of the optimum search radius over dominant height 333 %-
4J
Figure %-I: 9elationship of diameter increment and the competition indices fitted in
the two spacing trials used for this stud! 33333333333333333333333333333333333333333333333333333333333333 %-H#
Figure %-J: Pairwise scatterplot matri/ of the various competition indices against
each other in the >elder Trial 3333333333333333333333333333333333333333333333333333333333333333333333333333333 %-H"
Figure %-$#: Pairwise scatterplot matri/ of the various competition indices against
each other in the Tweefontein Trial 3333333333333333333333333333333333333333333333333333333333333333333333 %-HF
Figure %-$$: PCA &iplot of the varia&le plotted in the transformed space of the first
two principle components in the >elder trial 33333333333333333333333333333333333333333333333333333333 %-HH
Figure %-$": PCA &iplot of the varia&le plotted in the transformed space of the first
two principle components in the Tweefontein trial 3333333333333333333333333333333333333333333333 %-HH
Figure %-$F: 9elative importance graphs using different methods for the Tweefontein
spacing trial 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-I$
/v

Figure %-$%: 9elative importance graphs using different methods for the >elder
spacing trial showing improved ::* importance as compared to the Tweefontein site
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-I"
Figure %-$G: -llustration of the potential modifier approach on the two spacing trials,
with the top right hand diagram representing the change of the modifier over the
size of competition 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-I4
Figure %-$4: Comparison &etween the o&served .red &ars0 and the simulated
diameter .D+H0 represented as a distri&ution of "3Gcm diameter classes3 The mean
D+H for the site is represented in the notched &o/plot3 This showed a s)ewed
prediction grouped around a narrower D+H &and 333333333333333333333333333333333333333333333333 %-II
Figure %-$H: 9esidual plot of the predicted values of the spacing trials 33333333333333333 %-IJ
Figure %-$I: GN and JGN linear 2uantile regression lines which represents the upper
and lower &ounds for the truncated normal distri&ution 33333333333333333333333333333333333333 %-J#
Figure %-$J: Predicted residual generated from a random deviate &etween two
&ounds .Figure $I0 &ased on a normal distri&ution 33333333333333333333333333333333333333333333333 %-J$
Figure %-"#: Se2uential process of generating random deviation, from plotting
residuals .top left0, predicting &ounds .top right0, generating random deviation
.&ottom left0 superimposed on the residual plot .&ottom right0 333333333333333333333333333 %-J"
Figure %-"$: ;&served and predicted scatterplots for the Tweefontein SS-CCT spacing
trial, with &lac) points representing the o&served and green representing the
predicted values3 The left hand image represents the scatter of the average model <
with the linear 2uantile in the top right, the &ottom left and right images represent
the scatter of the model with added modelled random variance 33333333333333333333333333 %-JF
/vi

Figure %-"": ;&served and predicted scatterplots for the *ottering >elder spacing
trial, with &lac) points representing the o&served and green representing the
predicted values3 The top right image shows the deterministic model, the &ottom left
and right images represent the scatter of the model with added modelled random
variance 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-J%
Figure %-"F: 9esidual scatter of the added random variance model for the
parameterised sites 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-JG
Figure %-"%: 9esidual scatter overlain on the o&served increment scatter of the
added random variance model for the parameterised sites3 The &lac) points
represent the o&served and the green points represent the predicted values from
the stochastic model3 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-J4
Figure %-"G: ;&served .red &ars0 vs3 simulated .&lue &ars0 for the >elder trial with
random deviation added at each point3 The model shows a clear overall
overpredicition of D+H, however with an improved distri&ution compared to the
model without deviation .Figure %-$403 33333333333333333333333333333333333333333333333333333333333333333 %-JH
Figure %-"4: Deviation of predicted average diameter increment for a more realistic
of planted stand densities for a plantation industr! setup in the >elder trial 33333333 %-JJ

/vii

Tables
Ta&le "-$: CCT unthinned series trial summar! 33333333333333333333333333333333333333333333333333333 "-$4
Ta&le "-": Thinning in advance of coemptition for weed control in the CCT trial data
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 "-$H
Ta&le "-F: 1nthinned SSS-CCT spacing trial desing 333333333333333333333333333333333333333333333333 "-"#
Ta&le "-%: 8easurement intervals for the *ottering >elder trial 333333333333333333333333333 "-""
Ta&le "-G: >elder spacing trial plot num&ers .rings0 with their corresponding stems
per hectare, &ased on the radii and arc distances3 333333333333333333333333333333333333333333333333 "-"F
Ta&le F-$: 9andom effect tests for the nonlinear mi/ed effects model3 The column
Aparameter chosenD indicates which parameters used as an additional random effect
in the model3 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-F%
Ta&le F-": Count of &est fit random effects models 3333333333333333333333333333333333333333333333 F-F%
Ta&le F-F: Anova and 98S( comparisons of different modelling fitting methods on
the eza dataset 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-FH
Ta&le F-%: Fitted S--age models for the CCT trials 33333333333333333333333333333333333333333333333333333 FJ
Ta&le F-G: Potential height fits &! plot for the four spacing trials 33333333333333333333333333333 %%
Ta&le F-4: Potential height - dominant height gradient 33333333333333333333333333333333333333333 F-%I
Ta&le F-H: Final model parameterised on the pooled CCT trial datasets from (2uation
F-% 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-G#
Ta&le %-$: Classification of the sites according to the FA;-1>(P classification and S-3
The Tweefontein and 8ac 8ac trials used the same weather station3 333333333333333333 %-GJ
Ta&le %-": Potential increment model coefficients according to (2uation %-$3 333333 %-4"
Ta&le %-F: Coefficients of the potential increment model .(2uation "0 using site inde/
and d&h as predictor varia&les 333333333333333333333333333333333333333333333333333333333333333333333333333333 %-4"
/viii

Ta&le %-%: -llustration of the different competition indices used in this stud! .Seifert
et al3 in review0, i refers to the central tree, j refers to the competitor trees3 8odels
shown &elow are discussed in more detail in te/t &elow3 3333333333333333333333333333333333333 %-4%
Ta&le %-G: Correlation of the *+A competition inde/ at different ages of the >elder
trial with the resulting search radius size included 333333333333333333333333333333333333333333333333 %-4I
Ta&le %-4: *inear regression coefficients of the optimum search radius &ased on
dominant height 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-4J
Ta&le %-H: *inear models coefficients of the s2uare root transformation of diameter
increment using the respective competition indices 333333333333333333333333333333333333333333333 %-H%
Ta&le %-I: Full linear model of the s2uare root diameter increment transformation
using all of the C-Os as regressor varia&les 333333333333333333333333333333333333333333333333333333333333 %-HG
Ta&le %-J: -mportance measures of the principle components 33333333333333333333333333333 %-H4
Ta&le %-$#: Principle component loadings of the respective principle components 33 %-
H4
Ta&le %-$$: *inear model coefficients for the com&inations of the competition indices
33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-HJ
Ta&le %-$": 9elative importance proportions .e/planation contri&ution0 of the ::*
and *+A indices respectivel! using different importance measures 3333333333333333333333 %-I#
Ta&le %-$F: Coefficients of the diameter increment potential modifier formula
.(2uation %-G0 3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-IF
Ta&le %-$%: Anova comparison if (2uation %-G with ::*, *+A and &oth indices
included in 8odel $, " and F respectivel! 3333333333333333333333333333333333333333333333333333333333333 %-I%
Ta&le %-$G: Coefficients of the diameter increment potential modifier formula
.(2uation %-H0 incorporating the water inde/ 3333333333333333333333333333333333333333333333333333333 %-I%
/i/

Ta&le %-$4: Anova comparison of the diameter increment model with .8odel$0 and
without .8odel "0 the water inde/ 33333333333333333333333333333333333333333333333333333333333333333333333 %-IG
Ta&le %-$H= Anova comparison of the diameter increment model with .8odel$0 and
without .8odel "0 the water inde/ &! randoml! su&setting data from the >elder trial
to match the num&er of o&servations in the Tweefontein trial 33333333333333333333333333333 %-IG
Ta&le %-$I: *inear 2uantile regression coefficients of #3#G and #3JG tau values
representing the upper and lower &ounds of simulated residual prediction 333333333 %-J#
Ta&le %-$J: Average of o&served and predicted values for the different >elder plots,
showing clearl! that the model underperforms at e/treme densities 3333333333333333333 %-JI

//

Table of Equations

(2uation $-$ 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-H
(2uation $-" 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$#
(2uation $-F 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 $-$$
(2uation F-$ 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"G
(2uation F-" 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-"I
(2uation F-F 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-FH
(2uation F-% 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 F-%G
Equation 4-1 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-4#
(2uation %-" 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-4"
(2uation %-F 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-H%
(2uation %-% 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-HG
(2uation %-G 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-IF
(2uation %-4 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-I%
(2uation %-H 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-I%
(2uation %-I 333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 %-J$
$-$

Chapter 1: Introduction and background

1.1 Problem statement
Due to the fast growing, even-aged and single-species nature of the local plantation stands,
forest growth modelling in South Africa has, for good reason, mostl! &een confined to
computer implanted stand models and !ield ta&le predictions .:otze et al. "#$"03 These
models have proven to pro7ect stand volume with high accurac! and are well suited to the
homogenous situation of the stands applied3 However, stand models li)e these have
limitations3 Top-down approaches have to model changes and distri&utions, or in other
words have to decompose the stand volume again to o&tain individual tree volumes3 Stand
models further are not designed to model irregular stand structures or deviations from
t!pical silvicultural regimes3 -ndividual tree growth models, following a &ottom-up approach
that models interactions &etween a mosaic of individual trees .8unro $JH%0, offer an
alternative to stand modelling3 Due to their interaction and feed&ac) loops &etween stand
structure and growth the! are more fle/i&le to changes in the stand structure and prove
ver! useful for scenario anal!sis, simulation for research purposes and academic tools
.Pretzsch et al3 "##"03
Competition indices are a )e! element of individual tree models since the! descri&e the
interaction &etween the individual trees in the stand3 Different indices capture different
modes of competition, which is related to the specific resource limitation influencing the
interactions among the trees as shown &! Seifert et al. .in review03 This also feeds &ac) to
the interaction &etween trees of different dimensions3 -n predominantl! light limiting
environments, overtopping of the crowns of the trees cause the competition of the trees to
&ecome size-as!mmetrical, where larger trees &enefit disproportionatel! to their size3 hen
edaphic resources such as nutrients and water &ecome more limiting the size s!mmetr!
shifts to situations where trees &enefit proportional to their size .Schwinning and einer
$JJI03 Competition models should &e a&le to capture the varia&ilit! and gradient &etween
these two e/tremes3
-n this stud! an individual tree modelling approach was underta)en for Pinus elliottii
plantations in South Africa as an initial attempt to parameterise a growth model following
the structure of an e/isting (uropean growth simulator called S-*EA .Pretzsch et al3 "##"03
S-*EA was parameterised for central (uropean growth conditions, which are predominantl!
light limited3 That made some model changes necessar! in order to adapt the simulation
approach to predominantl! edaphic limited sites in South Africa3 Two aspects of the model
were addressed: the potential height modelling re2uired for the simulation initialisation, as
well as diameter increment modelling3 ith application to South African forest inventor!
$-"

standards in mind, potential height predicted from site inde/ was modelled3 For the
development of diameter increment models, different competition indices were com&ined
in order to capture the varia&le nature and shift of resource limitation and competition
mode3

1.2 Background and literature review
1.2.1 Pinus elliottii plantations in outh !frica
Pinus elliottii .(ngelmann0, commonl! )nown as slash pine, is an introduced species grown
t!picall! in even-aged commercial plantation forests in South Africa3 -t is indigenous to the
South (astern 1nited states= found predominantl! in the coastal plains of >orth and Central
Florida, although its range e/tends into neigh&ouring states as well .Po!nton $JHJ03 -n South
Africa, it has a relativel! long histor! of use in the commercial forestr! sector, with seeds
first imported in $J$4 and e/tensive e/pansion occurring since3
-n South Africa, Pinus elliottii has a ver! wide planted range in &oth the summer and all-!ear
rainfall regions, including a ver! wide altitudinal gradient3 -t is )nown as a hard!, relativel!
slow growing species that is adapta&le to man! different site conditions .du Toit "#$"03 The
thic) outer &ar) and itLs specific &ar) structure also ma)es it one of the most fire resistant
species .;dhiam&o et al. "#$%0, allowing it to &e ameliora&le to preventative under canop!
&urning and use as a &uffer in fire prone areas3
This species was chosen for this thesis due to its representation in almost all of the growing
regions in South Africa3
1.2.2 "orest growth modelling
Although man! modelling approaches e/ist, in this chapter three main modelling
approaches are mentioned: statisticall! &ased stand models and individual tree models and
process &ased models3
Stand models represent the whole stand as a unit and do not consider individual tree
interactions for model construction or parameterisation3 These growth models usuall! ma)e
use of varia&les such as stems per hectare .SPHA0, &asal area .+A0 per hectare and dominant
height .Eancla! $JJG, :otze et al. "#$"03 Stand models can model individual tree or
individual tree classes of diameter at &reast height .D+H0 for e/ample &! modelling
distri&utions, e3g3 :assier .$JJF0, in a t!pical top down approach3 +! com&ining stand ta&le
pro7ection methods with the stand level model approach, pro7ection from an o&served
inventor! into the future can provide accurate stand ta&le details .Corral-9ivas et al. "##J0
-ndividual tree models use information of individual trees in the simulation and model
prediction of tree growth, and re2uire at least the size of ever! tree in a stand and model
interactions &etween the trees in a mosaic in the stand .Pretzsch et al3 "##", Eancla! $JJG03
$-F

The spatial position of the individual trees is an optional parameter included depending on
the structure of the model3 Competition indices are often noted as distance dependent or
distance independent competition indices .Pretzsch "##J03 hile statistical individual tree
models have the advantage to &e sensitive to irregular tree distri&utions for e/ample due to
insect damage, wind or snow &rea)age or inappropriate silvicultural practice .Ac)erman et
al. "#$F0 the! share a ma7or trait with statistical stand models: The! are strictl! spea)ing
onl! valid in the range of their parameterisation3 (/trapolations must &e done with care,
which limits their application in pro7ections during transitional stages such as the
e/perienced climate change3
(coph!siological process &ased models do also follow the individual tree .e3g3 9Ptzer et al3
"#$"0 or stand .*ands&erg and aring $JJH0 paradigm3 +ig-leaf stand models such as FP'
.*ands&erg and aring $JJH0, that ma)e use of mechanistic processes, and allometric
relationships to model resource allocation on a stand level have &een successfull!
parameterised for some South African tree species .D!e et al3 "##%03 Process &ased models
offer superior climate sensitivit!, since the! predict growth from the &asis of
ecoph!siological processes .Awhite-&o/D approach03 1nfortunatel!, developing mechanistic
process models tends to &e an e/tremel! complicated and time-consuming tas) due to the
comple/ nature of these processes, and these models are often parameterised from intense
measurements of a few sites .Pretzsch "##J, 9Ptzer et al3 "##J03 Further limitations of the
mechanistic process models, in comparison to currentl! applied statistical models, are that
the! lac) the accurac! and practical output options such as log classes, harvesting costs and
wood 2ualit! considerations, necessar! for decision s!stems to support forest management
on a commercial scale3 However, this ma)es them currentl! more suited as research tools3
H!&rid models represent a compromise &etween empirical models, such as the individual
tree and stand models mentioned previousl!, and process &ased models, &! estimating
productivit! in relation to primar! factors .Dzierzon and 8ason "##4, Pretzsch "##J0 and
com&ining a solid forestr! output with increased climate sensitivit!3
Currentl!, growth and !ield modelling in the South African plantation industr! is
characterised &! A&lac) &o/D statistical stand models, which are reasona&l! accurate, &ut
una&le to cater for changing site conditions, and are in danger of &ecoming less useful due
to the environmental changes &rought a&out &! climate change .Pretzsch "##J03 The stand
models currentl! in use are also not designed for the comple/ities of intra-specific
competition in even-aged, single species plantations under changing conditions or stress3
This is a ma7or concern in the climate change conte/t, since statistical models are a&le to
model growth onl! within a range or close to the conditions under which the measurements
for the model were made as pointed out &efore3 (/trapolation &e!ond this parameterisation
range could lead to false conclusions3
-ndividual tree growth models are a&le to account for changes to stand structure, which
occur due to mortalit!, mechanised row removal, etc3 Changes to silvicultural regimes, such
$-%

as changing planting or thinning densit!, age mi/ture, etc3, are easier to model &! virtue of
the &ottom up approach ta)en to individual tree interactions and competition anal!sis
.Pretzsch "##J03 Prefera&l! the! should have certain climate sensitivit! in a h!&rid approach3
1.2.# Competition Indices
There are different competition indices .C-Ls0 applied in individual tree modelling, position
dependent and position independent &eing the two ma7or distinctions3 hile position
independent C-s onl! use the relative size of a tree in comparison to other trees in the
stand= position dependent competition indices calculate competition &ased on the e/plicit
positions of the trees in relation to each other3 Firstl! the neigh&ouring trees that compete
with the central tree are determined &ased on their position and whether the! would
influence the tree in 2uestion3 ;nce the relevant neigh&ours have &een found, the strength
of the competition for each of the trees and their effect on that tree is determined3
hen stands are homogenousl! structured, position independent indices do not differ from
position dependent indices significantl!= however the! are not deemed fle/i&le and accurate
enough to capture irregularit! in the stand, thus position dependent models are &etter
suited to e/trapolating across a &road range of conditions and stand structures .Pretzsch
"##J03
8an! methods e/ist for the determination of the competitor trees3 Fi/ed radii can, for
e/ample, &e defined around the central tree3 All trees with a distance less than the radius
awa! from the central tree are identified as competitors, as in the case of Heg!i .$JH%0 who
used a radius of F3#%Im .$#ft03 Fi/ed radii have severe disadvantages though as the! are
onl! ade2uate for certain sizes of trees under a specific competitive circumstance .Pretzsch
"##J03 The search radius would have to ad7ust for tree size or tree age for instance3
The ne/t step in calculating a position dependent C- would &e to determine the strength of
the competition determined from specific attri&utes of the trees such as diameter, height,
crown size, or a search crown3
1.2.$ Competition s%mmetr%
Competition s!mmetr! refers to a plant population where the size of a plant in competition
to other plants determines its relative competitive advantage over neigh&ouring plants
.Schwinning and einer $JJI, Stoll et al. "##", ichmann, "##$03 Size s!mmetr! of
competition can simplisticall! &e grouped into size as!mmetric, size s!mmetric and
s!mmetric competition3 This point is illustrated in Figure 1-1.
$-G

Figure 1-1 !"pot#esis on t#e relations#ip of plant si$e on growt# rate in a gi%en stand wit# respect to t#e si$e s"mmetr"
of competition. &tands are usuall" in a continuum between t#ese e'tremes w#ere lig#t limitation result in si$e
as"mmetric relations#ips and si$e s"mmetric relations#ips w#ere underground resource limitations are pre%alent.
&"mmetric competition occurs w#en competition is not related to tree si$e (figure from )ret$sc# and *iber+ ,-1-..
-n forest communities growth is either size as!mmetric when dominant or larger plants
&enefit disproportionatel! to their size or size s!mmetric where plants &enefit proportional
to their size .Schwinning and einer $JJI, ichmann "##$03 The theor! &eing that in light
limited circumstances < as!mmetric competition is more prevalent &ecause light is a
directional resource, where dominant trees not onl! gain &ecause their canopies are larger
and a&le to capture more sunlight, &ut also shade out their competitors giving those trees a
distinct advantage disproportionate to their size3 -n more size s!mmetric circumstances,
edaphic factors .water or nutrients0 are usuall! limiting and therefore, since these
components are not as strictl! spatiall! dependent, the competition is s!mmetric with size,
meaning larger trees &enefit proportional to their size as the! are a&le to o&tain more
resources3
This phenomenon can act on two scales3 ;ne is where a site inherentl! has certain
characteristics, for e/ample an ample water suppl! and is dominated &! size as!mmetric for
instance3 The mode of competition can also var! with time, either seasonall! or &etween
different !ears, for instance in drought !ears or !ears of a&ove average rainfall3 ichmann
."##$0 found that in the same sites for different !ears, trees in their respective stand
d!namics can actuall! shift &etween these two t!pes of competition mode3
Silvicultural regimes can &e catered to the specific mode of competition in productive forest
stands3 -n predominantl! light limited stands, Athinning from a&oveD is applied, where
certain trees with large canopies are removed to allow for more light to reach neigh&ouring
trees, which can result in overall higher productivit!3 -n more size s!mmetric and water
$-4

limiting circumstances, Athinning from &elowD is mostl! practiced, where&!
underperforming suppressed trees or smaller trees are removed to allow space and &oost
growth for larger, &etter performing neigh&ouring trees which results in optimum size and
volume growth .Pretzsch "##J0
-ndividual tree forest growth models rarel! cater for these comple/ities of the mode of
competition .Pretzsch and +i&er "#$#03 ;ne option would &e to com&ine different
competition indices under such different sites .Figure 1-,0, with the relative strength of each
inde/ changing for the different nature of the sites < i3e3 one competition inde/ would
account more for competition &etween light, while another would account for &elow
ground competition for resources .e3g3 soil water0 3

Figure 1-, Figure illustrating two different t"pes of competition indices t#eoreticall" more suited to o%ertopping and
local crowding respecti%el".
As will &e shown in this thesis, parameterisation of such models re2uire an ade2uate
num&er of sites of different average resource conditions, and longitudinal data to capture
temporal changes as well, ma)ing these t!pes of modelling strategies difficult to
parameterise3 However, the value of these t!pes of models would &e in their a&ilit! to cater
for changing climatic conditions and their a&ilit! to ad7ust silvicultural regimes specificall! to
sites &ased on their inherent resource limitation3
-n South Africa the commercial plantation forest environment is predominantl! water
limited with ade2uate light suppl!, so water or edaphic limitations are usuall! prevalent,
leading to the h!pothesis that growth is more size s!mmetric3 However, it is not )nown at
which point water is not limit an!more and light &ecomes a limitation .if such sites e/ist0,
and furthermore whether this changes seasonall! or annuall! during different climatic
weather conditions3
$-H

