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Transparents of my presentation at the Center for Research into Ecological and Environmental Modelling (CREEM), University of St. Andrews, Scotland 18th of June, 2008.

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**Spatial point processes in aid of rainforest ecology
**

Tuomas Rajala

University of Jyväskylä, Finland

Supervisors: A. Penttinen, J. Illian Funding: COMAS

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

What is this talk about:

• Example of ecological question related to biodiversity • Introduction to spatial point processes • Measuring diversity in spatial context

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Rainforest data: Barro Colorado Island, Panama The 50-hectare permanent tree plot was established in 1980 in the tropical forest of Barro Colorado Island (BCI) in Gatun Lake in central Panama. Censuses have been carried out in 1981-1983, 1985, 1990, 1995, 2000, and 2005. In each census, all free-standing woody stems at least 10 mm diameter at breast height were identied, tagged, and mapped.

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Topography of area

160

Intensity map of the trees

Tuomas Rajala, University of Jyväskylä, Finland

1000

3000

120

130

140

150

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Spatial point processes in aid of rainforest ecology

Questions of biodiversity 1

Global, community level questions: Q1 Species richness: How many species? • S := #species Q2 Species evenness: How even is the abundance distribution?

• Relative abundances: τ = 1, . . . , S, • Several indices are used to measure evenness, e.g.

πτ := nτ /n.

Simpson index α :=

Census n S

α

S

τ =1

2 πτ .

'81-'83 235282 285 0.051

'85 242046 287 0.052

'90 243999 288 0.052

'95 229020 281 0.052

'00 213769 280 0.051

'05 208370 282 0.049

**Now we have more detailed data so we can ask more...
**

Tuomas Rajala, University of Jyväskylä, Finland 5/24

Spatial point processes in aid of rainforest ecology

Questions of biodiversity 2

**Local, individual level questions: Q1 Intensity around individuals
**

• How dense is the surrounding area, size of neighbourhood, • how it aects the individual's survival?

and

**Q2 Interspecies relationships
**

• Do species dier in their neighbourhoods? • What is the role of a species in the community?

Let's try to answer Q2.

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Mathematical framework

**Local level questions require
**

• Treatment of individual units with known locations • denition of 'local' • possibility to statistically estimate global and species specic

features

**• stochasticity, as the forest is highly complicated system
**

1

Suitable mathematical framework

is given by

**Spatial point processes
**

1

e.g. Matérn '60, Rippley '76, Diggle '83, Stoyan et al. '95, Illian et al. '08 Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Spatial point processes

• Spatial point process is in this context understood as a

random, locally nite set X = {xi } of discrete points in Rd . • Data pattern x is a single instance X (ω) = x of spatial point process model. • The interest is in the distributional properties of X : intensity λ, spatial correlation of points, homogeneity, isotropia,...

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

• The complete spatial randomness is described by the Poisson

process: no interaction between points. • Models can be given trough a density fX with respect to the Poisson process p:

P(X ∈ A) =

• Example: left: Poisson fX ∝ 1.

A

fX (x)dp (x)

**right: Hard core process fX ∝ 1(min||xi − xj || > 0.05).
**

Poisson

1 1

Hard core,h=0.05

0

0

1

0 0

1

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Multitype spatial point processes

• Multitype (spatial) point processes are spat. point processes

with additional information on the points, M = {[xi ; t (xi )]}. The types t (xi ) ∈ {1, ..., S } can represent things like species, color, size class, event (on/o), role (factory/contamination), state of growth, sex...

betacells ants

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Tools for analysing point processes

• When a point pattern data is given summary statistics are

calculated, e.g.

n • Intensity λ ≈ |W |

• K -function: λK (r ) =

Eo

x ∈X

1(x ∈ B (o , r ) \ {o }).

**• Multitype versions also possible • Intensity λτ ≈ |nτ | W
**

• λγ Kτ,γ =

Eo ,τ

x ∈ Xγ

1(x ∈ B (o , r ) \ {o }).

4

Ants’ nests

λÃ´Öµ

0 0

1

2

3

2

4

6 r

8

10

12

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Back to the jungle

• Now, write M={[xi ; t (xi )]} for a multitype point process with

interpretations

• xi ∼ tree location • t (xi ) ∼ tree species

• In the small sample S = 56, so roughly 1500 dierent

**K -functions to compare. • How about summing up the diversity in the 'neighbourhoods' ?
**

Tuomas Rajala, University of Jyväskylä, Finland 12/24

Spatial point processes in aid of rainforest ecology

Measures of Diversity: Simpson index

**• Recall: denition of Simpson index
**

S

α :=

τ =1

(

λτ 2 ) = λ

S

τ =1

2 πτ

• Shimatani & Kubota (2004) introduced the Spatial Simpson

index:

S

α(r ) :=

τ =1

2 πτ

Kτ,τ (r ) . K (r )

• Summarizes the information in the pattern: No distinction

between species...

α(r)

0.00 0

0.02

0.04

0.06

10

20 r

30

40

50

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Measures of Diversity: ISAR

• Wiegand et. all. (2007): Individual Species-Area-Relationship

**(ISAR) function for a species τ :
**

S

Iτ (r ) :=

γ=1

Po ,τ ( Xγ ∩ B (o , r ) = ∅ )

• The expected number of species present around a typical tree

of species τ

**• Use Iτ (r ) to study Q2: Look for specieses which deviates from
**

0 Poisson process Iτ (r ). 0 • If Iτ (r ) > Iτ (r ), the species has more diversity around it than

would be expected. Call these species diversity accumulators.

0 • If Iτ (r ) < Iτ (r ), we call the species diversity repeller.