1.2.& 'ulnerabilit% of forestr% to climate change
Currentl!, the outcome of climate change in South Africa, and specificall! the area under
afforestation, is still uncertain .ar&urton and Schulze "##403 The predicted effect on
precipitation and temperature is diverse .ar&urton and Schulze "##40= some regions ma!
e/perience increased precipitation, while others e/perience drier conditions3 Temperature
in general is predicted to increase < &ut with var!ing levels in different regions3
The impact of climate change is thought to have su&stantial effects on the pest and disease
occurrences and out&rea)s, due to shifts in the climatic gradient and the e/pansion of pests
and diseases into new environments .van Staden et al. "##%03 >ew regions for forest growth
ma! also &ecome availa&le due to the reduction of frost occurrences and a shorter frost
season .ar&urton and Schulze "##40= in particular the high-altitude high rainfall sites of the
Dra)ens&erg and the Highveld regions of South Africa3
'enerall!, the effect on plantation forestr! is thought to &e severe, due to the long planning
horizons that are characteristic of forestr! and vulnera&ilit! of plantations in the current
sites, man! of which are on the marginal scale of production .Fair&an)s and Scholes $JJJ,
ar&urton and Schulze "##403
-mproved predictive models and decision support s!stems will &e necessar! to &e a&le to
adapt to such changes, &! allowing proactive management and anticipating e/pected
climate outcomes3 For this to &e realised, a high level understanding of forest growth and
development under a range of conditions is necessar! .Seifert et al. in press03 Due to the
significant potential impact of climate change on forestr! and the relative speed at which it
is developing, it is clear that the time period for response, especiall! for an industr!
dependent on long rotations, is e/tremel! short3 +efore an! ma7or adaptive and reactive
approaches can &e made, a significant advance in the understanding of the growth of South
African forests under a wide range of site conditions is necessar!3
1.2.( Potential modifier approach
The potential modifier method is an approach to controlling individual tree growth in a
simulation model3 -n this approach, an assumed potential increment is o&tained, usuall!
from potential height-age or diameter-age curves of the upper &oundar! lines of a given site
.Pretzsch "##J0, which then represents the growth of a tree in the a&sence of competition3
The real or predicted tree growth .i
pred
0 is o&tained &! multipl!ing this potential growth .i
pot
0
&! a modifier .mod.0, which reduces the potential growth .Equation 1-103

Equation 1-1

The modifier is a representation of competition state of the individual and has a value of
&etween # .for e/treme competition0 and $ .for no competition03 This competition is
$-I

e/pressed &! C-, which 2uantifies the competitive status of trees3 The competition status is
then included into a modifier function which scales the competition appropriatel!3
Potential )rowth
Potential growth is defined as the ma/imum level of production possi&le for a tree or stand
under a given state of optimal growing conditions .9eed et al. "##F03 This is an important
part of man! model components, as it represents the starting point for growth modelling
&efore the real growth is determined &! the modif!ing factors3 Determining the potential
growth is commonl! seen as a pro&lematic component, &ecause it is often difficult to
o&serve .+ragg "##$0, and presents further pro&lems when deciding on a definition of
potential growth3
Potential height is often used as a starting point to characterise the potential growth in a
stand or single trees3 The &enefit of using the height to determine the potential growth is
that dominant stand height can &e used, or is closel! lin)ed to a predetermined potential, as
it is not strongl! affected &! thinning .9itchie and Hann $JJ#03 8an! forest inventor!
s!stems alread! measure dominant height and thus the information is often readil!
availa&le3
The QA+;A model series .+ot)in et al3 $JH"0, a precursor to most >orth American gap
models, uses inferred leaf area for its calculation of ma/imum height and diameter in its su&
model A'9;D3 The individual tree-&ased growth simulator S-*EA .Pretzsch et al3 "##"0 on
the other hand, incorporates a site model, determined form a predefined list of site
conditions, resulting in a site factor .Figure 1-/0, allowing determination of the potential
height growth of a single trees through the use of a Chapman 9ichards t!pe e2uation < the
&asis for further growth calculations in S-*EA3

$-J

Figure 1-/ 0llustration of t#e site factor model used in &012A+ used as t#e precursor to modelling potential #eig#t growt#
( )ret$sc# et al. ,--,..

The site dependent potential growth can &e determined &!:
Defining and measuring a top percentage of trees under o&served conditions
1sing open grown trees
Appl!ing treatments to stands to provide conditions for optimal growth3
The potential growth ma! &e o&tained &! selecting a predefined top percentage of trees
representing a ma/imum growth range, usuall! from an e/tensive data&ase reference, for
e/ample in S-*EA .Pretzsch et al. "##"03 This can &e useful as it represents realistic, o&served
values for practical forest management as these values are often o&tained from large
data&ases of repeated measurements .sample plots, etc30 and, as mentioned previousl!, are
often alread! measured in man! forest inventor! s!stems3 Eancla! .$JJG0 suggested that
one possi&le pro&lem with this approach is that the estimates ma! sometimes select for
measurement errors rather than real growth3
The potential growth ma! also &e determined &ased on open grown trees3 +ot)in et al.
.$JH"0, including other gap models, used this definition to determine ma/imum growth for a
forest gap model3 This method is in man! wa!s theoreticall! sound as it represents a
competition-free state, &ut it has some limitations as it is often ver! difficult to find open
grown trees in realit!, especiall! for frost intolerant species .+ragg "##$0 and in particular
shade tolerant &road-leaved species will not show a ma/imum height growth in a solitar!
state &ut rather grow e/tensive lateral crowns .1hl et al. "##403 So the use of solitar! trees
might &e restricted to frost resistant pioneering species that have a clear acroton! in their
growth pattern3
$-$#

(daphic limitations on their own are often used to determine the potential3 The >orth
American gap model QA+;A reduces the ma/imum height and diameter formed under
optimal conditions with modifications made for shade tolerance, soil 2ualit!, and average
climate .+ot)in et al. $JH"03
9eed et al. ."##F0 used a different approach to determine the potential growth .height and
diameter0 for ucalyptus globulus in Portugal &! opting to eliminate nutrient and water
limitations &! fertilisation and irrigation3 The potential height or diameters were then
modelled &! using the cumulative air temperature heat unit .not descri&ed here0 using a
modified Chapman 9ichards t!pe e2uation

Equation 1-,
here:

This approach was ver! successful in determining the potential growth and was uni2ue in
the sense that it tried to create and parameterise the model according to optimal conditions
created &! removing &elowground limitations to growth, although modifiers were not
developed for a feasi&le model and a large amount of information regarding am&ient
temperature was necessar!3 The added &enefit of such an approach is that it can o&serve
and then model responses for predefined treatments and conditions .e3g3 water suppl!,
stand nutrition, etc303 However, o&taining a full range of such conditions and separating
response factors could &e pro&lematic3
The *odif%ing "actors
The modifier is &asicall! a reduction factor, which represents competition or an! other
limitation to growth, e3g3 light, water, C;
"
, etc3 .Porte and +artelin) "##"03 Theoreticall!,
these factors are usuall! &ased on the assumption descri&ed &! *ie&igLs *aw of the minimum
which states that the resource that is in the shortest suppl! will most affect the growth rate
of the plant3
These multipliers are t!picall! e/ponential in form, especiall! under high competition .()
and Dude) $JI#03 Diameter and height responses to competition, and their manifestation in
the modifier response, are usuall! different .Seifert "##F03 Figure 1-4 shows the common
form of this response3
$-$$

Figure 1-4 Effect of competition on t#e modifier %alues of db# and #eig#t. From Ek and Dukek 134-
Competition is a common varia&le used for determining the modifier3 S-*EA uses a
com&ination of competition indices and crown dimensions on the individual tree for &oth
height growth and &asal area growth .Pretzsch et al3 "##"03

Equation 1-/

here: zh is potential height growth, CSA is the crown surface area, ::* is the competition
inde/, >D-ST is a measure of the centre of competition from the stem centre of the su&7ect
tree and :8A is a conifer-&roadleaf tree neigh&our effect3
-n this wa! light limitation with regards to competition is ta)en into account, &ut in the site
model .which determines the potential growth0 S-*EA ta)es into account a variet! of site
conditions such as mean and minimum temperature, soil nutrient suppl!, C;
"
, soil water
retention, etc3 which gives the model a complete structure with added sensitivit! to site
changes such as glo&al climate change .Porte and +artelin) "##"03 Thus while not including
these factors e/plicitl! as modif!ing factors, the potential is determined, with competition
doing the rest, resulting in a simplified model structure without the interactions &etween
competition and site conditions3
-n the growth simulator (F-8;D", :omarov et al. ."##F0 used a slightl! different approach,
focussing on tree nutrition in &oreal forests, where&! each tree occupies a certain space
a&ove and &elow ground in a Asingle plant ecos!stemD3 -n this case the focus was on
nutrient limitations with a comple/ set of soil nutrient models, primaril! &ecause the &oreal
forests in the stud! were highl! dependent on nitrogen availa&ilit!, with light as a secondar!
growth limitation, which usuall! comes into pla! in su&-dominant trees .Chertov $JJ#,
:omarov et al. "##F03 This soil fertilit! &ased approach is rare, especiall! at its rate of
sensitivit! .Porte and +artelin) "##"03
$-$"

1.2.+ ilva
The distance dependant individual tree forest growth simulator S-*EA, has &een successfull!
implemented in 'erman! and other (uropean forests, and provides the fle/i&le, high level
understanding and application to forest growth necessar! to predict changes in forest
growth under various site conditions and climate change scenarios .Pretzsch et al. "##",
Pretzsch "##J03
As a conse2uence of its individual and full! spatial model approach S-*EA has proven to &e a
versatile tool for prediction of forest growth3 -t is for instance currentl! used &! the +avarian
State Forest (nterprise one of the &iggest forest owner in Central (urope as a standard tool
for sustaina&ilit! planning3 S-*EA has proven its worth as a tool for scenario simulations in
order to optimise silvicultural thinning regimes in a variet! of applications, including long
term sustaina&ilit! planning, wood 2ualit! prediction .Seifert and Pretzsch "##%0, pest
management .Seifert "##H0, &iomass prediction, etc3 S-*EA is &eing e/tensivel! used for
practical growth modelling and application for forestr!, it is used as an education tool,
scenario anal!sis, climate change pro7ections and visualisation for virtual forest stands for a
wide range of applications3
Parameterisation of this model though, has not !et &een performed in a South African
forest conte/t3 This tas) re2uires su&stantial remodelling and re-parameterisation in order
for the model to &ecome functional in South Africa3 A first >9F-financed pilot pro7ect at the
Department of Forest and ood Science of Stellen&osch 1niversit! in colla&oration with the
wor)ing group of Prof3 Hans Pretzsch at T1 8Rnchen 'erman!, showed that due to the
different resource limitations S-*EA cannot simpl! &e re-parameterised &ut needs to &e
structurall! changed in the su&-module for competition calculation3
To achieve this adaptation to South African forests and growth conditions two main steps
are addressed in this thesis: the potential height stand initialisation model .Figure 1-50 and
the diameter increment model &ased on competition indices .Figure 1-603
$-$F

Figure 1-5 &il%a flow diagram and t#e potential #eig#t-age relation in &012A predicted from site qualit". T#is cur%e is
used for t#e simulation initialisation

Figure 1-6 T#e diameter increment model function in &012A determined b" diameter (D*!.. )redicted increment is t#en
based on a modifier w#ic# takes competition into account.

1.# ,b-ectives
The main aim of the stud! was to introduce a methodological approach for individual tree
models for South African forestr! using the S-*EA structure as an e/ample3 Two important
$-$%

su&-components of the model were addressed: the potential height model and the
diameter increment modelling3 The su&-o&7ectives of these two main components were
addressed &elow:
1.#.1 Potential height model:
The o&7ective was to model potential height as a function of site inde/, the South African
standard for site 2ualit! description3 Thus three wor)ing steps were identified as the su&-
o&7ectives:
$3 8odelling site inde/ using different model fitting methodologies
"3 Finding a suita&le method to fit potential height models on o&served data
F3 Predicting potential height from site inde/
Step $ was used as a stud! into different methodologies for site inde/ model fitting
techni2ues3 These estimations were then used for the prediction of potential height .Step
F03 Step " involved finding a methodolog! to create potential height-age functions using the
Chapman 9ichards e2uation, while Step F involves using S- to model potential height3
1.#.2 .iameter increment model:
As diameter increment is highl! sensitive to competition &etween trees in a stand, the
o&7ective was to model diameter increment using the potential modifier methodolog!
under changing resource limitations3 The su&-o&7ectives .steps0 used to achieve this were:
$3 Classif! sites according to water availa&ilit!
"3 Determine the potential increment &ased on site conditions
F3 Fit different competition models
%3 Select a suita&le com&ination of indices to capture overtopping and local crowding
G3 1se C-Ls in com&ination in a deterministic potential modifier model
43 Create a stochastic model mimic)ing natural varia&ilit!
The stud! was thus limited to two )e! aspects, which are deemed important for the
potential application of an individual tree model, such as S-*EA, in South African plantations3
The two components provided insight into potential pro&lems and future application of the
model for forest growth modelling3
1.$ The use of / in the stud%
For all statistical purposes 9 .! Core Team "#$F0 was used in this stud!3 9 is an open source
software pro7ect freel! availa&le on the internet, with multiple pac)ages designed for
multiple purposes= updated and reviewed fre2uentl!3 The pac)ages used and the software
$-$G

itself proved ver! useful and ro&ust, and allowed the researcher to com&ine statistical,
spatial modelling and illustrative purposes simultaneousl!3 Select e/amples of the code
constructed in the stud! are included in Appendi/ F either &! the researcher or with
assistance from peers3 -t is not referred to in te/t, &ut is included for e/ample purposes3
"-$4

Chapter 2: .ataset description

-ndividual tree growth models and distance dependent competition indices re2uire
ade2uatel! designed spacing trials or sampled measured data in forest compartments to
capture the range of possi&le spacing and distri&ution of trees3 The pro7ect received support
from a wide range of industr! and research components, mentioned in the
ac)nowledgements3 Data from a few spacing trials were o&tained representing a large
num&er of o&servations and spacing designs3
-n a nutshell, these are the correlated curve trend .CCT0 spacing trials .;LConnor $JFG,
+reden)amp $JI%0 initiated in $JFH, the Pinus elliottii trials consist of four locations3 -n
addition one ongoing SSS-CCT .Standardised Sample Size0, .+reden)amp $JJ#0, trial initiated
in $JJ$ was included and a >elder spacing trial, which was measured from $JH4-$JJI3 The
datasets are e/plained &elow and were used as deemed appropriate for the different
purposes and o&7ectives of this thesis3 A map of the spacing trial locations is illustrated in
Figure ,-6.
2.1 The correlated curve trend 0CCT1 data
The CCT trial concepts were laid down &! ;LConnor in $JFG as spacing trials to determine
optimum planting and thinning regimes for the South African plantation industr!3 The CCT
trials can &e split into two series: an unthinned series called the &asic series that were
planted under a wide range of planting densities comprising of eight stand densities in
stems per hectare .spha03 -n this stud! the unthinned series was used for modelling
purposes with the design shown in Table ,-13
Table ,-1 77T unt#inned series trial summar"
Plot
Nominal Stand density
(spha)
Plot size
(ha)
Measurement
Trees/Plot
1 2965 0.081 240
2 1483 0.081 120
3 988 0.081 80
4 741 0.081 60
5 494 0.081 40
6 371 0.081 30
7 247 0.081 20
8 124 0.081 10

To overcome suppression &! competing weeds all of the plots were planted at ver! dense
stoc)ing levels and thinned in advance of competition .Table ,-,03 -n retrospect, this ma!
not &e the optimum solution as the high densities at these ages could include competition in
an! case, or lead to facilitation or other un)nown effects3
"-$H

For the purposes of this stud! this was assumed not to have a significant effect on the
results and the stands were treated for their intended SPHA3 The thinned plots incorporated
various thinning regimes and management practices such as weed control3
Table ,-, T#inning in ad%ance of coemptition for weed control in t#e 77T trial data
Plot
Age (years)
0 2 5.08 6.17 7.5 8.83 9.42 10.25
1 2965
2 2965 1483
3 2965 1483 988
4 2965 1483 988 741
5 2965 1483 988 741 494
6 2965 1483 988 741 494 371
7 2965 1483 988 741 494 371 247
8 2965 1483 988 741 494 371 247 124

The original CCT trials proved to &e a difficult dataset to use, with measurement histor!,
e/planations, etc3 not availa&le to the researcher3 For instance, man! trees were simpl!
sampled and it was not possi&le to determine which trees succum&ed to mortalit! or were
not included in the measurement sample3 Tree positions were not availa&le through
repeated re-num&ering and, &ecause the trials do not e/ist an!more, could not &e
reconstructed3 For this reason the data were used onl! for the potential height and site
inde/ modelling section of this thesis .Chapter F03 For this purpose, the data proved to &e a
good tool as it covered a wide range of site conditions and, &! South Africa standards, were
measured to a ver! high age .G#!rs0, which proved to &e of great importance for the shape
and as!mptotic development of the height-age growth models3
This Pinus elliottii dataset comprised of four sites called eza, :wa&onam&i, Du)udu)u and
8ac 8ac3 8easurements were ta)en at various intervals for the four trials < for e/ample
the height measurements are illustrated in Figure ,-1 and Figure ,-, &elow illustrate the
four CCT trials with regards to the height measurements over time and the height
measurements of the different stand densities of each of the sites and plot densities
respectivel!, showing differences &etween site and densit! of each stand3
"-$I

Figure ,-1 !eig#t measurements on t#e four 77T spacing trials s#owing a clear stratification between sites

Figure ,-, !eig#t measurements on t#e four 77T spacing trial indicating different growt# patterns and growt# trends
for different planting densities
"-$J

Fig ,-, illustrates the clear differences in height growth in sites and stand densities
encountered in the spacing trials3 -t also illustrates the pro&lems of re-measurement periods
ta)en at different ages with large gaps &etween measurements3 Figure ,-/ and Figure ,-4
identif! trends in competition encountered in the sites, with ma/imum tree height
responding less to competition compared to diameter= which is wh! the stud! focussed on
the effect of competition on diameter increment3

Figure ,-/ /D plot of #eig#t growt# trends in t#e 77T spacing trials wit# a linear a%erage response cur%e indicating little
c#ange between ma'imum #eig#t growt# between different stand densities
"-"#

Figure ,-4 /D plot of diameter growt# trends in t#e 77T spacing trials wit# a linear a%erage response cur%e indicating
significant c#ange between #eig#t growt# between different stand densities
2.2 Triple 2CCT
The Triple S-CCT concept .SSS-CCT0 was esta&lished and designed in the late $JI#Ls,
introduced &! +reden)amp .$JJ#0 in order to overcome the statistical shortcomings and the
cost implications of the CCT trials3 Si/ unthinned stand densities were planted at the stems
per hectare indicated in Table ,-/ &elow3 The SSS-CCT trial used in this thesis was one of
two such trials for P. elliotttii planted in Tweefontein at an altitude of appro/imatel! $"##m3
Tree positions could &e reconstructed from the planting pattern and num&ering s!stem
provided &! the compan!3 For this reason this dataset was ver! useful as competition
indices could &e calculated on the site3
Table ,-/ 8nt#inned &&&-77T spacing trial desing
Plot
Planting density
(SPHA)
Measurement
Plot size (ha)
Measurement
Trees/Plot
1 245 0.102 25
2 403 0.062 25
3 665 0.038 25
4 1097 0.023 25
5 1808 0.0138 25
6 2981 0.008 25
2.# 3elder spacing trial
The >elder spacing trial concept is an unthinned spacing e/perimental design .>elder,
$J4"03 Different designs were created for specific o&7ectives .Figure ,-503 The trial used in
"-"$

this thesis was planted in $JH" in the *otterring plantation of the coastal plateau of the
Tsitsi)amma region in the all-!ear rainfall Southern Cape 9egion of South Africa, &ased on
the conventional >elder spacing design .a in Figure ,-50, where the rings .or circles0
represent different spacings increasing with distance from the centre3 The trial &urnt down
in $JJI, with the last measurement age at "4 !ears3 The measurement intervals and dates
are shown in Table ,-4 &elow3

Figure ,-5 9elder trial designs based on different spacing geometries. 9elder (136,..

"-""

Table ,-4 :easurement inter%als for t#e 1ottering 9elder trial
;emeasurement no. Date Age ("ears. 2ariables measured
$ $JH4-$"-$F %3GI D&h, Ht
" $JHI-#G-#I 43## D&h, Ht
F $JHJ-#G-"4 H3## D&h, Ht, +ranch thic)ness
% $JIF-#4-#$ $$3#I D&h, Ht
G $JIG-#J-"F $F3FF D&h, Ht
4 $JIH-$"-#I $G3GI D&h, Ht
H $JJ$-#H-$$ $J3$H D&h, Ht
I $JJ"-#I-$4 "#3"G D&h, Ht
J $JJ4-#F-$G "F3IF D&h, Ht
$# $JJI-#G-"# "43## D&h, Ht

Tree positions could &e recalculated from the positions of the trees on the Aspo)eD and
AringsD of the >elder wheel3 This means that although orientation of the spacing wheel in
cardinal directions could not &e determined, the relative positions of the trees with all of
their neigh&ours could &e easil! calculated3
"-"F

Table ,-5 9elder spacing trial plot numbers (rings. wit# t#eir corresponding stems per #ectare+ based on t#e radii and
arc distances.
Arc No
(Ring in
Design)
Arc No
(Ring no. in
field)
Radii of
Arcs
(m)
Arc
distances
(m)
Distance
between Arcs
(m)
Area per
tree (m
2
)
Corresponding
stems per ha
3 0 Border 7.43 1.06 1.13 1.12 8900
4 1 8.56 1.22 1.31 1.49 6700
5 2 9.87 1.41 1.51 1.98 5043
6 3 11.38 1.62 1.74 2.63 3796
7 4 13.11 1.87 2.00 3.50 2857
8 5 15.11 2.16 2.31 4.65 2151
9 6 17.42 2.49 2.66 6.18 1619
10 7 20.08 2.87 3.06 8.21 1219
11 8 23.14 3.30 3.53 10.90 917
12 9 26.67 3.81 4.07 14.48 691
13 10 30.74 4.39 4.69 19.24 520
14 11 35.44 5.06 5.41 25.56 391
15 12 40.84 5.83 6.23 33.95 295
16 13 47.08 6.72 7.18 45.11 222
17 14 54.26 7.75 8.28 59.92 167
18 15 62.54 8.93 9.54 79.61 126
19 16 Border 72.09 10.29 11.00 105.76 95

2.$ Permanent sample plots 0PP1 data
The permanent sample plot data was o&tained with the permission of contri&utors and
custodians of PSP inventor! data from forestr! companies in South Africa3 These represent
re-measured plots of active commercial plantations .not spacing trials03These were not used
for model parameterisation as the! onl! represented a narrow range of stand densities, &ut
for illustrative and short validation purposes &ased on a few candidate sites3
"-"%

Figure ,-6 1ocations of t#e spacing trials

F-"G

Chapter #: ite inde4 and potential height modelling

#.1 Introduction
Silva emplo!s a potential modifier approach for predicting height and diameter increments3
Thus one of the o&7ectives of this thesis is to o&tain a potential height which could &e
o&tained &! determining potential height from site inde/ in a model in order to o&tain the
potential height from a widel! used and readil! availa&le site 2ualit! measure3 This chapter
investigates whether this is possi&le, how this should &e done and provides an initial
wor)ing model3
#.1.1 ite inde4
Site inde/ is widel! used in the South African forestr! industr! as a measure of site class and
is an important predictor for man! modelling and growth prediction applications .von
'adow and +reden)amp $JJ"03 8an! definitions of top height e/ist, the approach most
widel! used in South Africa is &ased on the definition that top height is the height of the
"#N largest trees .according to their D+H0 in a stand, which is usuall! estimated &!
calculating the 2uadratic mean diameter of the largest "#N of trees and su&stituting this for
D in the following formula .+reden)amp $JJF0:

Equation /-1

-n this stud!, the relationship &etween site inde/ and potential height curves was sought
out3 Site curves over age were modelled to understand the change in relationship over time3
#.1.2 Potential height growth
Potential height over age is a measure of a standLs height growth and represents an upper
&oundar! line or curve of measured tree heights for a given site .Pretzsch "##J, Seifert
"##F03 -n the S-*EA methodolog!, a potential height<age curve is developed as an
initialisation of the model process .Pretzsch et al. "##"03 Therefore, a methodolog! had to
&e developed using the availa&le data to 2uantif! potential height development over age3
Site inde/ values are t!picall! o&tained from plantation inventor! and are not e/plicitl!
modelled in this thesis3 ;ne possi&le pitfall of using site inde/ in this conte/t is that site
inde/ on the same site can var! according to var!ing .stems per hectare0 densities .Figure /-
1-03 -n this chapter, while on the same site, each plot representing a planting densit! was
treated as an individual with its own site inde/ in order to determine the relationship
&etween site inde/ and potential height3
#.1.# 3onlinear regression assumptions
Developing site inde/ curves on a longitudinal, repeated measures dataset presents certain
pro&lems3 Standard regressions rel! on inherent assumptions to the modelling process such
F-"4

as homoscedasticit! of residuals and independence of the residual errors3 *ongitudinal,
repeated measures violate the assumption of independence
erial autocorrelation
hile simple least s2uares estimation has &een used for modelling data of this )ind, a
relativel! simple and proven method= the longitudinal nature of the data presents a
significant pro&lem3 (ach of these datasets represents repeated measurements over time,
which violates the assumption of independence of errors= in this case the errors are
correlated with the error of the previous and later measurements of the same tree3
5eteroscedasticit%
Heteroscedasticit! is a common pro&lem in model fitting, where&! the residuals increase
along a predictor gradient < for e/ample age3 This was a common pro&lem in the modelling
of height in the stud! sites
#.1.$ Chapter ob-ectives
The o&7ectives of this chapter are thus to:
Develop continuous site inde/ curves that ta)e into account heteroscedasticit! and
autocorrelated time series errors
Develop a suita&le methodolog! to develop potential height-age curves
Assess the effect of densit! on site inde/ for the same sites and over a comparison of
sites
Fit a model that predicts potential height from dominant height
Thus the results of this chapter are split into three steps
$3 The development of dominant height-age curves
"3 >onlinear 2uantile regression for potential height modelling
F3 Prediction of potential height from site inde/
#.2 tep 1: ite inde4 modelling
This section deals with the calculation of site inde/3 -n the following sections the eza
Dataset was used to demonstrate the modelling methodolog!3 -t was deemed more suita&le
than the !ounger CCT datasets as it was assumed that onl! a data set with older trees would
reflect as!mptotic growth < which will &e shown to &e a ver! important factor3 This section
outline Figure /-1 shows the conceptual flowchart of the outline used in this section with
&rief descriptions3

F-"H

Figure /-1 Flowc#art of site inde' modelling section of t#is c#apter (&tep,.
#.2.1 Identification of dominant trees
(ach plot from each site of the spacing trials was modelled separatel!3 The "#N largest trees
in respect to their diameter were selected &! using the 2uantile function in 9 to &in the data
into five "#N classes and then su&-set the data for the largest "#N3 The trees selected were
then used for further height model development, as illustrated in Figure F-"3 -n the older
CCT trials where the num&er of trees measured differed for the different spacing densities
.lower amount of trees for low densities0 < this represented a pro&lem due to the differing
amount of o&servations3 However, it was decided to maintain the South African standard
site inde/ definition in this thesis and outline potential pitfalls with recommendations for
possi&le improvements where necessar!3
F-"I

Figure /-, Dominant #eig#t modelling e'ample for t#e :ac :ac ,365sp#a plot wit# red dots representing t#e dominant
trees+ t#e red and black das#ed lines representing t#e dominant and mean #eig#t cur%es respecti%el"

#.2.2 *odel selection
As with the nonlinear 2uantile regression, the Chapman-9ichards three parameter form
e2uation was used .Equation /-,0 to develop anamorphic dominant height-age growth
curves, which were used for site inde/ classification for an! given reference age3

Equation /-,

-n this stud!, the nonlinear least s2uares .nls0 approach was used as the standard
methodolog! for fitting the site inde/ function in the South African Forestr! industr!3 The nls
approach was compared to some alternative methods in order to identif! the &est fitting
method to deal with independence violations and homoscedasticit! errors3 These are:
>onlinear 8i/ed (ffects 8odel .nlme0
F-"J

'eneralised *east S2uares (stimation .glns0
-t should &e noted that parameters .slope of the curve0 are often fi/ed in anamorphic site
height-age models, often noted as b and c, and var! the as!mptote .a0 onl!3 hile this is
common practice in man! growth models in South Africa it was decided in this case not to
fi/ an! of the parameters in order to &e a&le to introduce and assess random effects in the
model3 The purpose of this e/ercise is not to develop reference site inde/ curves for
management, &ut to model site inde/ accuratel! to use as a predictor for potential height
and to investigate the use of mi/ed effects models for site inde/ modelling in South Africa3
#.2.# .ataset and trial !ge
As might &e e/pected, significant differences were seen &etween the !ounger SSS-CCT
spacing trials and the older CCT trials, with much more volatilit! in the as!mptote due to the
more linear growth at these ages without the realisation of the approach towards an
as!mptote3 For this reason all of the models were fit on the original CCT datasets3
These were all tested on the eza Dataset, whereafter the methodolog! was standardised
for all sites3 1sing different random effects, weighting, autocorrelation, etc3, produced
mar)edl! different results in some cases, especiall! at higher ages3
#.2.$ tarting values:
Starting values .sometimes called initial values0 for iteration of nonlinear models can have a
significant effect on the results and wrong starting values can cause significant pro&lems in
parameter estimation3 The method used for the selection of starting values is outlined &!
Fe)edulegn et al3 .$JJJ0 and *e)wadi et al3 ."#$"0= the parameters for the Chapman
9ichards e2uation .Equation /-,0 are estimated &! a simple algorithm, where:

& is defined as the rate constant at which the response varia&le approaches it ma/imum
possi&le value &
#

;r for this e/ample rewritten as .*e)wadi et al., "#$"0

c lies &etween zero and $ for the Chapman-9ichards as recommended &! Fe)edulegn et al.
$JJJ3 The c parameter was fi/ed at #344 or changed as seen fit to foster model conversion3
This methodolog! wor)ed well for the purpose of the stud!= improving calculation time and
F-F#

producing estimates that were within the e/pected ranges for the parameters, resulting in
model convergence3
#.2.& 3onlinear least s6uares
>onlinear *east S2uares .>*S0 estimation is a commonl! used fitting techni2ue in nonlinear
regressions3 -t uses an unconstrained minimisation algorithm, which simpl! defines a model
curve which is fit &! minimizing the sum of s2uares that occur on the !-a/is .Dalgaard "##I03
Figure /-/ provides an e/ample of a >*S fit in one of the CCT spacing trial plots, with some
visual diagnostic plots in Figure /-43

Figure /-/ E'ample of an 91& fit on t#e <e$a ,365 plot

F-F$

Figure /-4 ;egression diagnostics for t#e <e$a ,365 plot
As can &e seen in Figure /-4 a&ove inherent pro&lems with heteroscedasticit! are prevalent,
as seen in the residual plots .top right and top left images03 Furthermore, while no
significant trend is apparent in the autocorrelation plot in this small dataset, it is o&vious
that error correlation occurs in a repeated measures stud! such as this3 For this reason,
alternative methods were sought to 2uantif! site inde/ growth, which do not have time
related autocorrelation errors3 hile somewhat trivial to the overall structure and
contri&ution to the thesis, this was sought to ade2uatel! define a methodolog! for guide
curve fitting of site inde/ curves3 The model fit shows also a model &ias .overestimation of
smaller values0, which can &e attri&uted to the infle/i&le Chapman-9ichards e2uation3 The
Chapman-9ichards e2uation is an often used model for S- modelling .(sler "#$"03 -t was not
in the scope of this thesis to compare different mathematical model formulations, however
several models could present alternatives, for e/ample the Hossfeld e2uation .'ea-
-z2uierdo, CaSellas, and 8ontero "##I03 -t is important to stress that models such as the
Chapman-9ichards model, which have a rigid, and sometimes infle/i&le structure .as
F-F"

compared to pol!nomial models for e/ample0 are used &ecause tree growth is &ased on
certain assumptions and that nonlinear models such as these are applied for their
interpreta&ilit!, parsimon! and validit! .e/trapolation and ro&ustness0 &e!ond the range of
the data .Pinheiro and +ates "###03 +ut as seen in Figure /-4 this can come at a cost of a
&ias in the prediction of height at !ounger ages3
#.2.( )eneralised nonlinear least s6uares
'eneralised nonlinear least s2uares .'>*S0 is compara&le to >*S, e/cept that when there is
reason to &elieve that the assumptions of e2ual variance and uncorrelated errors
.independence0 are violated, '>*S is a possi&le option to overcome some of these issues &!
the incorporation of autocorrelated error functions .ACF0 and variance weighting
transformations3
'ariance and !utocorrelation
-n order to cater for une2ual variance and autocorrelation, variance weighting
transformations including an autocorrelation function .ACF0 were applied to the '>*S and
the >*8( models3 A power weighted variance transformation for residuals and the ACF
function for the lag factors significantl! improved the models and were included from the
outset= these improve the heteroscedasticit! and the autocorrelated time errors in the
model .shown in the heteroscedasticit! improvement in Figure /-6 and improvements of fit
in Table /-/03
#.2.+ 3onlinear mi4ed effects model
>onlinear 8i/ed (ffects modelling .nlme0 is a modelling techni2ue used for grouped data
.Pinheiro and +ates "###03 8i/ed models effectivel! split the variance in fi/ed effects that
can &e e/plained &! factors and random effects that cannot &e e/plained &ut are
nonetheless inherentl! present in the dataset such as o&served varia&ilit! within trees and
&etween trees and sites and can &e at least attri&uted to those clustering entities3 -n this
case no distinction was made according to the differences in site= however the deviation of
the parameters from ever! tree were defined as random effects3 Thus in this case the
deviation of parameter estimates for ever! tree .the random effects0 must &e chosen &!
deciding, which parameters to include as random effects3
The methodolog! applied to developing site inde/ curves with mi/ed effects modelling was
done &! following the procedures set out &! Pinheiro and +ates ."###0 for mi/ed effects
model fitting, and Fang and +aile! ."##$0 for application to forestr! related e/amples
.incidentall!, also fitted for P. elliottii03
-n descri&ing the steps to specif! fi/ed and random effects Fang and +aile! ."##$0 suggest
that the nature of the Chapman-9ichards parameters .a, &, c0 &e specified as fi/ed and
random effects or purel! mi/ed effects3 According to Fang and +aile! ."##$0 model
comparison can start &! e/amining the full model with all the parameters as random effects
without considering covariates, and then pic)ing the parameters or a com&ination one &!
F-FF

one, as descri&ed in Pinheiro and +ates ."###03 hile the full models .considering ever!
coefficient as random effects0 can sometimes improve model fits, the! often do not
converge3 There is also a ris) of over-parameterisation when appl!ing such a methodolog!
.Pinheiro and +ates "###03
Conse2uentl! either one or a com&ination of two of the parameters was tested as random
effects3 For this reason the >*8( section starts &! descri&ing how the different parameters
affected the model in Table /-1 and Appendi' A over a wider range of plots3
/andom 7ffects
As mentioned earlier, a decision had to &e made on which components to include as
random effects3 First it is necessar! to see whether there is correlation &etween the
parameter estimates= this can simpl! &e seen visuall! in a scatter plot matri/ .Figure /-503

Figure /-5 &catter plot matri' of t#e relations#ip between t#ree parameters of t#e 7#apman ;ic#ards equation for a
model fit+ s#owing significant correlation between t#e parameters.
From Figure /-5 it is clear that with significant correlations &etween coefficients not all have
to &e included in the random effects < this pattern was consistent for all of the plots3
However, there is no clear methodolog! to determine which should &e included without
testing the models first &! alternating the coefficients chosen for random effects, as
e/plained &! Pinheiro and +ates ."###03
Appendi/ A summarises the results from the eza dataset < which was used as a sample to
decide on which parameters to include in the random effects, an e/ample of one site is
shown in Table /-13 8odel % in Appendi/ A, with onl! the as!mptote as a random effect,
F-F%

provided the most consistent results, with the resulting models providing improved A)ai)e
-nformation Criterion .A-C0 values, often significantl! lower compared to the models using
the other parameters as random effects3 The counts of the num&er of times a model, with
its corresponding random effect, was significantl! the &est performing model tested on the
eza dataset is summarised in Table /-,3
Table /-1 ;andom effect tests for t#e nonlinear mi'ed effects model. T#e column =parameter c#osen> indicates w#ic#
parameters used as an additional random effect in t#e model.
)arameter c#osen
(as random
effects.
7on%ergence
(?+9.
df A07 *07 Test p-%alue
a,&,c >
a,& 6 J "4J3GH4I "JG3J""
a,c 6 J "4J3GH44 "JG3J"$J
a 6 H "4G3GHGG "I43#44"
&,c 6 J "H"3#4HG "JI3%$"I
& 6 H "4I3#4HI "II3GGI4 4 vs G #3JJJJ
c 6 H "4J3$G#$ "IJ34%#J

Table /-, 7ount of best fit random effects models
;andom effects models
Parameters -ncluded >o3 of *owest A-C values
a,&,c #
a,& #
a,c $
a H
&,c #
& F
c G

As shown in Ta&le F-", including the as!mptote .a0 onl! as the random effect was resulted in
improved model fits over a num&er of sites3 Thus the as!mptote was used as the standard
random effect for all further >*8( models, which were tested against the >*S models, as
the &enchmar), and the '>*S models as an alternative3
F-FG

#.2.8 *odel comparisons
Diagnostics for nonlinear regression is a contentious issue as nonlinear regression curves are
fi/ed to the definition of the model, and thus drawing meaningful conclusions for the 2ualit!
of the fit .such as the 9
"
value0 is difficult3 -n this case a straightforward approach was ta)en,
&! simpl! anal!sing the visual structure of the model and the significance of the parameters3
9esidual plots for ever! model t!pe and site were compared < these give a good idea on
how the data is scattered around the mean curve, with priorit! given to homoscedastic
residual plots3
Different models were then compared with the A)ai)e -nformation Criterion .A-C0 descri&ed
&! A)ai)e .$JH"0, which can &e used to compare models with different covariance
parameters as fi/ed and random effects .Fang and +aile! "##$03 The root mean s2uare error
.98S(0 was also used as an indication of model fit3
A comparison of all of the main t!pes of residuals and improvements is shown in Figure /-6
and Table /-/ &elow: what was noticed from the summar! of the models .Table /-40 is a
depreciation of the as!mptote compared to the >*S fitting method < although small3

F-F4

Figure /-6 ;esidual plots of an e'ample dataset using different modelling tec#niques
Clearl! the >*8( models are superior in &oth the results of the residual plots as the residual
plots are more staggered, with less heteroscedasticit! and a smaller une/plained variance3
ACF and weighting significantl! improve the model output, as can &e seen from the
conversion of >*S to '>*S, and the standard >*8( model to the variance weighting and
autocorrelated error inclusion to the >*8( model3
Ano%a comparison and ;:&E
Comparison &etween the different models was performed using A>;EA, where the A-C and
98S( were calculated .Table /-/03 hile often 8ean S2uared error is used for model
evaluation which includes &ias and precision elements .Seifert and Seifert "#$%0 the 9oot
8ean S2uare (rror .98S(0 provides the advantage to &e in the same unit as the modelled
varia&le3 -t is an aggregation of the residuals o&tained from a predicted model and is a good
measure of how well a model fits overall, especiall! when compared to other models3
F-FH

n
X X
RMSE
n
i
i del mo i obs
=
=
1
2
, ,
) (

Equation /-/

From the >*8(, '>*S, and >*S model fits, an Anova comparison was tested, loo)ing closel!
at the A-C and 98S( values as a measure of comparison3
Table /-/ Ano%a and ;:&E comparisons of different modelling fitting met#ods on t#e <e$a dataset
Plot .spha0 8odel df A-C +-C Test p-value 98S(
1,4
'>*S 4 %H34G G%3%4 #3J$F$G"J
>*8( H G$3GJ GJ3G% $ vs " #3$4FI #3I%$GH44
>*S % 4J3#H HF34$ " vs F T3###$ #3J$"H#J$
,4@
'>*S 4 $#"3#G $$F3%# #344H$4J4
>*8( H JJ3I4 $$F3$# $ vs " #3#%#4 #344H"#4J
>*S % $#43F4 $$F3JF " vs F #3##GI #34G4HJ$H
/@1
'>*S G $II3$# $JJ3HG #3I#FH%#$
>*8( H $%I3G" $4%3IF $ vs " T3###$ #3I$G$%J%
>*S % $J#3"$ $JJ3GF " vs F T3###$ #3I#"F4#J
434
'>*S 4 "%$3JJ "G43JF $3$GGFGG
>*8( H $4G3$" $I"3G% $ vs " T3###$ #3JGI$4%
>*S % "I43$$ "J43#4 " vs F T3###$ $3$G%"%J
@41
'>*S 4 FIJ3$H %#43H% $3#%IG$J
>*8( H "4G3GI "I43#H $ vs " T3###$ #34HIH4F"
>*S % %$"34J %"%3%# " vs F T3###$ $3#%I%H"
344
'>*S G %4"3G4 %HI3$G $3#44G#H
>*8( H F"$34H F%F3G# $ vs " T3###$ #3HJFFIHJ
>*S % G#"3%G G$%3J" " vs F T3###$ $3#4FFHJ
144/
'>*S 4 GIJ3H$ 4$#3F4 #3JJ#$$JH
>*8( H %II3IG G$"3JG $ vs " T3###$ $3"%G$"H
>*S % 4F#3H# 4%%3%H " vs F T3###$ #3JF$FG4J
,365
'>*S 4 IH"3H# IJ43$I #3I%HI4I%
>*8( H GH%3IF 4#"3"" $ vs " T3###$ #3GIJ444H
>*S % JFG3"# JG#3IG " vs F T3###$ #3I%H#HG4

According to the A-C values, &esides one plot, the >*8( fitted model outperformed the
other model t!pes with p-values all &elow #3#G, suggesting a significantl! improved fit on all
of the plots3 Furthermore, it most resulted in lower 98S( values, indicating an overall
improved fit3
#.2.9 3:*7 final results 0model selection1
The summar! of the >*8( models for all of the four sites is represented in Table "#$= with
illustrated curves n Figure /-@3 hat is noticea&le is that the site inde/ is not strictl!
sensitive to the stems per hectare .as opposed to mean height0, there is a general tendenc!
F-FI

of a densit! effect on site inde/ .Figures /-@ and /-1-03 This tendenc! must &e ta)en into
consideration when site inde/ is used for prediction of growth3 However, as previousl!
stated, each plot was treated as an individual with its corresponding potential height
.calculated in step two0, which are e/plained in the third section of this chapter results3
The >*8( model was finall! chosen for model fitting as it provided a &etter fit for the
relevant data range .G# !ears03 However, with the associated pro&lems using the as!mptote
as a random effect, to achieve an improved fit for the entire data range, e/trapolation
&e!ond G# !ears ma! &e compromised as the as!mptote seems to &e lower than the other
fitting methods used3 -t was decided that, seeing as it is unli)el! that plantations will &e
grown for such long periods for commercial purposes, this would &e an accepta&le
compromise3
The overestimation of the model at !oung ages, which is most li)el! an effect of the
infle/i&le Chapman-9ichards e2uation was not solved &! the >*8(3 However, to remain
compati&le to S-*EA the compromise of appl!ing the Chapman-9ichards e2uation was
made3
FJ

Table /-4 Fitted &0-age models for t#e 77T trials
<e$a :ac :ac Dukuduku Awambonambi
Densit" 2alue
&td.
Error
DF t-%alue
p-
%alue
2alue
&td.
Error
DF t-%alue
p-
%alue
2alue
&td.
Error
DF t-%alue
p-
%alue
2alue
&td.
Error
DF t-%alue
p-
%alue
1,4
a $$H34G H%3IH $H $3GH #3$F%G %G3GF $3FJ I# F"3IG # "G3$$ $3F# %G $J3"4 # "I3GF $3JF %H $%3HI #
b -#3#$ #3#$ $H -$3#" #3F"$4 -#3#% #3## I# -$"3HI # -#3#4 #3#$ %G -43%H # -#3#4 #3#$ %H -4344 #
c #3IF #3#4 $H $F34" # $3$I #3#F I# FH3$J # $3#$ #3#J %G $$34J # $3#J #3#H %H $43F% #
,4@
a %"3FI F3I" %$ $$3#I # FH34% $3G# J$ "G3#H # "I3"F $3"$ I# "F3"I # %I3JI G3#$ H% J3HI #
b -#3#F #3#$ %$ -%3GI # -#3#H #3#$ J$ -$$3GI # -#3#4 #3#$ I# -I34H # -#3#" #3## H% -G3$G #
c #3J4 #3#I %$ $$3G4 # $3%F #3#G J$ "43#J # $3$" #3#H I# $43J% # #3IJ #3#% H% "%3H% #
/@1
a %$3$# "34$ 4" $G3H% # FI3FH #3IJ $$F %F3"% # "J3%4 $3"F $$% "%3## # %"3G# $3J4 J$ "$34% #
b -#3#F #3#$ 4" -43#% # -#3#4 #3## $$F -$43JJ # -#3#% #3## $$% -J3$4 # -#3#F #3## J$ -J3F% #
c $3#" #3#I 4" $F3"% # $3FH #3#% $$F FG3IH # #3J% #3#% $$% "$3$4 # #3IJ #3#F J$ F#3#4 #
434
a F%34" $3GH HF ""3#4 # %$3%4 $3I# $"H "F3#G # "I3HG $3$$ $F4 "G3JJ # FJ3IG $3G$ $$H "43%# #
b -#3#G #3#$ HF -I3I% # -#3#G #3## $"H -$$3GJ # -#3#% #3## $F4 -$#3#F # -#3#F #3## $$H -$$3#G #
c $3$G #3#H HF $H34F # $3"F #3#% $"H F"3#$ # #3JG #3#% $F4 "F3$I # #3J" #3#F $$H F$3%# #
@41
a FI3#I $3%J $$H "G34% # %"3"4 "3$F $G$ $J3IH # F#344 $3$G $GJ "43GI # G#3FJ F3F$ $GG $G3"" #
b -#3#% #3## $$H -$#3"G # -#3#G #3## $G$ -$$3$% # -#3#F #3## $GJ -J3"$ # -#3#" #3## $GG -H3"% #
c $3#" #3#% $$H ""3JG # $3"4 #3#% $G$ FF3$H # #3IF #3#% $GJ ""3FH # #3I% #3#F $GG F#3%J #
344
a %G3F4 F3F% $%F $F3GI # %G3$H "3FG $I% $J3"F # "J3$I #3H" ""I %#34H # %H3"H "3"4 $I$ "#3J# #
b -#3#F #3## $%F -434# # -#3#G #3## $I% -$$3"% # -#3#% #3## ""I -$F3#% # -#3#" #3## $I$ -J3GG #
c #3JF #3#% $%F "%3"G # $3"% #3#% $I% F%3HI # #3J4 #3#% ""I "F3$% # #3IG #3#" $I$ F43$" #
144/
a F#3H% #3HH $I" FJ3H4 # %$3J% $3F4 "4I F#3II # F"3%F $3FJ "I$ "F3%$ # %"3JF $3HG "%4 "%3G% #
b -#3#4 #3## $I" -"$3HI # -#3#G #3## "4I -$43$4 # -#3#" #3## "I$ -I3IG # -#3#" #3## "%4 -$#3IJ #
c $3%4 #3#F $I" %J3$J # $3$J #3#F "4I %F3HG # #3HJ #3#F "I$ "H3"I # #3I4 #3#" "%4 FI3"F #
,365
a "I3%FH #3GIGJ4 F4" %I3GF #
%"3FH #3JH %J$ %F3IG # "H3"I #34$ G$I %%3I" # F%34F $3$G FII F#3#4 #
b -#3#GJJ #3##"$H F4" -"H34F #
-#3#G #3## %J$ -"%3I$ # -#3#G #3## G$I -$H3F4 # -#3#% #3## FII -$F3I" #
c $3F4J$H #3#$I$ F4" HG344 #
$3$J #3#" %J$ HF3$# # $3#" #3#F G$I F43"4 # #3J$ #3#" FII %43GI #
%#

Figure /-@ Fitted dominant #eig#t cur%es for t#e 77T trials

%$

#.# tep 2: Potential height modelling
>onlinear 2uantile regression is one possi&le method to 2uantif! potential height growth3
Kuantile regression was introduced &! :oen)er and +assett .$JHI0 as a statistical set of
methods for defining conditional means in data anal!sis3 Another option would &e to su&set
the data into 2uantiles and perform some t!pe of least s2uares estimation to achieve a
nonlinear fit for that su&set= however 2uantile regression was preferred as dividing the data
into su&sets and achieving a mean, instead of median response delivers differing values=
more elo2uentl! descri&ed in :oen)er and Halloc) ."##$03
#.#.1 .escription of the 3:/; procedure
Kuantile regression is a generalisation of the median regression3 hile the latter was
introduced as a ro&ust method for dealing with outliers, which used the median instead of
the arithmetic mean to fit a regression curve, 2uantile regression is a&le to use an! 2uantile
.denominated &! the AtauD value0 of the distri&ution to fit a regression curve to it .Cade and
>oon "##F03 Thus it is an appropriate techni2ue to fit potentials3 >onlinear 2uantile
regression was fit using the nlrq function in the quantreg pac)age in 9 .:oen)er "##403
-n this stud!, tau vectors of #3J, #3JG, #3JHG and #3JJ 2uantiles .which represent the
conditional 2uantile fits, e3g3 #3G represents the G#N - or median fit0 were used to determine
the sensitivit! of the nonlinear 2uantile regression on the parameterisation data3 As a
starting point for the potential modifier approach, the ma/imum possi&le definition must
first &e determined as the modifier onl! reduces the potential height value .Pretzsch "##J03
After careful consideration and visual inspection, it was decided to use the #3JHG 2uantile
for the potential height definition3 hile it does not achieve the ma/imum values for height
growth, it seems more fle/i&le than the #3JJ tau vector and does not e/clude too much of
the ma/imum potential height series3 The effects of these choices are discussed further on3
>onlinear 2uantile regression proved to &e a ro&ust and eas! method to o&tain potential
height-age growth series3 +! specif!ing the #3JHG 2uantile the fits were more consistent3
The potential height fits are shown in Figure /-4 &elow, fitted over their respective spacing
trial series for each plot .spha03 The results per plot are summarised in Table /-5.

%"

Dukuduku Awambonambi
<e$a :ac :ac
Figure /-4 Fitted potential #eig#t cur%es for t#e 77T dataset for different stems per #ectare.

From simpl! o&serving the growth curve series < a trend appears .seen within each trial
series0 that the #3JHG 2uantiles seem to &e affected &! densit! onl! to a small degree,
although the e/treme high and low ranges of stand densit! .e3g3 $"% and "J4G spha plots0
tend to dominate the upper and lower &ounds respectivel!3 However the difference
&etween sites does not seem to overtl! densit! dependent, &ut ma! &e more strongl!
dependent on the site 2ualit! or location of the plots, suggesting that a site 2ualit! measure
ma! &e useful for predicting potential height3
%F

-n order to see whether these potential heights are representative, visual assessment was
done on the PSP dataset3 Figure /-3 &elow shows that for the &est site in the CCT trials .the
8ac 8ac lowest densit! plot0= the potential captures the upper &ound of the PSP height
series 2uite well, &esides a few outliers, suggesting that the potential models fitted on the
spacing trials represent the upper &oundar! of o&served potentials3

Figure /-3 )otential #eig#t of t#e #ig#est 77T trial %alue (:ac+ sp#a B 1,4. plotted o%er )&) data of a wide range of
sites+ t#e blue line is t#e potential of t#e 77T plot+ t#e red line represents t#e mean #eig#t of t#e )&) dataset

%%

Table /-5 )otential #eig#t fits b" plot for t#e four spacing trials
<e$a Dukuduku :ac :ac Awambonambi
Densit" 2alue
&td.
Error t %alue )r(CDtD. 2alue
&td.
&td.
&td.
Error t %alue )r(CDtD.
,365
a %$3"4 "3I$ $%34H # FJ3"H "34J $%34$ # GJ3"F G34$ $#3GG # %43$4 F3JG $$34I #
b -#3#F #3## -43%F # -#3#" #3## -43F$ # -#3#F #3## -43"H # -#3#" #3## -G3GJ #
c $3#% #3#4 $H3$# # #3H% #3#" F#3IH # $3#" #3#F F"3%# # #3I" #3#F "J3G$ #
144/
a %%3HH F3%% $F3#F # FF3$F "3$$ $G34I # HJ3J$ $J3G4 %3#I #3####G %I3$G %3HJ $#3#G #
b -#3#F #3## -G3FH # -#3#F #3## -G3I% # -#3#" #3#$ -"34% #3##I%I -#3#" #3## -%34I #
c #3J4 #3#H $%3$G # #3H% #3#% "#34J # #3J# #3#% "F34H # #3HJ #3#F "F3I" #
344
a 4J3"G $"3IH G3FI # F#34" $3$H "43"$ # 4H3FI $I3"# F3H# #3###"" G#3JH F3"# $G3J# #
b -#3#$ #3## -F3#G #3##"F" -#3#% #3## -I3#4 # -#3#" #3#$ -"3"H #3#"F$ -#3#" #3## -43H$ #
c #3IH #3#% "#3$J # #3IF #3#G $H3F" # #3JI #3#H $%3#$ # #3HH #3#F "I3GI #
@41
a %"3G# F3%F $"3FI # FJ3H% F3FF $$3JG # 4%3HI H3#F J3"$ # GF3G% F3H4 $%3"4 #
b -#3#% #3#$ -G3"" # -#3#" #3## -%344 # -#3#" #3## -G3$% # -#3#" #3## -G3FJ #
c $3#% #3#I $"34# # #3H# #3#% $I3FI # #3JH #3#% "F3JJ # #3HG #3#F ""3"F #
434
a FI3FF #3I$ %H3%4 # F#3I" $3JI $G3GF # HF3$F $I3"" %3#$ #3####H %#34$ F3FJ $$3JI #
b -#3#G #3## -"#3%4 # -#3#% #3#$ -%3HI # -#3#" #3#$ -"3%" #3#$GH4 -#3#F #3#$ -%3I% #
c $3"% #3#F FH3%J # #3J" #3#J $#344 # #3J" #3#G $43JJ # #3I4 #3#4 $G3FF #
/@1
a %#3#J $3"G F"3$G # F"34G $3G4 "#3JI # %F34G $3%$ F#3IJ # %"3H" "3IF $G3$# #
b -#3#% #3## -$43"" # -#3#F #3#$ -G3JH # -#3#4 #3#$ -$#3HJ # -#3#F #3#$ -G3GJ #
c $3$4 #3#F FF3H4 # #3HJ #3#4 $%3#H # $3"% #3#4 "#34" # #3HJ #3#G $43I$ #
,4@
a FJ3FI $3#G FH34% # FI3#I "3"4 $43I% # GI3"I 43"G J3F" # %"3H" F3$F $F344 #
b -#3#G #3## -"#3$4 # -#3#F #3#$ -G3J4 # -#3#F #3#$ -%3%H #3####$ -#3#F #3#$ -G3"" #
c $3"4 #3#F G#3GI # #3I" #3#G $43J" # #3JJ #3#H $G3$I # #3IG #3#4 $%3FH #
1,4
a %I3"" F3F" $%3G$ # F#3#" $3"" "%3GH # GG3HI 43"G I3JF # F%3J# $3#F FF3I" #
b -#3#% #3## -J3GI # -#3#% #3## -J3#G # -#3#F #3#$ -F3$J #3##$G$ -#3#G #3## -$#3F$ #
c $3"$ #3#F FH3#G # #3I4 #3#% "#34% # $3#F #3$$ J3F# # #3J% #3#% "$3"" #
F-%G

#.$ tep #: Prediction of potential height from ite Inde4
-t was decided to use S-
"#
, the dominant stand height at the &ase age of "# !ears, as a
reference inde/3 First the relationship of the potential height and site inde/ curves was
plotted and anal!sed after which the corresponding dominant height age "# is used as the
site inde/3
The e2uation used to descri&e this relationship is a Chapman 9ichards height-age function
with site inde/ as a factor .Pa!andeh $JH%0:

pot
= o (SI
20
)
b
(1 c
cugc
)
d(SI
20
)c

Equation /-4

h
pot
is the potential height .m0, SI
,-
the e/pected site inde/, age is measured in !ears, and
a1, a2 and a3 are regression parameters3 This model was chosen due to its parsimonious
structure3
The model incorporates an effect of the site 2ualit! in S%
"#
, which was o&tained from the
predicted site inde/ model of the different sites .Step $03 Thus the potential height
development of the stand is modelled according to their respective S-
"#
values3 This was
done for each site first and finall! for all of the sites com&ined3 -n order to validate the final
model, first the potential height series predicted from dominant height was compared to
the actual potential height in the CCT plots3
#.$.1 7ffect of stand densit%
-n the dataset used, stand densit! affected site inde/3 Figure /-1- clearl! illustrates this
point with linear trendlines applied for each of the four sites used in the stud!, although
some variations around the trend e/isted3 This was possi&l! due to microsite and
management differences of the plots3 This was not significant to the overall performance of
the predictive model, as each site inde/ plot was used as an input for the parameterisation3
-t is included here as a possi&le pitfall of using measured site inde/ that does not ta)e into
account changing the possi&le changing densit! in a following rotation= although the
gradient is 2uite low for the range of commonl! planted stand densities3
F-%4

Figure /-1- &ite 0nde' %alues on different stand densities for t#e 77T dataset
3
The JGN confidence &ands are e/pectedl! wide due to the low num&er of points3 hat is
noticea&le from Fig F < $# is that each site has a different S--densit! gradient and that the
lines shift upwards or downwards dependent on the inherent site 2ualit!3 This further
emphasises the need for a site 2ualit! predictor &ased on edaphic conditions as proposed &!
.(sler "#$", *ouw and Scholes "##"03
#.$.2 /elationship between potential height and dominant height
-t is important to see what the relationship &etween dominant height and the fitted
potential height on the same site over age is3 As an e/ample, Figure /-11 illustrates this for
the eza dataset for each of the plots3
F-%H

Figure /-11 E'ample of potential and dominant #eig#t-age cur%es for t#e <e$a trial
This shows how the difference &etween potential and dominant height increases over age3
-n order to assess this relationship potential height is plotted over dominant height for all of
the four CCT trials in Figure /-1, &elow3

F-%I

Figure /-1, )otential #eig#t plotted o%er dominant #eig#t for all of t#e t#e 77T dataset plots
Figure /-1, shows a generall! linear relationship for the dominant and potential heights
over age, although the values &egin to var! as age, and conse2uentl! dominant height,
increase3 This gradient was modelled &! a least s2uares linear fit, forcing the intercept
through zero, which suggests a&out a $#N difference in potential and dominant height
values over age .Table /-60, i3e3 the difference &etween potential and dominant height
increases over age, as e/pected3
Table /-6 )otential #eig#t - dominant #eig#t gradient
&ite Eradient &td. Error t %alue )r(CDtD. ;
,
Du)udu)u $3#J%4"F #3##$4FG 44J3F T"e-$4 #3JJJ$
:wam&onam&i $3$"%JJF #3##"%44 %G43" T"e-$4 #3JJI$
eza $3#I#I4I #3##$J$J G4F3$ T"e-$4 #3JJIH
8ac 8ac $3$"%JJF #3##"%44 %G43" T"e-$4 #3JJI$

This linear relationship and the relativel! similar gradients suggest that a reference S-
"#

could &e introduced as an added effect, as specified in Equation /-43
F-%J

#.$.# Predictive e6uation
Site inde/ will change over two gradients: the site and, to a smaller degree, the densit! .a
potential source of error in the model03 The o&7ective here is to o&tain potential height
models for a given site inde/ .in this case, S-
"#
03 The potential height over site inde/
relationship is defined for all sites com&ined3 -t must &e noted that the effect of densit! on
site inde/, which was calculated on the South African top height definition, is not ideal, and
a great improvement could &e made &! &asing the site inde/ on site factors mentioned in
the previous section3
"inal Combined *odel
The four CCT spacing trials were pooled into the final model for potential height-age
prediction from site inde/ using Equation /-43 Pooling all of the sites together will prevent
the occurrence of e/treme cases and provide a &alanced model that is a&le to fit most cases
sufficientl!3 Figure /-1/ represents the final proposed model for prediction of potential
height from site inde/3

Figure /-1/ Final parameterised model of potential #eig#t-age using &0 as a predictor
F-G#

Table /-@ Final model parameterised on t#e pooled 77T trial datasets from Equation /-4
)arameter 2alue &td. Error t %alue )r(CDtD.
a #3IFFI #3#%"FH $J34HH"H #
& $3F$F#4 #3#$JI" 443"4%H4 #
c -#3#"J4G #3##$#$ -"J3FH"J #
d #3$44$F #3##J%I $H3G"#%4 #
e #3GGG4F #3#$HJG F#3J%I44 #

#.$.$ 'alidation
,bserved vs. Predicted Potential height
-t was decided to see how the potential height compared with the potential height
predicted from the site inde/ .in the pooled model03 This was done &! calculating the
difference in predicted potential height compared to the o&served potential height fitted for
each of the spacing trial plots .Fig /-4, Table /-503The models fits tested on the individual
sites a relativel! high error margin .over and under prediction0 &efore age $# .Fig /-15.3
The! &egin to converge age "# and then fan out again representing an increased error
predicted for higher ages .Fig /-140, although the values are small considering the actual
height of the trees at those ages3

F-G$

Figure /-14 De%iation from t#e obser%ed potential #eig#t-age compared to t#e potential #eig#t predicted equation

F-G"

Figure /-15 :edian de%iation in percentage of t#e obser%ed and predicted potential #eig#t cur%es
;verall, considering the vastl! differing site conditions, growing conditions and the different
shape of the height-age growth curves, the com&ined model reacts well, and although
seems to underpredict slightl! at after age "# .Fig /-150, it seems to sta&ilise to some
degree3 -t seems that site inde/ can indeed &e used as a predictor for potential height
modelling, although the values will range at ver! !oung and ver! old ages3 The high error
&efore age $# could also mean that this Chapman 9ichards &ased model ma! &e unsuita&le
for pulpwood rotations, although as these are onl! potential height values it would first
need to &e determined how the final predicted model performs once a modifier is applied3
/eferencing against independent PP data
The a&ove validation used sites in which the model was parameterised= however it is
necessar! to see how this model wor)s for independent data3 For this reason a few sites
were selected from the PSP dataset which had a suita&le num&er of re-measurements3 From
this an inspection of how the o&served vs3 the predicted potentials compare for sites of a
given site inde/ can &e seen .Fig /-,103

F-GF

Figure /-16 )otential #eig#t cur%es plotted o%er )&) data of different classes. T#e red lines represent t#e predicted
potential #eig#t for t#e upper bound of t#e &0 classes presented abo%e. T#e top left image presents all of t#e data wit#
15+ ,-+ ,5 and /- &0 predicted potentials
-n Figure F-"$, the predicted potential from site inde/ seems to capture the upper &ound of
the PSP dataset, with the top left hand graph representing all of the sites, with lines of the
predicted potentials for S-Ls of $G, "#, "G and F#3 (ach of the other graphs represents S-
classes within this dataset with the respective potential height curves predicted from S- of
"#, "G, and F# respectivel!3
To see how this performs on a few selected sites, five sites were selected from the second
PSP series, where measured S-Ls were not availa&le, and thus had to &e calculated from the
methodolog! proposed in this chapter3 The S- values would then predict a potential curve
which would &e superimposed on the plot height-age data for visual inspection .Fig /-1@03

F-G%

Figure /-1@ Fitted predicted potential #eig#t cur%es fitted on selected independent )&) data
The predicted potential seems to capture the potential heights of each site 2uite well, with
onl! a few trees which fall a&ove the predicted potential curves3

F-GG

#.& Chapter conclusion

The main o&7ective for this chapter, split onto three steps, was to model potential height
&ased on measured site inde/3
Site inde/ models and potential height models were developed in order to develop a
methodolog! to predict potential height from site inde/3 The relationship &etween site
inde/ and potential height was shown to &e a linear relationship, and a reference site inde/
of S-
"#
was used to predict potential height from site inde/3
The use of nonlinear mi/ed effects modelling has proved a superior method for modelling
dominant height-age curves with the associated clustered data structures and
heteroscedasticit! and it also represents a potential improvement for other height-age
models3 However, care must &e ta)en to ensure that including the as!mptote as a random
effect does not inflate or deflate the as!mptote implausi&l! < as it tends to change the
as!mptote to fit the o&served data, which ma! affect e/trapolation &e!ond the measured
!ears in the parameterisation training set3
>onlinear 2uantile regression proved to &e a ro&ust method of fitting o&served height
potentials3 The model training set .CCT trials0 covered the range of heights o&served PSP
data3
Potential height seems to &e well correlated to a standLs site inde/3 Eisual validation of the
results seem to suggest that site inde/ can indeed &e used to model the potential height,
which covers the first step of the potential modifier method and simulation initialisation &!
deriving a height potential from an industr! standard site inde/ information3

%-G4

Chapter $: *odelling diameter increment in response
to resource limitations and site classification

$.1 Introduction
The main purpose of this chapter is to create an age-independent diameter increment
model, which predicts diameter increment from D+H and the competitive conditions of the
tree at an! point in time3 Figure 4-1 illustrates this relationship for all of the plots in the 8ac
8ac spacing trial, where the gradient for the increment-diameter relation flattens out
.decreases0 over time, with each scatter cloud representing a different measurement
activit! at a certain age3 -n the proposed approach, which is following the S-*EA
methodolog!, the age effect is su&stituted &! tree size .D+H0, while the competition
interaction is supposed to cater for the change in increment-diameter relations over age3

Figure 4-1 D*! 0ncrement - D*! scatterplot on t#e :ac :ac 77T trial+ s#owing decreasing linear gradient o%er age
(mplo!ing a potential-modifier methodolog!, two steps were thus re2uired3 First the
potential increment for an! given tree diameter had to &e found3 Second, the modifier,
&ased on a competition inde/, had to reduce the increment and displa! a structure similar
%-GH

to Figure 4-1 a&ove, where&! the gradient of diameter increment for a given D+H
decreases3
Different competition indices are developed and descri&e growth differentl! according to
their mathematical structure3 For instance the ::* inde/ .Pretzsch et al. "##"0, with its
search crown is intrinsicall! more suited to descri&ing overtopping and thus competition in
light limited environments3 ;ther indices, &ased solel! on distance &etween individuals or
groups of individuals in an area, will &e intrinsicall! more size s!mmetric, such as the *ocal
+asal Area .*+A0 inde/, descri&ed later .Seifert et al3 in press03
Thus the sensitivit! of diameter increment to an inde/ can change according to site location
and the resource limitation which is e/perienced as demonstrated &! Seifert et al. .in press03
For instance, competition inde/ A might descri&e more of the variation in the predicted
model than inde/ + in a wet environment3 This can also change according to the 2ualit! of
the site3 The performance of competition indices ma! also change according to age, densit!
and longitudinal climate changes .wet and dr! spells03
$.1.1 .ataset
The >elder spacing design and the SSS-CCT design at Tweefontein were used for these
purposes3 -t must &e noted upfront that these are two ver! different designs < thus when
ma)ing comparisons &etween the &ehaviour of the indices, some differences could &e due
to the different spacing design, o&servation, etc3 However, these were the onl! trials where
tree positions could &e o&tained and most of these pro&lems should &e negated &! the
nature of the competition indices3
$.1.2 Chapter outline
ith onl! two sites from which to test competition with different water availa&ilit!, this
Chapter should &e strictl! seen as a methodological guideline for predicting diameter
increment, instead of an investigation on changing competition mode with different
resource limitations, although an indication of shift in importance of competition indices on
different sites is seen .%3G3F03 The chapter presents possi&le methodologies for future testing
of changing competition modes and their effect on diameter -ncrement3 The methodolog!
was developed according to the following steps:
Step $: Classif! sites according to water availa&ilit!
Step ": Determine the potential &ased on site conditions
Step F: Fit multiple competition indices
Step %: Select competition indices
Step G: 1se C-Ls in a deterministic potential modifier e2uation
Step 4: Create a stochastic model incorporating natural varia&ilit!
%-GI

Figure 4-, Flowc#art of t#e c#apter outline s#owing working steps of t#e met#odological approac# used in t#e stud"

%-GJ

$.2 tep 1: ite classification according water availabilit% and
site inde4
ith the h!pothesis in mind that the mode of competition shifts with the availa&ilit! of
edaphic factors, a simple categorisation of the sites according to water availa&ilit! was
sought, su&7ect to the availa&ilit! of data3 The FA; < 1>(P inde/ .1>(P $JJ"0 where aridit!
is calculated &! dividing the precipitation &! the potential evapotranspiration, as calculated
&! the Thornthwaite method .Thornthwaite $J%I03
-n this instance, the aridit! inde/ was fi/ed &! using monthl! weather data supplied &! the
Agricultural 9esearch Council .A9C0 climate data&ase3 This provides an added static
classification for the site3
Defining the water inde/ longitudinall! .changing over time0, either using this inde/ or other
candidate indices .8c:ee, Does)en, and :leist $JJG, Palmer $J4G0, would improve the
interaction with diameter increment3 1nfortunatel! measurements in the trials were not
ta)en at annual intervals= often at "-G !ears, which would mas) correlations3
Table 4-1 7lassification of t#e sites according to t#e FAO-89E) classification and &0. T#e Tweefontein and :ac :ac trials
used t#e same weat#er station.
1ocation )recipitation Aridit" inde' 7lassification (FAO-
89E).
A%erage &0
*ottering >elder JG# $3$#4 Humid "$3"
UTweefontein SSS-CCT $""" #3I4 Humid "F3#
:wam&onam&i $"#I $3" Humid "#3F
Du)udu)u J4# #3H4 Humid $H
eza J"H #34J Humid "#3F
U8ac 8ac $""" #3I4 Humid "%3#

Table 4-1 shows this inde/ for all of the spacing trials used in this thesis3 For the aridit!
inde/, onl! two sites were relevant, the >elder trial and the Tweefontein SSS-CCT trial, as
these were the onl! availa&le trials with tree positions necessar! for modelling the effects of
competition in this case3 However the average site inde/ .averaged over the S- values
presented in Chapter F0 was used for the potential increment estimation in Section %3F and
for the testing of the model in Sections %34 and %3H3
ith this is mind, a tentative linear model was drawn &etween the water inde/ values of the
two sites < accepting that more wor) would need to &e done to full! incorporate water
availa&ilit!3 This simple methodolog! would then &e developed and tested for future
e/periments, using this simple water inde/ as a pointer to determine whether there are an!
%-4#

functional relationships &etween the water availa&ilit! and the competition indices in this
model3
$.# tep 2: .etermine the potential based on site conditions
For the purpose of this stud!, the methodolog! proposed &! Pretzsch and +i&er ."#$#0 was
used to determine a wor)a&le simulation routine for diameter increment modelling3 -n this
procedure the potential diameter growthVincrement was first defined using the nlrq
pac)age in 9 for nonlinear 2uantile regression application .as done in Chapter F0, using the
#3JJ tau values, where:

Equation 4-1

here di
pot
is the predicted potential increment, d is the diameter .D+H0 of the tree and a
0
,
a
1
and a
2
are coefficient to &e determined in the model3 This represents the ma/imum
potential diameter increment for a given D+H < while not a true potential, it is an ade2uate
appro/imation for the purpose of this thesis3
$.#.1 Comparison of sites
Four sites were considered for potential increment parameterisation, the 8ac 8ac,
:wam&onam&i and Du)udu)u CCT trials and the >elder spacing trial3 The eza trial was not
included as there was a large period of measurements gaps= the Tweefontein SSS-CCT trial
was not included as it was too !oung3 The potential curves fitted for the considered sites are
presented in Figure 4-/ &elow3

%-4$

:ac :ac Awambonambi
Dukuduku 9elder
Figure 4-/ Fitted potential increment cur%es for t#e four sites considered for increment potential estimation
-ncluding the >elder trial to the model results in a much flatter curve which gives poor fit to
the data upon visual inspection3 This was &ecause the >elder trial was onl! measured until
"4 !ears, which did not include the flattening of the -ncrementVD+H relationship, resulting
in an interference with the gradient3 Thus the results of the potential increment curves of
the three CCT trials according to Equation 4-1 are represented &elow3

%-4"

Table 4-, )otential increment model coefficients according to Equation 4-1.

S- $H3#
S- "#3F
:wam&onam&i
S- "F3J
Du)udu)u 8ac 8ac
Parameter (stimate S( (stimate S( (stimate S(
a #3#GF" #3#$#F #3I##" #3""%$ F3JH$% #3GIGI
& "3"FIF #3#JHF #3HJ4H #3$FFH #3""I" #3#HJJ
c #3$"I #3##%" #3#GFJ #3##G" #3#F$4 #3##FJ

From Figure 4-/ and Table 4-, it can &e seen that site inde/ had an effect on the
determination of potential increment .as seen in the a&ove figures03 Thus dominant height <
or #
dom
- can &e included as a predictor varia&le to Equation 4-1, where a site 2ualit! effect
can &e included .Pretzsch and +i&er "#$#0 as was done in in Chapter F, resulting in Equation
4-, &elow

Equation 4-,

The resulting fit of the a&ove model is ta&ulated in Table 4-/ and the curves are illustrated
in Figure 4-43
Table 4-/ 7oefficients of t#e potential increment model (Equation ,. using site inde' and db# as predictor %ariables
7ombined 0ncrementF D*! model (Equation 4-,.
2alue &td. Error t %alue )r(CDtD.
a
1
#3GFH" #3"HFHH $3J4""$ #3#%JHG
a
,
#3$$%F% #3#$G4% H3F#II4 #
a
/
#3F%%"$ #3#I4"I F3JIJF #3####H
a
4
#3#FH"% #3##%$F J3#$"HH #

%-4F

Figure 4-4 )otential increment o%er D*! cur%es parameterised from t#e 77T trial dataG t#e different cur%es represent
different &0 %alues
These potentials are the JJN 2uantiles representing the ma/imum annual diameter
increment that a tree can o&tain for a given D+H and site inde/3 The estimated increment
was then modelled &! including a suita&le competition inde/, discussed in the following
sections, which should mimic the structure presented in Figure 4-13
$.$ tep #: "it various competition models
$.$.1 .istance dependent competition indices
-n this stud! five distance-dependent competition indices were used3 These indices were
chosen to capture a gradient, which would descri&e overtopping or local crowding, with the
o&7ective that two indices will &e selected which &oth ade2uatel! descri&e competition and
capture different modes of competition .Seifert et al. in review03 These, summarised in
Table 4-4 and descri&ed &elow, are the ::* .which is used in S-*EA0, the local &asal area
.*+A0, &asal area of larger trees .+A*0, Heg!i and Eoronoi pol!gons3

%-4%

Table 4-4 0llustration of t#e different competition indices used in t#is stud" (&eifert et al. in re%iew.+ i refers to t#e
central tree+ j refers to t#e competitor trees. :odels s#own below are discussed in more detail in te't below.

The ::* inde/ .Pretzsch "##J0 uses a search for competitors &ased on a search cone at an
angle of 4#W which starts at a point of 4#N of the tree height3 As most competition indices it
wor)s in a com&ination of competitor selection and the 2uantification of the competition
effect of those identified competitors3 >eigh&ouring trees, which fall inside the search cone,
are included as competitors and the angle from the tip of the neigh&ouring tree and its
ma/imum crown e/tension to the cone mantle &angle ' in Table 4-4( is calculated3 This is
used as a measure of competition, which is then multiplied &! the cross-sectional crown
area of the competitor in relation to the su&7ect tree .CCA
i
VCCA
7
03 Species specific values for
crown dimensions for P. elliottii were not availa&le, for this reason the S-*EA model was
used to calculate the ::* for the stands using Pinus sylvestris crown model as a pro/!3 The
::* is &! its design strongl! focussing on competition induced &! crown competition and
overtopping3
%-4G

The local &asal area .*+A0 is simpl! the sum of the &asal area of all trees within a
competition search radius and the reference tree located in the centre of the circle
.Stene)er and Qarvis $J4F03 -t has &een suggested as an effective measure of local crowding
and is more sensitive to measuring edaphic limitations as it does not discriminate &etween
the sizes of the trees included in the influence zone, e/cept for their &asal area contri&ution
.Seifert et al. in review03
The &asal area of larger trees .+A*0 is identical to the *+A e/cept that it onl! includes trees
which are larger in D+H than the reference tree, which would then provide a good
indication of overtopping and radiation e/clusion3
The Heg!i -nde/ .Heg!i $JH%0 calculates size ratios of the reference tree with its competitors
multiplied &! an inverse distance weighting3 These are then all summed up for each
reference tree within a zone of competition3
The Eoronoi inde/ is a simple growing space inde/ where the space in a given stand is
divided e2uall! among trees, first &! drawing distance lines &etween each tree and its
neigh&ours, these lines are then &isected and lines are drawn connecting the &isected lines,
resulting in a pol!gon for each tree &ased on its growing area with regards to its neigh&our
.Figure 4-503 This is thus simpl! a refined measure of a treeLs growing area and the
relationships would change with age and competition3 -t is included here as a &enchmar) <
to illustrate the performance of the other indices in relation to a simplistic growing area
inde/3 -t must &e noted that refinements of the Eoronoi e/ist, where the size of the
pol!gons is changed proportional to the size ratio of the tree compared to its neigh&ours or
even to measured crown dimensions .Seifert and 1tschig "##"03 This was not e/amined in
this stud!, &ut would &e a potential point of interest for future comparison3

%-44

Figure 4-5 2oronoi pol"gons calculated for t#e 9elder spacing trial as an e'ample
$.$.2 7dge effects
-n the Tweefontein SSS-CCT trial, although &order trees were present, the! were not
measured3 ith the small size of each stand, "G trees in a stand, man! of the indices will
have search zones which fall outside of the &oundar!3 This is noted as a possi&le limitation
of the stud!3
Pretzsch ."##J0 mentions three methods to simulate or e/trapolate stand structure outside
of the edge of the measured stand: plot mirroring, shifting and linear e/pansion3 -n this
stud!, the plot shifting techni2ue was used for the SSS-CCT trial, where the plot is shifted
along the sides and corners creating eight edge plots, with the measured plot in the centre3
This was not necessar! for the >elder trial, the first and last rings were simpl! repeated
along the gradient for positions3
$.$.# Competition search radius 0influence <one1
The definition of the size of the search radius is critical to the performance of the
competition indices < if the zone is too &ig or too small, information on competition will &e
%-4H

lost3 The first decision to &e made is whether the search radius should &e fi/ed or relative
.to stems per hectare for instance03 -n this stud! a fi/ed radius for the different stand
densities was chosen, however on which would change relative to the dominant height of a
stand at a certain age, the h!pothesis &eing that the size of the influence zone would change
as trees &ecome larger in a stand3 The Heg!i, *+A and the +A* indices use fi/ed search radii
and it was decided to standardise the radius for all three indices in order to draw reasona&le
comparisons3
The *+A was used as a reference to determine how large the search radius should &e as it is
the simplest of the three indices and is not complicated &! additional factors such as size of
competitors, etc3 Furthermore, the *+A inde/ has a much clearl! linear correlation with
diameter increment .Figure 4-40, with a much higher lin) to linear correlation than the other
indices, where more sophisticated nonlinear or transformation applications would have
&een necessar! to determine the ma/imum correlation with the search radius3
To determine the optimum search radius, different sizes of search radii were tested on
ever! measurement age of the >elder trial and the correlation of the *+A with diameter
increment determined .the minimum of each correlation was chosen since the size of the
competition has a negative effect on diameter increment03 This is represented in Figure 4-6
and summarised in Table 4-5 &elow3

Figure 4-6 9egati%e 7orrelation of t#e 1*A competition inde' wit# diameter increment at different measurement "ears
(ages. using different competition searc# radii+ t#e correlation was multiplied b" -1 for illustrati%e purposes.
%-4I

Table 4-5 7orrelation of t#e 1*A competition inde' at different ages of t#e 9elder trial wit# t#e resulting searc# radius
si$e included
Age
Dominant
#eig#t
:inimum correlation
Optimum searc#
radius
%3GI %3F$%HFH%I% -#3F4$I4 "34""$HF
4 G3J"J%HGH4G -#344HGF G3I4$G%J
$$3#I $$3HH4F%H#4 -#3IG"I %3F$"F#I
$F3FF $%3"IIH$F"G -#3HJ$H$ H3JH#44$
$G3GI $43H$%IJ""H -#3IF##F H3JH#44$
$J3$H "#3FHH$4#JJ -#3I"4F" H3JH#44$
"#3"G "$3%"GF#"#4 -#3GHHG" H3JH#44$
"F3IF "%3H$H%%"$ -#3I$JG$ H3JH#44$
"4 "43GH4J#$4F -#3I%HFJ $#3$$%%%

A simple linear model was then fitted for the values from Ages %-"4 < with their respective
dominant heights in order to e/clude age from the calculations illustrated in Figure 4-@, with
the resulting model in Table 4-63

%-4J

Figure 4-@ 1inear regression of t#e optimum searc# radius o%er dominant #eig#t

Table 4-6 1inear regression coefficients of t#e optimum searc# radius based on dominant #eig#t
1inear (O1&. competition $one model
)arameter
Estimate &td. Error t %alue )r(CDtD.

(stimate Std3 (rror t value Pr.XYtY0
(0ntercept. "3J#IJG $3##HI$ "3II4 #3#"F%% U
!dom #3"G#F4 #3#G4%4 %3%F% #3##F#F UU
Signif3 codes: # @UUUL #3##$ @UUL #3#$ @UL #3#G @3L #3$ @ L $
9esidual standard error: $3"G4 on H degrees of freedom
8ultiple 9-s2uared: #3HFHG, Ad7usted 9-s2uared: #3H

Thus the competition search zone will increase with the given dominant height, which was
used for all three competition indices that re2uired a search radius .*+A, +A* and Heg!i03
$.$.$ Performance of competition indices
(ach of the competition indices introduced in Section %3%3$ was applied to the *ottering and
Tweefontein spacing trials resulting in the following diameter increment in relation to the
competition inde/ plots &elow .Figure 4-403
%-H#

1ottering 9elder Tweefontein &&&-&77T
::*

*+A

+A*

Heg!i

Figure 4-4 ;elations#ip of diameter increment and t#e competition indices fitted in t#e two spacing trials used for t#is
stud"
%-H$

The Heg!i and ::* indices &oth had a clear negative e/ponential trend of increment over the
C- value, the +A* inde/ also showed a nonlinear trend and the *+A inde/ shows a linear
response3 Significant variation e/ists in the plots, especiall! when competition indices
approach zero .state of no competition03 The Eoronoi inde/ did not show much correlation
.Appendi/ +0= however this could &e &ecause the correlation changes at different ages or
stages of development of the stand, which this investigation is tr!ing to avoid3
$.& tep $: electing competition indices
As seen in the previous section, each competition inde/, &! virtue of the different aspects
that the! measure, covers different e/planator! aspects of competition and thus would
potentiall! contri&ute e/planator! value3 Thus, com&ining two or more C-Ls to the modifier
e2uation &! creating a multiple regression e2uation, more aspects of competition might &e
covered and a &etter fit ma! &e o&tained with respect to diameter increment3
However, overlap of the e/planation &etween competition indices or collinearit! ma! distort
the e/planation value of each inde/ used3 Collinearit! .or multicollinearit!, when more than
two varia&les are included in a model0 occurs when predictor varia&les in a multiple
regression are highl! correlated .8!ers $JI403 Collinearit! does not alwa!s affect the
predictive power of a model on the data that it is fit3 However, collinearit! significantl!
affects the sta&ilit! of the model and hinders the a&ilit! to draw valid conclusions a&out
individual regressor varia&les= small changes in !-values can significantl! alter model
coefficients even though measures of fit .e3g3 9
"
values0 remain relativel! unchanged .8!ers
$JI403 This would compromise one of the o&7ectives of this chapter < to determine how the
importance of different varia&les changes under different edaphic and site 2ualit!
conditions3 Additionall!, although it is tempting to add regressor varia&les .the C-Ls0 to
o&tain a &etter fit, the concept of ;c)hamLs razor should &e followed, where parsimonious
models are sought3 Furthermore, tedious calculation of ever! competition inde/ would not
&e ideal for an! future model application3
-n view of the o&7ectives of this chapter, the set of chosen competition indices was thus
tested individuall! as well as in com&inations to identif! inde/ com&inations that were not
significantl! collinear3 -deall!, a com&ination of two C-Ls was to &e o&tained that ade2uatel!
descri&e diameter increment3 The resulting model should provide a good e/planator! power
with regards to overtopping .light limitations0 and local crowding .edaphic limitation0 < as in
the e/ample of Figure 1-,3
This re2uired a varia&le selection e/ercise, where correlation .collinearit!0 and &ehaviour of
the respective indices was sought through principle component anal!sis .PCA0 and variance
inflation factors .E-FLs03 Different com&inations of C-Ls varia&les were tested se2uentiall! to
determine the &est com&ination of C-Ls3 9elative importance measures were then carried
out with the two final selected C-Ls on different sites3
%-H"

Figures 4-3 and 4-1- show the pairwise matri/ scatterplots of the different competition
indices against each other in the >elder and SSS-CCT trials, indicating correlation &etween
certain varia&les3

Figure 4-3 )airwise scatterplot matri' of t#e %arious competition indices against eac# ot#er in t#e 9elder Trial

%-HF

Figure 4-1- )airwise scatterplot matri' of t#e %arious competition indices against eac# ot#er in t#e Tweefontein Trial
$.&.1 'ariable selection
As seen in Figure 4-4 most of the competition indices were nonlinear in their effect on id3 A
simple s2uare root transformation was found to &e ade2uate to linearise the response=

where f(x) represents a linear com&ination of one, several, or all of the competition indices3
S2uare root transformations have the advantage over logarithmic transformations that, for
diameter increment where # values are prevalent, no infinite values are produced3 The
transformation produced visuall! linear fits .ordinar! least s2uares0 for all of the models,
e/cept for the ::* and Eoronoi3

%-H%

Table 4-@ 1inear models coefficients of t#e square root transformation of diameter increment using t#e respecti%e
competition indices
:odel ;
,
A07
s2rt.D&h-ncrement0 Z +A*
#34##" "#II3%#J
.-ntercept0 $3%#%44I #3##%G#F F$" T"e-$4 UUU
+A* -#3#$I4% #3###$HH -$#G3$ T"e-$4 UUU
s2rt.D&h-ncrement0 Z *+A
#3GIF% "FJ"3$"F
.-ntercept0 $3%J4$$4 #3##G"J4 "I"3G T"e-$4 UUU
*+A -#3#$%%% #3###$%" -$#$3G T"e-$4 UUU
s2rt.D&h-ncrement0 Z HgC-
#3%4#4 %"J$3H#H
.-ntercept0 $3FG%FI #3##G$%4 "4F3$H T"e-$4 UUU
HgC- -#3#H##G #3###II% -HJ3"% T"e-$4 UUU
s2rt.D&h-ncrement0 Z ))l
#3%G"% %%#F3F""
.-ntercept0 $3"%#H%G #3##%F%G "IG3GJ T"e-$4 UUU
))l -#3"GH#H #3##F"JJ -HH3JF T"e-$4 UUU
lm.formula M s2rt.D&h-ncrement0 Z Eoronoi, data M sss0
#3$JJG H$JG3#"%
.-ntercept0 #3IJF"HH #3##4"J4 $%$3II T"e-$4 UUU
Eoronoi #3##I%IG #3###$JI %"3I$ T"e-$4 UUU

Table 4-@ shows that the *+A and +A* indices e/plain the variance well, .showing the
highest 9
"
values0, although it must &e noted that the ::* could &e &etter descri&ed with an
alternative transformation3
Com&ining all of the indices into a full model to descri&e diameter increment according to
Equation 4-/ shows how a much improved fit can &e o&tained &! adding varia&les together,
indicated &! their respective names in the e2uation, with parameters a-e to &e determined
.Table 4-403

_BE
I
=o kkl +b Ecgyi +c IBA+J Ioronoi +c
Equation 4-/

However, due to interactions and collinearit! &etween varia&les, a decision has to &e made
of which varia&les should &e included in the model that represents a good compromise
&etween model fit and reduced correlation &etween the varia&les3 Eariance inflation is one
method used to detect collinearit! .8!ers $JI40:
%-HG

Equation 4-4

where the VI for a varia&le is the reciprocal of the inverse of 9
"
from the regression3
Eariance inflation is calculated for each of the e/planator! varia&les3 As a guideline a E-F of
G, or a s2uare root of the E-F larger than two, indicate collinearit! in the model3
Table 4-4 Full linear model of t#e square root diameter increment transformation using all of t#e 70Hs as regressor
%ariables
8odel: s2rt.Diameter -ncrement0 M *+A [ +A* [ HgC- [ ::* [ Eoronoi
Parameter (stimate Std3 (rror t value Pr.XYtY0 E-F s2rt.E-F0
.-ntercept0 $3G#%4JI" #3##IJHH4 $4H34#4 T "e-$4 UUU
*+A -#3##H"FIJ #3###"F%4 -F#3I4F T "e-$4 UUU F3%J444G $3I4JJFH
+A* -#3##4G"$$ #3###F%HI -$I3H%J T "e-$4 UUU %3HG#$II "3$HJ%JF
HgC- -#3#$4G%H4 #3##$%IGH -$$3$FI T "e-$4 UUU %3H$#"J$ "3$H#F"$
))l -#3#%F%$#H #3##G"J%$ -I3" "3I"(-$4 UUU %3F4$$J$ "3#IIF%4
Eoronoi -#3###%GIH #3###$HJF -"3GGI #3#$#4 U "3#"4%I" $3%"FG%4
8ultiple 9-s2uared: #34H4H, Ad7usted 9-s2uared: #34H4G
F-statistic: F#HH on G and HF%J DF, p-value: T "3"e-$4

Table 4-4 shows a significant fit for all of the parameters, however E-F is 2uite high for most
of the varia&les indicating that the model needed to &e reduced and dependencies &etween
varia&les &etter understood3
$.&.2 Principle component anal%sis
Principal component anal!sis .PCA0, .Hotelling $JFF0, can &e used to reveal similarities in
e/planation value and thus collinear structures &etween varia&les3 -t is a multivariate
statistical feature e/traction method that wor)s &! pro7ecting the data onto orthogonal
vectors, called principal components, which e/plain the ma/imum variation of the data3
These principal components are the features of the data3
Detailed information of PCA can &e found in multiple te/ts3 +riefl! e/plained though: -f I is a
matri/ with the columns representing varia&les and the rows representing sample
o&servations, the first principal component p
$
is the linear com&ination where the
pro7ection onto p
$
, given &! + !ields the ma/imum variance su&7ect to 3
The pro7ection onto the second principal component p
"
is the com&ination that
gives the second highest variance su&7ect to and p
"
&eing orthogonal to p
$
3 This is
e/tended to all further principal components3 The orthogonalit! criterion ensures that each
component is completel! uncorrelated with all other components, there&! ensuring that the
components e/plain the ma/imum variation3 The principal component loading vectors, pi .i
%-H4

M $,\, m0, are the eigenvectors of the covariance matri/ of the data set, therefore the! can
&e o&tained from spectral decomposition of the covariance matri/3
;nce the principal components have &een determined a &iplot can &e used to visualise
which varia&les contri&ute most to each principal component, it also shows similarities or
collinearit! &ehaviour of the varia&les in relation to each other in the transformed space3
hen a &iplot is applied to PCA results, the a/es are a pair of principal components3 The
points represent the principal component scores of the o&servation, and the vectors
represent the coefficients of each varia&le on the principal components3 So in the &iplot the
longest vector will represent the varia&le that contri&utes most to the variation in the data
and therefore provides the most important information for the model3
9 has a function called princomp in its stats pac)age for PCA3 A data matri/ consisting of the
competition indices is passed into it and it performs PCA on it3
Table 4-3 0mportance measures of t#e principle components
0mportance of components
:easure 7omp.1 7omp., 7omp./ 7omp.4 7omp.5
&tandard de%iation $34%4#"$ $3#F%#$" #3IHJ%4F #3G4#H%I #3F4G%"J
)roportion of 2ariance #3G%$IHH #3"$FIF4 #3$G%4J$ #3#4"III #3#"4H#I
7umulati%e )roportion #3G%$IHH #3HGGH$F #3J$#%#G #3JHF"J" $

Table 4-3 a&ove shows that Component $ accounts for G%N of the variation in the data: The
loadings of each varia&le .C-0 of the principle components a&ove can &e shown numericall!
in Table 4-1-3
Table 4-1- )rinciple component loadings of t#e respecti%e principle components
)rinciple 7omponent 1oadings
0nde' 7omp.1 7omp., 7omp./ 7omp.4 7omp.5
AA1 -#3%GG #3%"% -#3%"$ -#3"IG -#3GJ4
*A&A1 -#3%HJ #3"I4 #3F#F -#3%J4 #3GJ"
1*A -#3%GG #34IH #3%%H -#3F%I
!g70 -#3%H4 -#3G#F #34 #3FJI
2or #3F4$ #3IGI #3FF4 #3$""

Eisuall! this is shown in the &iplots for &oth sites .Figures 4-11 and 4-1,0, where the length
of the arrow for each varia&le indicates its contri&ution to the component loading3

%-HH

Figure 4-11 )7A biplot of t#e %ariable plotted in t#e transformed space of t#e first two principle components in t#e
9elder trial

Figure 4-1, )7A biplot of t#e %ariable plotted in t#e transformed space of t#e first two principle components in t#e
Tweefontein trial
%-HI

>ot much can &e determined from the length of the vectors .or their loadings0 as the! load
relativel! e2uall! on the two main components3 However, Figures 4-11 and 4-1, show
consistent performance on the two sites with regards to &ehaviour .grouping0 of the C-
varia&les3 The Eoronoi inde/ is negativel! correlated to the other potential predictors < a
high Eoronoi area will mean that there is more growing space and thus a higher increment,
as opposed to the other varia&les which increase in values with increasing competition3
However, what is interesting is the correlation &etween the other four varia&les, which will
&e necessar! for stratification of the varia&les to ma)e deductions a&out their e/pected
similarit!3 The ::* and the +A* are ver! similar, as the! characterise competition strongl! &!
overtopping3 The Heg!i and *+A, which might e/plain edaphic competition .local crowding0
to a higher degree, are closel! grouped compared to the other indices3
As e/plained earlier, collinearit! will &e a pro&lem for creating a com&ined model3 The PCA
loadings a&ove give a 2ualitative idea of which varia&les to include3 Clearl!, the two groups
can &e seen, with the ::* and +A* closel! related, and the Heg!i and *+A closel! related as
well3 -t was decided to include one varia&le from each grouping .e3g3 the ::* and Heg!i0 for
multiple collinearit! pro&lems and for parsimon! in the model3 The Eoronoi inde/ was not
considered for further modelling purposes due to its low e/planation value .Table 4-@ and
Table 4-603 Table 4-11 &elow shows the results for the various pairings of indices:

%-HJ

Table 4-11 1inear model coefficients for t#e combinations of t#e competition indices
:odel 20F &qrt(20F. ; , A07
sqrt(Db#0ncrement. J kkl K 1*A
$3G4F $3"G# #34GG $##G34GH
.-ntercept0 $3%4H #3##G F##3JG T"e-$4 UUU
))l -#3$"I #3##F -FJ3#I T"e-$4 UUU
*+A -#3#$$ #3### -4G3HF T"e-$4 UUU
sqrt(Db#0ncrement. J kkl K !g70
"3J$G $3H#H #3G#% F4H$3HHG
.-ntercept0 $3F""JJ% #3##G#IG "4#3$H T"e-$4 UUU
))l -#3$F4%H4 #3##GFGI -"G3%H T"e-$4 UUU
HgC- -#3#%#$HJ #3##$%%H -"H3HH T"e-$4 UUU
sqrt(Db#0ncrement. J 1*A K *A1
F3#FF $3H%" #34G$ $#IJ3H4F
.-ntercept0 $3%I%$%J4 #3##%IGH F#G3GG T"e-$4 UUU
*+A -#3##H%"I #3###""H -F"3HF T"e-$4 UUU
+A* -#3#$#J#% #3###"IJ -FH3HH T"e-$4 UUU
sqrt(Db#0ncrement. J !g70 K *A1
"3#"% $3%"F #34FF $%GH3FI#
.-ntercept0 $3%F"%IJG #3##%%%H F""3$" T"e-$4 UUU
HgC- -#3#"444$ #3##$#FH -"G3H$ T"e-$4 UUU
+A* -#3#$%""$ #3###"%" -GI3I" T"e-$4 UUU

The com&ination of the ::* and *+A indices had the &est 9
"
values, lowest A-C values and
had lowest E-F < suggesting that the! were the least collinear of the a&ove com&inations
and represented the &est fit3 A com&ination of *+A and +A* also resulted in a good fit=
however the E-F was the highest as the! are &ased on the same competition inde/3
The com&ination of ::* and *+A intuitivel! represent different modes of competition, which
is 2uantified in the &etter fit o&tained and the low collinearit! &etween the two C-Ls3 These
two were thus selected as a candidate com&ination to test the changing mode of
competition and com&ination of C-Ls for the modifier function3
$.&.# /elative importance
>ow that a candidate com&ination was o&tained, where collinear effects would &e minimal
to the e/planation value of the two C-Ls - a comparison &etween the importance of varia&les
in each site is given3 The full model and the suggested reduced model .::* and *+A0 are
introduced to see how the! change over the two sites < assuming that the water inde/ is
representative of a gradient3
%-I#

The relaimpo pac)age developed &! 'rPmping ."##40 in 9 was used for this purpose3 The
pac)age provides different methods for decomposing the contri&ution of 9
"
with different
predictor varia&les provided that the regressors are not correlated3 'rPmping ."##40
recommends that two particular methods AlmgD method and Apm%dD method, with lmg
more appropriate for causal anal!sis and pm%d more appropriate for predictive anal!sis
.'rPmping "##403 The other methods were included here for a complete picture to anal!se
whether the relative importance changes consistentl! with other variance decomposition
methods3
The results for the >elder and Tweefontein trials are summarised in Table 4-1, &elow, using
different variance decomposition methods for illustration and to see consistenc! with other
methods, although the lmg and pmvd methods are of importance3
Table 4-1, ;elati%e importance proportions (e'planation contribution. of t#e AA1 and 1*A indices respecti%el" using
different importance measures
9elder Tweefontein
:et#od AA1 1*A AA1 1*A
lmg #3%F$ #3G4J #3%#H #3GJF
pm%d #3F"J #34H$ #3"GG #3H%G
betasq #3F"J #34H$ #3"GG #3H%G
car #3%$F #3GIH #3FHJ #34"$
last #3F"J #34H$ #3"GG #3H%G
first #3%GH #3G%F #3%%F #3GGH
Total ;, 4$3H$N 4J3$4N

The *+A was attri&uted consistentl! a higher importance to the variance e/planation of the
model on ever! method t!pe3 -n the lmg method, this was small, suggesting a small
difference &etween sites, however the pm%d method showed a much larger difference3 The
results are illustrated in Figure 4-1/ and Figure 4-14 for the Tweefontein and >elder sites
respectivel!, with JGN &ootstrapped confidence intervals for the respective importance
values for the different C-Ls3
%-I$

Figure 4-1/ ;elati%e importance grap#s using different met#ods for t#e Tweefontein spacing trial

%-I"

Figure 4-14 ;elati%e importance grap#s using different met#ods for t#e 9elder spacing trial s#owing impro%ed AA1
importance as compared to t#e Tweefontein site
9egardless of the method it is clear the *+A has the largest contri&ution to the 9
"
value in
&oth sites, with the ::* increasing in importance in the >elder site, which was classified as a
wetter site according to the aridit! inde/ .Table 4-10 for &oth the lmg and pm%d methods
consistentl!3 -t can &e tentativel! h!pothesised that this could &e due to the &etter moisture
conditions on the site3 This is an encouraging result for changing importance of competition
indices &ased on resource limitations and changing mode of competition3 However more
sites are necessar! for proper validation of such a h!pothesis3 For the purpose of this thesis
water inde/ was used as a considered addition to the modifier function3
$.( tep &: =se CI>s in a deterministic potential modifier
e6uation
Step " defined the potentials, which can &e modelled for an! given diameter on a certain
site3 1sing the information gained in the previous section, the competition indices can now
&e incorporated into a modifier3 Two o&7ectives are represented here: to see whether the
%-IF

incorporation of an additional competition inde/, which would &alance the light oriented
::* with an inde/ more focussed on local crowding and edaphic limitations, would improve
the model3 The second o&7ective is to see if the incorporation of a water inde/, which can
scale the C-Ls according to the availa&le water, improves the model fit3
$.(.1 ,b-ective 1: Incorporating the :B! competition inde4
1sing the ::* and the *+A in a linear model within the modifier of the potential modifier
approach results in Equation 4-5:

Equation 4-5

here is the mean annual diameter increment, is the potential diameter
increment for that specific site with its given site inde/ calculated in Equation 4-, and
illustrated in Figure 4-4, and the e/ponential function with the linear e2uation representing
the modifier3 For the >elder and Tweefontein sites together this was represented &!:
Table 4-1/ 7oefficients of t#e diameter increment potential modifier formula (Equation 4-5.
Formula Equation 4-5
)arameter Estimate &td. Error t %alue )r(CDtD.
a -#3%""%J4" #3##4HF"" -4"3H4 T "e-$4 UUU
b -$3$JJ$JF4 #3#%#I%%% -"J3F4 T "e-$4 UUU
c -#3##F4$$F #3###GFI" -43H$ "3#J(-$$ UUU
9esidual standard error: #34H#F on H%JF degrees of freedom

The e/ponent of the linear e2uation scaled the linear e2uation &etween # .a&solute
theoretical competition: no growth0 and $ .no competition: ma/imum growth03 The
intercept presented a potential pro&lem as it will alwa!s reduce the potential .i3e3 the
modifier will never reach $ .the potential growth03 However, e/cluding this intercept
resulted in an over scaled, unrealistic model where too man! trees are growing at the
potential or not growing at all, which would not &e ideal for the simulation3 For this reason,
it was decided not to e/clude the intercept from the model in order to o&tain a good
average, with a stochastic component to &e added later .Step 403
As stated, the first o&7ective is to see whether including the local &asal area in addition to
the ::* improved the model3 This was done &! onl! including either the *+A or ::* in
Equation 4-5, comparing each of them in addition to the com&ined model3

%-I%

Table 4-14 Ano%a comparison if Equation 4-5 wit# AA1+ 1*A and bot# indices included in :odel 1+ , and / respecti%el"
Anal"sis of 2ariance Table
:odel ;es.Df ;es.&um &q Df &um &q A07 ;:&E F %alue )r(CF.
1 H%J% FFIG3G $GF"#3F% #34H"#%
, H%J% %$FJ3J # # $4I"I3FI #3H%F$GH
/ H%JF FF443G $ HHF3FH $G"I#3"J #34H#$GI $H"$3F T "3"#(-$4 UUU

The Anova comparison shows a significant improvement to the A-C, 98S( and F-statistic3
-ncluding &oth indices seems to indicate that including the *+A in con7unction with ::* in
Equation 4-5 improves the predictive fit for diameter increment modelling3
$.(.2 ,b-ective 2: Incorporating a water inde4
-n order to include the water availa&ilit! with the aridit! inde/ presented in Table 4-1, a new
linear model inside of the modifier can &e incorporated:

Equation 4-6

here ! represents the FA; < 1>(P .$JJ"0 water inde/, ""# and #$% are the C-Ls and a is
the intercept3 This can &e incorporated as the modifier into Equation 4 -@:

Equation 4-@

Table 4-15 7oefficients of t#e diameter increment potential modifier formula (Equation 4-@. incorporating t#e water
inde'
Formula Equation @
)arameter Estimate &td. Error t %alue )r(CDtD.
a -#3%F#"G #3##4I4I -4"34%H T "e-$4 UUU
b -$3$G4"H #3#%#""" -"I3H%H T "e-$4 UUU
c -#3##"JI #3###GF -G34"" $3J4(-#I UUU
9esidual standard error: #34HI" on H%JF degrees of freedom

Section %3G3F .9elative importance0 showed that for the two sites &eing used for
parameterisation, the importance of the indices changed for the s2uare root transformed
model3 Thus the ne/t o&7ective was to see whether the water inde/ does indeed improve
the model &! comparing Equation 4-@ and Equation 4-5

%-IG

Table 4-16 Ano%a comparison of t#e diameter increment model wit# (:odel1. and wit#out (:odel ,. t#e water inde'
Anal!sis of Eariance Ta&le
8odel 9es3Df 9es3Sum S2 Df Sum S2 A-C 98S( F value Pr.XF0
$ H%JF F%%43J $G%GH3#" #34HI$#%
" H%JF FF443G # # $G"I#3"J #34H#$GI

Table 4-16 shows no significant difference &etween the two models &ased on the F-statistic3
This could mean that with onl! two sites containing num&ers of o&servations and onl! two
water inde/ values, not enough information was availa&le to test whether this should &e
included in the full model, despite the plausi&le relative changes of the varia&le importance
o&served .%3G3F03 Furthermore, as the water inde/ was a static value for each site, it ma! &e
improved &! a water availa&ilit! inde/ in order to introduce d!namic effects3 1nfortunatel!,
such an inde/ was not availa&le in this stud!3 -n order to test whether the model
performance was due to the relative size of the datasets < random samples from the >elder
e/periment were ta)en to match the num&er of o&servations of the Tweefontein site and a
comparison tested .Table 4-1@03
Table 4-1@G Ano%a comparison of t#e diameter increment model wit# (:odel1. and wit#out (:odel ,. t#e water inde'
b" randoml" subsetting data from t#e 9elder trial to matc# t#e number of obser%ations in t#e Tweefontein trial
Anal"sis of 2ariance Table
:odel 9es3Df 9es3Sum S2 Df &um &q A07 ;:&E F %alue )r(CF.
1 "%FJ $#JF3F %JHG3HF" #344J$$I
, "%FJ $#%I3I # # %IH%3"F% #34GGFG4

This result was consistent with multiple randomised samples, suggesting that the water
gradient provided here &etween the two sites ma! not have &een large enough to cover
changes in C- &ehaviour with water availa&ilit!3 For further modelling it was decided to use
the model .Equation 4-@0 with the water inde/ on the different sites nonetheless since it
showed a logical &ehaviour and was statisticall! not different in the e/planation value than
Equation 4-5 without the water inde/3
$.(.# *odel behaviour
Predictions from (2uation H were used on the two datasets to anal!se the structure of the
predicted values compared to the o&served increment values3 Figure 4-15 shows the
procedure where the potentials for each given site are calculated .a0, after which a modifier
.&0 reduces the increment3 The o&served and predicted increments for each site are shown
se2uentiall! .c-f03

%-I4

a. )otential increment cur%es b. :odifier

c. 9elder obser%ed d. 9elder predicted

e. Tweefontein obser%ed f. Tweefontein predicted

Figure 4-15 0llustration of t#e potential modifier approac# on t#e two spacing trials+ wit# t#e top rig#t #and diagram
representing t#e c#ange of t#e modifier o%er t#e si$e of competition
%-IH

The predicted increment follows a pattern that mimics the trend of competition at different
D+H values .Figure 4-10= however the predicted values show much less varia&ilit! than the
o&served increments shown a&ove3
hat is also evident is that the predicted increments are constrained &oth &! the potential
and &! the ma/imum value of the modifier .which was #34G in this case0, which means that
the increment cannot increase a&ove #34G times the increment potential for a given D+H3
The depression of the modifier was due to the inclusion of an intercept in the modifier
e2uation .a in Equation 4-@0, which was nonetheless included &ecause it includes variation
from factors une/plained in the model and prevents e/treme values in the modifier3 -t was
decided to test the performance of this model, and then to incorporate random varia&ilit!
as a stochastic component for further improvement in the ne/t section3
$.(.$ *odel validation
The chosen model .Equation 4-@0 was tested on the >elder spacing trial, with the first
measurement age .%3GI !ears in the >elder trial0 used as a starting point3 The simulation
time step period was not initiated .in S-*EA it is G !ears03 -n this case the simulation is
performed &etween measurement periods to test how the model reacts in the different
time steps3 This means that the effect of competition is constant &etween two
measurement ages < thus the simulated increment will remain the same for that period3
The simulated series of the deterministic model .without variance component0 produces a
series where the diameter increment and thus D+H is overpredicted from age 4 to "F, after
which point it &egins to converge again .Appendi/ C03 The full range of simulated periods is
shown in Appendi/ D3 Figure 4-16 &elow shows the end of the simulation at "4 !ears of the
>elder trial .the final measured age of the trial03
%-II

Figure 4-16 7omparison between t#e obser%ed (red bars. and t#e simulated diameter (D*!. represented as a
distribution of ,.5cm diameter classes. T#e mean D*! for t#e site is represented in t#e notc#ed bo'plot. T#is s#owed a
skewed prediction grouped around a narrower D*! band
As can &e seen from the simulation end .Figure 4-160 and Appendi/ D the diameter
simulated D+H distri&ution shifts towards higher D+H classes, clustered around a narrow
range of D+H3 hile this is still a significant improvement from a simple mean model, this
could &e pro&lematic in the simulation as it will reduce the varia&ilit! of the diameter
classes in the model and reduce the competitive comple/it!3 Thus with each simulation step
the model continues to shift in this trend, there&! compounding the error3 For this reason it
was necessar! to see whether the increment prediction with varia&ilit! improved the model
< and finall! in which rings .and corresponding SPHA0 of the >elder trials it overpredicted3
$.+ tep (: Create a stochastic model incorporating natural
variabilit%
$.+.1 Incorporating natural variation
Due to the comple/ nature of &iological s!stems, and our ina&ilit! .or difficult!0 to capture
this comple/it! in a model with distinct varia&les, it is often necessar! to account for this
varia&ilit! around the mean value with the help of stochastic models .Pretzsch "##J03 -n this
case it is desired to appro/imate .or mimic0 the high degree of varia&ilit! of diameter
increment, which could &e caused &! factors not included in the model, e3g3 micro-site
variation in water and nutrient suppl!, weather, genetics, etc3 As is seen &! the scatter plot
of Figure 4-1@, which represent a residual plot of the predicted value deviation, while much
of the increment patterns can &e discerned from stand ageVcompetition and the diameter
of the tree, there remains a need to incorporate random variance into the model in order to
mimic natural varia&ilit!3 Furthermore, the application of the model led to a mismatched
%-IJ

diameter distri&ution, s)ewed to the right and highl! concentrated around a narrow &and of
diameter classes .Figure 4-1603 For this reason a stochastic model was tested that
incorporates varia&ilit! &! including a random deviate in the increment function3
-t was decided to incorporate natural variance &! anal!sing the residual scatter plots of the
predicted values for the two parameterisation sites, with the residual standard deviation of
the o&served minus the predicted values plotted over the predicted values .Figure 4-1@03
*inear 2uantile regression models of the residual plots were created to represent the upper
and lower &ounds and a new random deviate would then &e generated &etween these two
&ounds &ased on a normal distri&ution3

Figure 4-1@ ;esidual plot of t#e predicted %alues of t#e spacing trials
The scatter plot shows that the variance seems to increase slightl! with increasing predicted
increment values3 This is more clear in the negative tail of the distri&ution, which is
e/pected since the increment is &ound &! the lower zero value .diameter does not usuall!
&ecome negative03 To model this relationship the #3JG and #3#G tau value .GN and JGN0
linear 2uantile regression lines were used to represent the upper and lower &ounds
respectivel! of the residual plot .Figure 4-1403 The &enefit of the 2uantile line is that it
allows continuous variance &ounds for an! given predicted value3
%-J#

Figure 4-14 5L and 35L linear quantile regression lines w#ic# represents t#e upper and lower bounds for t#e truncated
normal distribution
This significant positive .tauM#3JG0 and negative .tauM#3#G0 slope values for the 2uantile
lines illustrate an increasing varia&ilit! for higher predicted values, with strong deviation in
the negative direction, while the variance in the positive residual direction onl! increases
slightl!3 The values of the 2uantile lines are shown in Table 4-14 &elow3 For instance this
means that &ounds of the variance for a diameter increment of $3G would &e &etween -#3J"
and $3F#3
Table 4-14 1inear quantile regression coefficients of -.-5 and -.35 tau %alues representing t#e upper and lower bounds
of simulated residual prediction
rq(formula B 0ncrement residuals J )redicted 0ncrement+ tau B c(-.-5+ -.35..
tau %alue )arameter 2alue &td. Error t %alue )r(CDtD.
tau -.-5
(0ntercept. -#3$I4%I #3#""GJ -I3"G%$4 #
0ncrement -#3%IHI% #3#$%4% -FF3FF"F #
tau -.35
(0ntercept. $3$G#44 #3#FH"J F#3IG%FH #
0ncrement #3#J%%H #3#"G% F3H$III #3###"

hile the 2uantiles do not capture all of the data points, the! proved to &e the most ro&ust
with some o&served variation sacrificed3
%-J$

As is seen from Figure 4-14 the predicted &ounds from the 2uantile regression is 2uite
large, indicating a high degree of varia&ilit!, however, the points are still strongl! clustered
around the mean or predicted value and the distance of the &ounds increases with
predicted increment3 For this reason and &ecause the distance &etween the &ounds changes
over the size of the predicted increment0, a weighting factor was added to the standard
deviation value of the normal distri&ution, where the standard deviation is defined &!:
Stc: = u.S (uppcr lowcr)
Equation 4-4

where St&e' is the standard deviation of the normal distri&ution, (pper and lo)er are the
truncation &ounds for an! predicted value3
The results of the predicted diameter increment &ased on the complete stochastic model
produced a scatter plot illustrated &elow overlain on the o&served residual plot .Figure 4-
130, with the full visual procedure illustrated in Figure 4-,-3

Figure 4-13 )redicted residual generated from a random de%iate between two bounds (Figure 14. based on a normal
distribution
%-J"

Figure 4-,- &equential process of generating random de%iation+ from plotting residuals (top left.+ predicting bounds
(top rig#t.+ generating random de%iation (bottom left. superimposed on t#e residual plot (bottom rig#t.
The new predicted scatterplot showed a similarit! to the o&served natural deviation3 -t
remained to &e seen how these deviate result in an improvement of the increment model3
The new predicted icrement values with the random deviates added had to &e compared to
the increment values3 This was done visuall! initiall! to see if it matches the structure of the
increment-D+H scatter plots, with its distinctive pattern3 Figure 4-,1 and Figure 4-,, &elow
shows the improvement of the stucture from the o&served increment for the >elder and
the Tweefontein sites respectivel!, with the predicted plots without deviation and the
predicted plots with deviation3

%-JF

Figure 4-,1 Obser%ed and predicted scatterplots for t#e Tweefontein &&-77T spacing trial+ wit# black points
representing t#e obser%ed and green representing t#e predicted %alues. T#e left #and image represents t#e scatter of
t#e a%erage model M wit# t#e linear quantile in t#e top rig#t+ t#e bottom left and rig#t images represent t#e scatter of
t#e model wit# added modelled random %ariance
%-J%

Figure 4-,, Obser%ed and predicted scatterplots for t#e 1ottering 9elder spacing trial+ wit# black points representing
t#e obser%ed and green representing t#e predicted %alues. T#e top rig#t image s#ows t#e deterministic model+ t#e
bottom left and rig#t images represent t#e scatter of t#e model wit# added modelled random %ariance

%-JG

Figure 4-,/ ;esidual scatter of t#e added random %ariance model for t#e parameterised sites
%-J4

Figure 4-,4 ;esidual scatter o%erlain on t#e obser%ed increment scatter of t#e added random %ariance model for t#e
parameterised sites. T#e black points represent t#e obser%ed and t#e green points represent t#e predicted %alues from
t#e stoc#astic model.
The new plots .Figure 4-,/ and 4-,40 seemed to mimic the o&served increment 2uite well,
matching the point clouds o&tained from the competitive situation at different
measurement ages, e/cept for a depressed tail of points at higher D+H values .with lower
predicted increment curves03 -t is now necessar! to see how the new random deviates
&ehave in a simulation over time3 This is done in the validation section &elow3
*odel 'alidation
Adding varia&ilit! should prevent model from collecting or converging towards a mean
around one D+H class, as was seen form the simulated model .Appendi/ D03 The same
simulation was done as in Section %343%, this time with the random variance added to the
prediction, shown in Appendi/ ( with the end point at "4 !ears shown in Figure 4-,53
Diameter increment is clearl! overestimated at most ages, for &oth the model including
varia&ilit! and without3
%-JH

Figure 4-,5 Obser%ed (red bars. %s. simulated (blue bars. for t#e 9elder trial wit# random de%iation added at eac#
point. T#e model s#ows a clear o%erall o%erpredicition of D*!+ #owe%er wit# an impro%ed distribution compared to t#e
model wit#out de%iation (Figure 4-16..
From a diameter distri&ution point of view, the predicted model is clearl! superior <
although shifted to the right due to the overpredicted d&h originating from the
deterministic model part3 The model overall showed an overprediction for the >elder trial,
however with the e/treme planted densities that e/ist .from 4H##- $"4 spha0 it is necessar!
to see at which densities the model is not predicting well3 For the end of the simulation run
the following Table 4-13 shows the average o&served vs3 predicted D+H values for the
different >elder rings .and corresponding stems per hectare0 at "4 !ears:

%-JI

Table 4-13 A%erage of obser%ed and predicted %alues for t#e different 9elder plots+ s#owing clearl" t#at t#e model
underperforms at e'treme densities
)lot
(ring.
&)!A
()lanted.
A%erage of predicted
D*!(cm.
A%erage of obser%ed D*!
(cm.
Difference
% $"4 %"3%4 GF3$G -$#34J
G $4H %F3$I G$3%# -I3""
4 """ %"34% %I34I -43#%
H "JG FJ3G4 %%3JF -G3FH
I FJ$ %#3$% %"3## -$3IG
J G"# FH3G4 F43%I $3#I
$# 4J$ F43FH F%34G $3H$
$$ J$H F%3$4 F$3J% "3""
$" $"$J F"3"" "I3II F3F%
$F $4$J "J3JJ "F3I4 43$F
$% "$G$ "H3%# ""3G# %3J#
$G "IGH "G3HJ $J34H 43$"
$4 FHJ4 "F3%$ $I3F$ G3$#
$H G#%F ""3J% $43%# 43G%
$I 4H## ""3FG $%3HI H3GH

Table 4-13 shows that the model overpredicts at high densities and underpredicts at ver!
low densities= however, at moderate densities at which most stands would &e planted and
managed under in plantation stands .highlighted in &lue0, the difference is relativel! small3
This difference is illustrated as a percentage in Figure 4-,6 &elow3

%-JJ

Figure 4-,6 De%iation of predicted a%erage diameter increment for a more realistic of planted stand densities for a
plantation industr" setup in t#e 9elder trial

$.8 Chapter conclusion
The main o&7ective of this chapter was to model diameter increment in as a function of
resource limitations and site classification for application of a methodological &ased
approach for a specific dataset to outline pro&lems and future wor)3 This was split into the 4
su&-o&7ectives which formed the outline of the wor)ing steps of the chapter3 This main
o&7ective was achieved, however some )e! issues arose which will &e discussed according to
the si/ wor)ing stepsVo&7ectives of the Chapter3
The water inde/ introduced in the first step proved not to &e ade2uate to capture a large
enough gradient &etween the two sites for modelling purposes3 However, it did result in a
shift &etween importance of the competition indices discussed later3 Potential increment
curves were applied &ased on a given D+H on different stands, which showed clear
differences &etween sites3 -ncorporating site inde/ as a site 2ualit! measure into the
potential increment model resulted in a gradient of predicted potentials from site 2ualit!3
-n order to include a modifier multiple distance-dependent competition indices were tested
on two sites with availa&le tree positions with the o&7ective to identif! a com&ination of
%-$##

indices that showed small collinearit! while e/plaining diameter increment well3 The )e!
idea &ehind this was to capture a gradient &etween overtopping .light limitation0 and local
crowding .edaphic limitations0 modes of competition as highlighted &! Seifert et al. .in
press03 The chosen competition indices reacted differentl!, &ut in order to identif! and
2uantif! the differences the &ehaviour and correlation &etween the indices were e/amined3
Differences in PCA &iplots and improved fit with low collinearit! resulted in the decision to
choose the *+A and ::* indices in a com&ined model3 -ncorporating a competition inde/
which captures more size s!mmetric competition .*+A0 seemed, under the fitted model
constructed a&ove, to improve prediction compared to model rel!ing purel! on the
standard S-*EA competition inde/ ::*3 The relative importance of the ::* and *+A to the
transformed model changed under different site conditions on the two sites, with the ::*
increasing in importance in the less drought affected site3 -ncorporating &oth indices in one
model has potential to capture changing competition s!mmetr! under changing water
availa&ilit! - although this needs to &e investigated under a much wider gradient of sites
with var!ing water availa&ilit! and perhaps of different !ears of the same site in a
longitudinal stud! approach3
The results have shown that including the aridit! inde/ in the modifier e2uation presents
potential for inclusion of a water inde/ into the diameter increment prediction3 Although
the chosen approach was ver! simple, restricted &! site and data availa&ilit!, and relia&le
conclusions are difficult to ma)e with regards to changing importance of C- models, it could
&e used for further parameterisation of S-*EA3 The ideal situation would &e to com&ine a
water inde/ and weather data with a soil water &alance model to estimate water
availa&ilit!, which was outside the scope of this thesis3 -n this stud! the longitudinal data
aspect was not considered due to time and resource limitations, however, it must &e noted
that this ma! have a significant effect, which should &e anal!sed in future studies3
The presented model matched competitive stages, achieving the o&7ective of o&taining an
age-independent model3 The potential modifier model with the competition indices were
still not a&le to capture the wide range of varia&ilit! o&served in diameter increment
predictions= this lead to a s)ewed, narrow prediction of D+H distri&ution of predicted
compared to o&served distri&utions3
The use of a linear 2uantile regression for the truncation of a normal distri&ution &etween
residuals, and a random prediction &ased on a normal distri&ution proved to &e a ro&ust
methodolog! to incorporate natural variation3 However, the captured varia&ilit! was not
large enough to mimic the variance in o&served stands3 -t is the opinion of the author that
the pro&lem originates from the deterministic model, where the competition indices were
still not sensitive enough to model diameter &ased solel! on a potential and competition in
the modifier3 -t is thought that including allometric relationships, such as diameterVheight or
crown dimensions into the model would greatl! improve the situation3 The structure of the
::* inde/ ma! also not currentl! &e suited to capture the competitive situation in the South
%-$#$

African conte/t= changes could &e made to the angle of the search cone which detects and
counts potential competitors3 This could &e tested in a sensitivit! anal!sis3 The pro&lem
could also &e related to the size of the trees < larger trees ma! &e e/pected to deviate in the
upper regions of the random spectrum for instance3 This was not addressed in the model
and represents a )e! issue for future wor)3
Further refinements to the stochastic model could &e made &! testing the normalit!
assumption and &! using a ei&ull distri&ution for instance3 The variation predicted also did
not ta)e into account densit! effects in the o&served residual plot, which ma! affect the size
of the variation of diameter increment under different degrees of competition .a higher
variation at low competition for instance0= this could &e a consideration for an investigation
for future studies, which ma! ma)e the stochastic model more sensitive to different stand
densit! ranges3
Eisual anal!sis of the new predicted increments showed a good li)eness to o&served
-ncrement-D+H scatterplots3 -ncorporating a varia&ilit! to move into stochastic modelling
drasticall! improved the D+H distri&ution pro&lem, matching o&served D+H values
reasona&l! well3 The model seemed to capture the average situation 2uite well3
This Chapter serves as an e/ample of a methodological approach to simulate diameter
increment com&inations of distance dependent competition indices and stochastic
modelling3 Future studies can greatl! improve the process &! considering further sites with
different water indices and site 2ualit! and &! stud!ing the shifting importance of
competition indices under different water availa&ilit! in order to increase the sensitivit! of
the model to changing climatic conditions3

G-$#"

Chapter &: Conclusion and recommendations

This chapter provides a &rief overview of what was achieved and recommendations for
future wor), as most of the issues have &een discussed in the individual chapters alread!3
This is divided into two sections: the wor) which was applied in this thesis .the potential
height and diameter increment models in Chapters F and %0 and steps for further
parameterisation for S-*EA, which were not applied in this thesis3
&.1 Potential height modelling
The overall o&7ective of this chapter was to model potential height and to see whether site
inde/ can &e used as a predictor varia&le for potential height3 -n this sense the overall
o&7ective was achieved as it seemed to &e a via&le approach3
>onlinear 2uantile regression proved to &e a ro&ust method for conditional median
modelling, in this case of the potential height3 The algorithm used seems to &e less affected
&! outliers than other least s2uares estimation techni2ues3 There were some limitations
worth noting: for one, as with man! models, it is &ound &! the o&served values of the data
represented, and ma! thus &e una&le to 2uantif! the true potential3 This limits the potential
height model as it is then &! definition una&le to further model e/ceptional trees, which
have a large effect on competition and neigh&ours3 This can &e remedied &! the inclusion of
stochastic modelling techni2ues, as applied in Chapter % where&! the allowance of a
random deviation procedure could allow some trees to var! a&ove the allocated potential
after the application of a modifier3
8odelling site inde/ using different fitting techni2ues provided potential new and
interesting techni2ues for site inde/ modelling3 >onlinear mi/ed effects modelling proved
superior in predictive 2ualit! compared to the >*S and '>*S techni2ues for the data range
ac2uired3 -ncluding the as!mptote as the random effect provided the most ro&ust and
accurate inclusion of random effects into the >*8( methodolog!3
1sing site inde/ as a predictor, the overall o&7ective of the chapter, proved to &e possi&le3
Some validation and refinements to the process could &e made, however it is thought that
site inde/ is a&le to model potential height 2uite well3 A ma7or concern would &e the effect
of densit! on site inde/, while this thesis used the South African site inde/ definition as is, it
could lead to su&stantial errors at e/treme .ver! high or low0 stand densities and is an issue
that should &e addressed in future wor)3
Future wor) should focus on a site 2ualit! predictor &ased on edaphic conditions .(sler
"#$", *ouw and Scholes "##"0, which should improve the sensitivit! of the model to site
conditions and move the model into a h!&rid modelling approach3
G-$#F

&.2 .iameter increment modelling
The overall o&7ective of the chapter was, under data limitations, to present a methodolog!
for future parameterisation and to highlight pro&lems associated with this3 -n this sense, the
o&7ective was achieved= however improvements to this methodolog! can still &e made3
Stratif!ing the indices &ased on the collinear relationships in order to o&tain models with a
com&ination of good predictive power to diameter increment and low collinearit! to each
other using PCA and E-FLs was a novel and powerful approach3
As noted earlier, the discussion on the &ehaviour of competition indices on different site
t!pes must &e ta)en ver! tentativel!, as two sites does not represent a good gradient3
However, some trends can &e noted and the validation produced some interesting results,
showing clearl! that the importance of the different indices3
-ncluding the *ocal +asal Area inde/, which captures a more growth s!mmetric competition
structure representing edaphic factors, improved the model and often performed &etter
that the ::* for P. elliottii under the water limited South African conditions3
-t is necessar! though to see how this changes for different growth periods, ta)ing into
account rainfall and water availa&ilit! over different seasons and !ears to see whether the
competitive nature of the trees can switch &etween s!mmetric and as!mmetric
competition3 -t is strongl! suggested that a stud! &e underta)en to understand the cross-
sectional .site stratification0 and temporal shifts in competition mode3 This could for
e/ample &e done in com&ination with a dendrochronological stud!3

&.# !dditions for model completion
As this thesis did not cover the entire modelling and simulation process done in Silva,
further wor) must &e done in the following areas, although no strong deductions can &e
made until the! are tested in the South African growing conte/t3
The omission of the species specific crown model and light transmission factor ma! have
&een a ma7or factor in the &ehaviour of the ::* model3 A model should &e developed for
South Africa to model the crown structure of P. elliottii and other species to &e used in
future parameterisations, which could &e used in the competition indices and allometric
e2uations to improve growth prediction3 Height increment modelling &ased on potential
height and the stand initialisation should &e studied3 Although height increment is not as
strongl! affected &! competition as diameter increment, competition in addition to
allometric models and site 2ualit! could &e investigated3 8ortalit! was not parameterised in
this stud!3 Some surrogates could &e used, however a more size and competition &ased
approach should &e used for parameterisation into S-*EA3
G-$#%

&.$ ,verall thoughts
hile the two components studied are ver! different in their model approaches and are not
com&ined into a full model !et, the overall o&7ectives for each were o&tained3 The a&ove
process in the thesis gives a good indication of the comple/it! of constructing single-tree
growth models3 However, the thesis resulted in a strong indication that this t!pe of
modelling process would &e feasi&le, with the main focus to shift on completing the
simulation structure of the entire growth modelling structure and to focus on shifts in
competition inde/ and competition modes under changing water availa&ilit!3 Pro&lems
encountered, and the solutions suggested, with the models tested could &e of use for
further research3

4-$#G

Chapter (: /eferences

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Site classification and growth models for Sit)a spruce plantations in -reland3 Forest cology
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Pa!andeh, +3 .$JH%03 >onlinear site inde/ e2uations for several ma7or Canadian forest
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in competition among plants3 :ecologia, 00".%0, %%H<%GG3
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4-$#J

Seifert, T3, Seifert, S3, Se!dac), A3, Durrheim, '3, ] von 'adow, :3 .n3d303 Comeptition effect
in an afrotemperate fores3 Forest (cos!stems .in revie40
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bet4een Forest !esources and 1ood DualityC Modelling Approaches and Simulation
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indices to model individual tree diameter growth in Afro-temperate forests3 G
th
>atural
Forests and oodlands S!mposium, 9ichards +a!, South Africa, $#3<$%3 April "#$$3
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+estimmung des achstums in +estanden3 +ericht des Forschungszentrums
aldP)os!steme, 1niversitat 'Pttingen, 9eihe +. 4I0, $$$-$$"3
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spruce < trem&ling aspen stand3 Forestry ;hronicles, "9, FF%<FF43
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competition alters &iomass-densit! relationships3 Proceedings. ?iological sciences E The
!oyal Society, ).9.$G#40, "$J$<G3
Team, 93 C3 ."#$F03 9: A *anguage and (nvironment for Statistical Computing3
Thornthwaite, C3 .$J%I03 An approach towards the rational classification of climate3
3eographical !evie4, "<, GG<J%3
1>(P3 .$JJ"03 1orld Atlas of =esertification3 *ondon: (dward Arnold3
1hl (, 8etzger H-', Seifert T ."##40 Dimension und achstum von solitaren +uchen und
(ichen3 Tagungs&and der Qahrestagung der Se)tion (rtrags)unde im Deutschen Eer&and
Forstlicher Forschungsanstalten, %H < GF3
Eancla!, Q3 :3 .$JJG03 'rowth models for tropical forests: A s!nthesis of models and
methods3 Forest Science, $0.$0, %<%"3
van Staden, Eida, (rasmus, +3F3>3, 9ou/, Q3, ingfield, 83Q3, van Qaarsveld, A3S3 ."##%03
8odelling the spatial distri&ution of two important South African plantation forestr!
pathogens3 Forest cology and Management $IH: 4$<HF3
4-$$#

Eon 'adow, :3, ] +reden)amp, +3 .$JJ"03 Forest management .p3 $G$03 Preotria: Academia3
ar&urton, 83, Schulze 93 ."##403 Climate change and the South African commercial
forestr! sector: an initial stud!3 9eport to Forestr! SA3 A;!Ucons !eport ,$* Decem&er "##43
ichmann, *3 ."##$03 Annual Eariations in Competition S!mmetr! in (ven-aged Sit)a
Spruce3 Annals of ?otany, <<.$0, $%G<$G$3 doi:$#3$##4Van&o3"##$3$%%G
!)off, 393, Croo)ston, >3*3 and Stage, A393 .$JI"03 1serLs guide to the stand prognosis
model3 1SDA For3 Serv3 'en3 Tech3 9ep3 >o3 ->T-$FF3

H-$$$

Chapter +: !ppendices
!ppendi4 !: 3:*7 random effects anova table

Densit"F)lot :odel )arameter 7on%ergence (?+9. df A07 *07 log1ik Test 1.;atio p-%alue
1,4
$ a,&,c >
" a,& >
F a,c 6 J GG3H""#" 4G3J%$%4 -$I3I4$#$
% a 6 H G$3GII%4 GJ3GF4J" -$I3HJ%"F
G &,c 6 J GG3H"F4G 4G3J%F#J -$I3I4$I"
4 & >
H c 6 H G$3H"F4I GJ34H"$% -$I3I4$I% G vs H F3$$(-#G $
,4@
$ a,&,c 6 $" $#J3FHG $F"3#H4I -%"34IHG
" a,& >
F a,c 6 J $#F3IH#GG $"#3IJ4J -%"3JFG"I $ vs F #3%JGGGGG #3J$JJ
% a >
G &,c 6 J $#F3FH%JI $"#3%#$% -%"34IH%J
4 & 6 H JJ3IGG4F $$F3#JI% -%"3J"HI$ G vs 4 #3%I#4%J% #3HI4%
H c 6 H JJ3IGG4F $$F3#JI% -%"3J"HI"
/@1
$ a,&,c >
" a,& >
F a,c >
% a 6 H $%I3G$H $4%3IF"" -4H3"GIG"
G &,c 6 J $G$3FG#" $H"3F"4I -4434HG#I
4 & 6 H $%J3$J%J $4G3G$ -4H3GJH%F G vs 4 $3I%%H #3FJH4
H c 6 H $%I3F$F% $4%34"IG -4H3$G44J
434
$ a,&,c 6 $" $H%34$JI "#%3%IF% -HG3F#JII
" a,& 6 J $4I34$I% $J$3#$4$ -HG3F#J$J $ vs " #3##$FHF $
F a,c 6 J $H%3"FGG $J434FFF -HI3$$HHH
% a 6 H $4G3$"%F $I"3G%%H -HG3G4"$%
G &,c >
4 & 6 H $4F3IFG4 $I$3"G4$ -H%3J$HI 4 vs F 43FJJJFG #3#%#I
H c 6 H $H#3"F4$ $IH34G44 -HI3$$I#G
@41
$ a,&,c >
" a,& 6 J "4J3GH4I "JG3J"" -$"G3HII%
F a,c 6 J "4J3GH44 "JG3J"$J -$"G3HIIF
% a 6 H "4G3GHGG "I43#44" -$"G3HIHH
G &,c 6 J "H"3#4HG "JI3%$"I -$"H3#FFI
4 & 6 H "4I3#4HI "II3GGI4 -$"H3#FFJ 4 vs G #3###"%G""" #3JJJJ
H c 6 H "4J3$G#$ "IJ34%#J -$"H3GHG$
H-$$"

Densit"F)lot :odel )arameter 7on%ergence (?+9. df A07 *07 log1ik Test 1.;atio p-%alue
344
$ a,&,c 6 $" FF$344FG F4J3#HJ% -$GF3IF$H
" a,& 6 J F"G34I"$ FGF3H%%$ -$GF3I%$$ $ vs " #3#$I4FF$HH #3JJJF
F a,c 6 J F"G34HG FGF3HF4J -$GF3IFHG
% a 6 H F"$34H$% F%F3%JH% -$GF3IFGH F vs % #3##FGF#J%J #3JJI"
G &,c >
4 & >
H c >
144/
$ a,&,c 6 $" %JI3IG%I G%#3$4FI -"FH3%"H%
" a,& 6 J %J"3IG%J G"F3IF44 -"FH3%"H%
$ vs
" "3"H(-#G $
F a,c >
% a 6 H %II3IG%I G$"3JG$I -"FH3%"H%
G &,c >
4 & 6 H %II3IG%I G$"3JG$I -"FH3%"H% 4 vs " "3%H(-#G $
H c 6 H %II3"IG G$"3FI" -"FH3$%"G
,365
$ a,&,c nlme3fit$ $" H4F3H$$% I$"3GII -F4J3IGGH
" a,& nlme3fit" J HGH3H"FH HJ%3FI$$ -F4J3I4$I $ vs " #3#$""4J4F4 #3JJJ4
F a,c nlme3fitF J HGH3H$#H HJ%3F4I$ -F4J3IGGF
% a nlme3fitH H HGF3H#HI HI"3"$J$ -F4J3IGFJ
G &,c nlme3fit% J HGI3"FF" HJ%3IJ#4 -FH#3$$44
4 & nlme3fitG H HG%3"F"I HI"3H%%$ -FH#3$$4% G vs 4 #3###%#F#G$ #3JJJI
H c nlme3fit4 H H%%3G$FH HHF3#"G -F4G3"G4J

H-$$F

!ppendi4 B: 'oronoi pol%gon increment relationship for the
3elder and Tweefontein sites respectivel%

H-$$%

H-$$G

!ppendi4 C: ,bserved and predicted .B5 for the
deterministic model

H-$$4

!ppendi4 .: imulation steps for the deterministic model

Period 1: 6 years

Period 2: 7 years

Period 3: 11.08 years
H-$$H


Period 5:15.58

Period6: 19.17
H-$$I

Period 7:20.25

Period 8:23.83

Period 9:26
H-$$J

H-$"#

!ppendi4 7: imulation steps for the stochastic model

Period 1: 6 years

Period 2: 7 years

H-$"$


Period 5:15.58
H-$""

Period6: 19.17

Period 7:20.25
H-$"F

Period 8:23.83

Period 9:26
H-$"%

H-$"G

!ppendi4 ": elect e4amples of /2 Code

#########################################################
####### Nonlinear quantile regression example ###########
#########################################################

Allccttrials <- subset(Allccttrials, Height > 0)

str(Allccttrials)
head(Allccttrials)

###1.2 Subset the data into the different trials

Weza <- subset(Allccttrials, Location == "Weza")
Mac <- subset(Allccttrials, Location == "Mac Mac")
Kwam <- subset(Allccttrials, Location == "Kwambonambi")
Duku <- subset(Allccttrials, Location == "Dukuduku")

###2. Deriv For functions

#2.1.1 Chapman Richards Three Parameter
height.chapman <-
deriv(~ a * (1 - exp(b*x))^c,
c("a","b","c"),
function(x, a, b, c){},
hessian = TRUE)

Weza2965 <- subset(Weza, Spha =="2965")

a <- max(Weza2965$Height)
b1 <- max(Weza2965$Height) - min(Weza2965$Height)
b2 <- max(Weza2965$Age) - min(Weza2965$Age)
b3 <- (b1/b2)
b <- b3/(max(Weza2965$Height))
c <- 0.66
a
b
c

Weza.0.9 <- nlrq(Height ~ height.chapman(Age, a, b, c),
start = list(a = a, b = -b, c = c),
data = Weza2965, tau=0.9, trace=TRUE)



H-$"4

#Test0.9
handy.Height.hat <- function(Age)
predict(Weza.0.9, newdata = data.frame(Age = Age))
#Call
par(las = 1)
Plotnlrq <- plot(Height ~ Age, data = Weza2965,
xlim = c(0, max(Weza2965$Age, na.rm=TRUE)),
ylim = c(0, max(45)),
ylab = "Height(m)", xlab = "Age (y)", main = "0.9 Quantile")
curve(handy.Height.hat, add = TRUE)

summary(Weza.0.9)

#Test0.95
handy.Height.hat2 <- function(Age)
#Call
par(las = 1)
ylim = c(0, max(45)),
curve(handy.Height.hat2, add = TRUE)

summary(Weza.0.95)

#Test0.975
handy.Height.hat3 <- function(Age)
#Call
par(las = 1)
ylim = c(0, max(45)),

+ curve(handy.Height.hat, add = TRUE, lty = 2, lwd = 2, col =
"Green")
+ curve(handy.Height.hat2, add = TRUE, lty = 2, lwd = 2, col =
"Blue")
+ curve(handy.Height.hat3, add = TRUE, lty = 2, lwd = 2, col =
"Red")

legend(1, 45, c("0.90","0.95","0.975"), lty=c(2,2,2),
lwd=c(2,2,2),col=c("Green","Blue","Red"))

summary(Weza.0.975)

#########################################################
###### Site index modelling example ############
#########################################################
H-$"H

Wezadom1 <- subset(dominantheightclass, Location == "Weza")

Wezadom247 <- subset(Wezadom1, Spha == "247")
Wezadom247 <- subset(Wezadom247, Height > 0)

a <- max(Wezadom247$Height)
b1 <- max(Wezadom247$Height) - min(Wezadom247$Height)
b2 <- max(Wezadom247$Age) - min(Wezadom247$Age)
b3 <- (b1/b2)
b <- b3/(max(Wezadom247$Height))
c <- 0.66
a
c
b
nlc <- nls.control(maxiter = 200, tol = 1e-05, minFactor = 1/1024,
printEval = FALSE, warnOnly = FALSE)
handy.nls2 <-
nls(Height ~ Height.growth(Age, a, b, c),
data = Wezadom247, control = nlc)
#Test
handy.Height.hat <- function(Age)
predict(handy.nls2, newdata = data.frame(Age = Age))
#Call
par(las = 1)
Plotted2 <- plot(Height ~ Age, data = Wezadom247,
xlim = c(0, max(Wezadom247$Age, na.rm=TRUE)),
ylim = c(0, max(45)),
ylab = "Height(m)", xlab = "Age (y)", main = "Average Height")
curve(handy.Height.hat, col = "red", add = TRUE)

summ <- summary(handy.nls2)
require(nlstools)
resid <- nlsResiduals(handy.nls2)
plotresid <- plot(resid, type = 0)

library(nlme)
Weza247group <- groupedData(Height~Age|Number, Wezadom247)
plot(Weza247group)
head(Weza247group)

cor(coef(handy.nls2))

####Nlme

a <- max(Weza247group$Height)
b1 <- max((Weza247group$Height) - min(Weza247group$Height))
b2 <- max(Weza247group$Age) - min(Weza247group$Age)
b3 <- (b1/b2)
b <- b3/(max(Weza247group$Height))
c <- 0.66

H-$"I

a
b
c

nlc1 <- nlmeControl(maxiter = 100000, tol = 1e-05, minFactor =
1/1024,

nlc2 <- nls.control(maxiter = 500, tol = 1e-05, minFactor = 1/1024,

Weza247nlslist <-
nlsList(Height ~ Height.growth(Age, a, b, c), data = Weza247group,
start = list(a = 36.74088, b = -0.03314, c = 1.05124), control =
nlc2)
summary(Weza247nlslist)

pairs(Weza247nlslist, id = 0.1, na.action = na.exclude)
plot(intervals(Weza247nlslist), layout = c(3,1))

start <- c(a = a,b = -b, c = c) # starting value
nlme.fit <- nlme(Height ~ Height.growth(Age, a, b, c),
fixed = a + b + c ~ 1, random = a+ b + c ~ 1,
data = Weza247group, start=c(start),
control=nlmeControl(opt='nlm'),
weights = varPower(form = ~ Age), corr =
corAR1(0.296739967))
summary(nlme.fit)
pairs(nlme.fit)

anova(nlme.fit, handy.nls2)
###3 - Substantial correlation between b and c random effects -
makes it difficult to converge
intervals(nlme.fit, which = "var-cov")

nlme.fit.a <- update(nlme.fit, random = a ~ 1)
nlme.fit.b <- update(nlme.fit, random = b ~ 1)
nlme.fit.c <- update(nlme.fit, random = c ~ 1)
nlme.fit.bc <- update(nlme.fit, random = b + c ~ 1)

anova(nlme.fit.a, nlme.fit.b, nlme.fit.c, nlme.fit.bc)
anova(nlme.fit.a, nlme.fit.bc)
summary(nlme.fit.a)
summ

##Fit diagonal variance covariance matrix assuming random effects
are independent

nlme.fit.diag <- update(nlme.fit, random = pdDiag(a + b + c ~ 1),
control=nlmeControl(opt='nlm'))

#doesnt converge, thus try other random effects
nlme.fit.diagbc <- update(nlme.fit, random = pdDiag(b + c ~ 1))
nlme.fit.diagac <- update(nlme.fit, random = pdDiag(a + c ~ 1),
H-$"J

nlme.fit.diagab <- update(nlme.fit, random = pdDiag(a + b ~ 1),
nlme.fit.diaga <- update(nlme.fit, random = pdDiag(a ~ 1),
nlme.fit.diagb <- update(nlme.fit, random = pdDiag(b ~ 1),
nlme.fit.diagc <- update(nlme.fit, random = pdDiag(c ~ 1),

anova(nlme.fit.diagac, nlme.fit.diagab, nlme.fit.diaga,
nlme.fit.diagb, nlme.fit.diagc)

####With a, b and c all substantially corellated, it may not be
necessary to include them all in the model
# Just using a seems to be the best model
summary(nlme.fit.diaga)
summary(handy.nls2)

anova(nlme.fit.diaga, handy.nls2)
plot(handy.nls2)
plot(nlme.fit.diaga)
plot(nlme.fit.diagb)
plot(nlme.fit.diagbc)

#Now use the weights
nlme.fit.diaga <- update(nlme.fit.diaga, weights = varPower(form = ~
Age) )


anova(nlme.fit.diaga, nlme.fit)

###gnls
library(nlme)
Weza247gnls <- gnls(Height ~ Height.growth(Age, a, b, c), data =
Weza247group,
start = list(a = 46.86677, b = -0.04293, c = 1.45860))
summary(Weza247gnls)
summ

Nelder126gnls.Power3 <- update(Weza247gnls, weights = varPower(form
= ~ Age), corr = corAR1(0.296739967))
summary(Nelder126gnls.Power3)

plot(Nelder126gnls.Power3)

gnlspowerwightedresiduals <- Nelder126gnls.Power3
nlmepowerweightedresiduals <- nlme.fit.diaga
nlme <- nlme.fit
nls <- handy.nls2

anova(Nelder126gnls.Power3, nlme.fit.a, handy.nls2)
H-$F#

####rmse
RMSE(Nelder126gnls.Power3)
RMSE(nlme.fit.a)
RMSE(handy.nls2)

anova(gnlspowerwightedresiduals, nlmepowerweightedresiduals, nlme,
nls)

plot(nls)
plot(nlme)
plot(gnlspowerwightedresiduals)
plot(nlmepowerweightedresiduals)

##Test the autocorrelation regression improvements for the best nlme
(weighted and unweighted)

#Unweighted:
plot(ACF(nlme.fit, maxLag = 10), alpha = 0.05)
ACF(nlme.fit)
nlme.fit.acf <- update(nlme.fit, corr = corAR1(0.11717144))
plot(ACF(nlme.fit.acf , maxLag = 10), alpha = 0.05)
summary(nlme.fit.acf)
summary(nlme.fit)
anova(nlme.fit, nlme.fit.acf)
plot(nlme.fit.acf)

# Weighted
plot(ACF(nlme.fit.diaga, maxLag = 10), alpha = 0.05)
ACF(nlme.fit.diaga)
nlme.fit.diaga.acf <- update(nlme.fit.diaga, corr =
corAR1(0.29005147))
plot(ACF(nlme.fit.diaga.acf, maxLag = 10), alpha = 0.05)
ACF(nlme.fit.diaga.acf)
summary(nlme.fit.diaga.acf)
anova(nlme.fit.diaga.acf, nlme.fit.diaga)
plot(nlme.fit.diaga.acf)

anova(nlme.fit, nlme.fit.acf, nlme.fit.diaga, nlme.fit.diaga.acf)

##See if the Nlmeweighted and unweighted acf's compare
summary(nlme.fit.acf)
summary(nlme.fit.diaga.acf)

anova(nlme.fit.acf, nlme.fit.diaga.acf)

##See if changing the parameters used for random effects has and
effect

nlme.fit.diagbc <- update(nlme.fit, random = pdDiag(b + c ~ 1))

plot(nlme.fit.diagbc)

H-$F$

nlme.fit.diag.bc <- update(nlme.fit.diagbc , weights = varPower(form
= ~ Age) )
ACF(nlme.fit.diag.bc)
nlme.fit.diaga.bc.acf <- update(nlme.fit.diag.bc, corr =
corAR1(0.29005147))
plot(nlme.fit.diaga.bc.acf)
#unweighted
nlme.fit.diaga.unweight <- update(nlme.fit.diagbc, corr =
corAR1(0.29005147))
plot(nlme.fit.diaga.unweight)

summary(nlme.fit.diaga.bc.acf)
summary(nlme.fit.diaga.unweight)

anova(nlme.fit.diaga.bc.acf, nlme.fit.diaga.unweight)

anova(gnlspowerwightedresiduals, nlmepowerweightedresiduals, nlme,
nls, nlme.fit.diaga.acf)

#########################################################
##### Competition indices exapmle #############
#########################################################

####BALIndex

#df <- read.csv("C:/Users/Gerard/Documents/Masters/r voronoi/Nelder
Year by year/1998.csv")
df <- read.csv("F:/Tweefontein BAL/Tweefonteinnew.csv")

#df<- subset(df, TPH0 =="245")
df<- subset(df, TPH0 =="1097")

head(df)
# computes the BAL competition index as follows:
# all neighbour trees inside the competion zone radius (CZR)
# contibute to the total sum of the Basal area, if their
# DBH is thicker than the central tree.
#
# alle trees are assumed to be on a axias allinged rectangular plot
#
# stefan seifert 2013-1

require(RANN)

df<- subset(df, Age =="1.83")
H-$F"


d <- df
head(d)
createtorus = function(d, dx=NA, dy=NA) {
if (is.na(dx))
dx=diff(range(d$x))
if (is.na(dy))
dy=diff(range(d$y))
dnew = d
dnew$outside=F
# centerrow
dc=rbind(dnew,transform(d, x=x-dx, outside = T))
dc=rbind(dc,transform(d, x=x+dx, outside = T))
#+top
dnew = rbind(dc,transform(dc, y=y-dy, outside=T))
#+bottom row
dnew = rbind(dnew, transform(dc, y=y+dy, outside=T))
return(dnew)
}

head(createtorus(d))

neighbours.BAL = function(x,y,r=plotsize,k=100) {
# returns all neighbours in a distance of r
# neighbour number is limited to k
# warning will be given if there might be more neighbous than k
require(RANN)
k = min(k,nrow(x))
neigh = nn2(x[,c("x","y")], x[,c("x","y")], searchtype="radius",
radius = r-1e-6, k=k)
if(max(neigh$nn.idx[,k])>0 & k<nrow(x)) {
warning("neighbours.BAL: k might be to less to find all
potential neighbours")
}
return(neigh)
}

p = createtorus(d)
head(p)
str(p)

BAL = function(p,CZR=plotsize) {
# compute the BAL index, BASAL AREA, and DIAM for all trees in p
H-$FF

# p is a data.frame with the columns x, y for the tree position
# and D for the DBH of the tree
# a column newID with unique IDs
# CZR is teh radius to which neighbours are counted
# if CZR is NA then CZR will be estimated as 2 times the
# squareroot of the specific tree area
# bounding
BAL = rep(NA,nrow(p))
BASAL = BAL
CR13 = BAL
mimax = range(p$x)
mimay = range(p$y)
if (is.na(CZR)) {
a = diff(mimax)*diff(mimay)
spa = a/nrow(p) # 1/intensity : specific area per tree
CZR = sqrt(spa) * 2 # k-facor 2 : radius is 2-times the
specific tree area
}
border = with(p, x<=mimax[2]-CZR & x>=mimax[1]+CZR &
y<=mimay[2]-CZR & y>=mimay[1]+CZR)
sqha = CZR^2*pi/10000 # circle ha
ne = neighbours.BAL(p,CZR, k=100) # all neighbours for all trees!
# sum up all valid neighbours squared DBHs
# we do it in a loop
for (ct in 1:nrow(p)) {
nonu = ne$nn.idx[ct,-1]
nonu = nonu[nonu>0]
d = p[nonu,"D"]
d1 = d[d>p$D[ct]]
d2 = d[d>10 & d <=30]

BAL[ct] = sum( d1^2 )*pi/40000 / sqha # [ basal area per ha]
BASAL[ct] = sum( d^2 )*pi/40000 / sqha
CR13[ct] = sum(d2) / sqha
}
return(data.frame(newID=p$newID, BAL=BAL,BASAL=BASAL, Age =
p$Age, DBH = p$D, DIncrement = p$Di,HtIncrement = p$Hti,
Ht = p$Ht, x = p$x, y = p$y, SPHA = p$TPH0,
flagBALOk=border, CR13=CR13, CZR=rep(CZR,nrow(p)) ))
}

BALCALL <- BAL(p)
head(BALCALL)
plot(BALCALL$BAL, BALCALL$DIncrement)
plot(BALCALL$BASAL, BALCALL$DIncrement)

#################Hegyi Index

p <- BALCALL
head(p)
names(p)[names(p) == "newID"] <- "ID"
H-$F%

p$newID <- 1:nrow(p)
p$D <- p$DBH

CZR <- plotsize

neighbours.heg = function(x,r,k=100) {
# returns all neighbours in a distance of r
# neighbour number is limited to k
# warning will be given if there might be more neighbous than k
require(RANN)
k = min(k,nrow(x))
neigh = nn2(x[,c("x","y")], x[,c("x","y")], searchtype="radius",
radius = r-1e-6, k=k)
if(max(neigh$nn.idx[,k])>0 & k<nrow(x)) {
warning("neighbours.heg: k might be to less to find all
potential neighbours")
}
return(neigh)
}

it.heg.stand = function(p,CZR, k=100) {
# p are all trees in the plot
# this data.frame must contain x,y as coordinates
# and d as diameter [cm]
# the column newID should contain a unique ID like the row
number
# if some trees ar excluded this ID helps to reconstruct the
# original data
require(plyr)

ne = neighbours.heg(p,CZR, k) # all neighbours for all trees!
HgCI = rep(NA,nrow(p))
newID = HgCI
flagBorder = rep(NA,nrow(p))

mimax = range(p$x)
mimay = range(p$y)
flagBorder = with(p, x<=mimax[2]-CZR & x>=mimax[1]+CZR &
y<=mimay[2]-CZR & y>=mimay[1]+CZR)
for (ct in 1:nrow(ne$nn.idx)) {
#print(ct)
# test if current tree ct is to near the maximum extent of
the plot (B:think this comment is meant for line 53)
z = c()
# number of neighbours
nonna = (ne$nn.idx[ct,]>0)
nc = length(na.omit(ne$nn.idx[ct,nonna])) # B:na.omit just
removes incomplete cases, i.e. more than number k, or out of CZR

neighb = ne$nn.idx[ct,nonna][-1] # all valid neighbour
indexes
neighbd = ne$nn.dist[ct,nonna][-1] # all valid neighbours
distances
HgCI[ct]=sum( (p$D[neighb]/p$D[ct])/neighbd )
newID[ct]=p$newID[ct]
H-$FG

}
return(data.frame(HgCI=HgCI,flagInside=flagBorder,newID=newID))
}

source("J:/B Fury/ci-Hegyi-iterNocea.R")#specifiy which script has
the functions being used

head(p)
str(p)

heg=it.heg.stand(p,CZR,35)
plot(p$x,p$y)
head(heg)
str(heg)
heg.1=data.frame(ID = p$ID, newID=p$newID,
BAL=p$BAL,BASAL=p$BASAL,HgCI=heg$HgCI, Age = p$Age,
DBH = p$DBH, DbhIncrement = p$DIncrement,
HtIncrement = p$HtIncrement,
Ht = p$Ht, x = p$x, y = p$y, SPHA = p$SPHA,
CZR=rep(CZR,nrow(p)))

plot(heg.1$HgCI, heg.1$DbhIncrement)
head(heg.1)

str(heg.1)

###########################Voronoi
p <- heg.1
head(p)
str(p)
treecoords <- subset(p, select=c(newID,x,y))
require(deldir)

x<-c(treecoords$x)
y<-c(treecoords$y)
plot(x,y)
delresult <- deldir(x,y)

summ<-delresult[["summary"]]
summ
summ8<-summ[8]
summ8merge <- merge(summ8, heg.1, all=TRUE, by="row.names")

plot(delresult)

plot(delresult,add=FALSE,wlines=c("tess"),
wpoints=c("both","real","dummy","none"),
number=FALSE,cex=1,nex=1,col=NULL,lty=NULL,
pch=NULL,xlim=NULL,ylim=NULL,xlab='x',ylab='y',
showrect=FALSE)

plot(delresult,add=FALSE,wlines=c("tess"),
H-$F4

wpoints=c("none"),
number=FALSE,cex=1,nex=1,col=NULL,lty=1,
pch=NULL,xlim=NULL,ylim=NULL,xlab='x',ylab='y',
showrect=FALSE)

head(summ8merge)
summ8merge$conc <- paste(summ8merge$ID,summ8merge$newID, sep = '.')
str(summ8merge)
plot(summ8merge$dir.area, summ8merge$DbhIncrement)

setwd("F:/B Fury/Tweefontein/hegyi and cvor")
write.csv(summ8merge, "2981.20.42.csv")


Potential Height Growth and Diameter Increment - 2014

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Potential Height Growth and Diameter Increment - 2014

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Development of potential height growth and diameter

increment models for the parameterisation of an

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