**• The statistical inference is based on Monte Carlo-simulations.
**

Tuomas Rajala, University of Jyväskylä, Finland 14/24

Spatial point processes in aid of rainforest ecology

The results for BCI

**Dataset: BCI census '95, all trees with dbh > 10cm. α = 2.5%
**

100

neutral repeller accumulator

Percentage cases

0 0

20

40

60

80

10

20 r

30

40

Tuomas Rajala, University of Jyväskylä, Finland Suprising amount of repellers.

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Spatial point processes in aid of rainforest ecology

Comparing ISAR's

• Another rainforest plot: 50ha plot Pasoh, Malaysia. More than

800 species, over 0.3mil individuals.

• Figure depicts ISARτ for subset of individuals with

dbh > 10cm for species with nτ > 70.

60

I(r)/S

BCI Pasoh

I(r)

40

20

0.10

0.20

0.30

80

0

10

20 r

30

40

50

0.00

0

BCI Pasoh

0

10

20 r

30

40

50

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Back to math: the neighbourhoods

• The neighbourhood denition used was

y ∈ ne (x ) ⇐⇒ y ∈ B (x , r ) for a xed r > 0.

• What if we want to dene the neighbourhood relation

dierently?

• The theory for studying neighbourhood relationships: Graph

theory ⇒ general framework for neighbourhoods

• Graph is dened as a pair G (V ) = (V , E ) where V is a

non-empty set called vertex set, and E ⊆ {xy :, x , y ∈ V } the edge set. (write xy ∈ E ⇐⇒ x → y ). ne (x ) := {y ∈ V : x → y }.

• Denition of

neighbourhood of a point x ∈ V :

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Tuomas Rajala, University of Jyväskylä, Finland

Spatial point processes in aid of rainforest ecology

**The type of information of X in G (X ) is coverned by the construction rule of E . Common examples:
**

• Geometric graph for R > 0:

**x → y ⇐⇒ d (x , y ) ≤ R for some metric d (·, ·).
**

• k-nearest neighbours graph, k > 0: if

**dk (x ) := inf {r > 0 : N (b(x , r )\{x }) = k } is the distance to the kth neighbouring point of x, then x → y ⇐⇒ d (x , y ) ≤ dk (x ).
**

Tuomas Rajala, University of Jyväskylä, Finland 18/24

Spatial point processes in aid of rainforest ecology

Random graphs

Graph theoretical features reect the structure of the point process. Example: • Mean connections per point or mean degree

deg := Eo

x ∈N

1(o → x ).

If neighbourhood is given by geometric graph with parameter r > 0, deg = λK (r ), i.e. the information of Ripley's K -function is an example of graph summary. • Same can be done to any function of some neighbourhood, e.g. the ISAR function:

S

Iτ (G (X )) =

γ=1

Tuomas Rajala, University of Jyväskylä, Finland

Po (Xγ ∩ ne (o ) = ∅)

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Spatial point processes in aid of rainforest ecology

BCI vs. Pasoh: k-nearest neighbours

**Upper: Metric neighbourhood, geometric graph Lower: Topological neighbourhood, k-nearest neighbours graph.
**

60 0.20 0.10

BCI Pasoh

20

I(r)/S

I(r)

40

0.30

80

0

10

20 r

30

40

50

0.00

0

BCI Pasoh

0

10

20 r

30

40

50

40

20

I(r)/S

BCI Pasoh

I(r)

30

10

0.04

0.08

0.12

50

0

20

40

60

80

100

0.00

0

BCI Pasoh

0

20

40

60

80

100

Tuomas Rajala, University of Jyväskylä, Finland

k−nn

k−nn

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Spatial point processes in aid of rainforest ecology

From 1D to 2D: General consept of Diversity

Ú Ö× ØÝ ÓÙÒØ×

Ê
Ò ××

Dominance

ËÔ

Ú ÒÒ ××

Equality Mingling

ÜÔÓ×ÙÖ

Segregation

Ë
ØØ Ö Ò

Clustering Regularity

• Two aspects of classical diversity: Richness and evenness • The two aspects of spatial diversity: Exposure and scattering1 • Problem: Exposure and scattering are not independent • Topological neighbourhoods might help separate the two

aspects

Pielou '77, Aguirre et al. '03, Shimatani et al. '04. Tuomas Rajala, University of Jyväskylä, Finland

1

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**Spatial point processes in aid of rainforest ecology
**

Mingling

Clustering

Evenness

Segregation

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Conclusions

• Rainforests biodiversity: Shown methods allows us to e.g. test

validity of dierent theories (neutral vs. niche) sciences, chemistry, genology...)

• General consept of diversity, also in 2D? (Sosiology, material • Neighbourhoods: mathematical framework (Graphs)

Tuomas Rajala, University of Jyväskylä, Finland

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Spatial point processes in aid of rainforest ecology

Literature Articles:

• Hubbell, Condit, Foster: Barro Colorado forest census plot data. URI:http://ctfs.si.edu/datasets/bci/ 2005 • Shimatani, Kubota: "Quantitative assessment of multispecies spatial pattern with high species diversity",Ecological research, v.19, 2004 • Wiegand, Gunatilleke, Gunatilleke, Huth: How individual species structure diversity in tropical forests, PNAS, nov. 16 2007

Books:

• Burslem, Pinard, Hartley: Biotic interactions in the tropics, Cambridge 2005. • Illian, Penttinen, Stoyan, Stoyan: Statistical analysis and modelling of spatial point patterns, Wiley 2008. • Marchette: Random graphs for statistical pattern recognition, Wiley 2004.

Tuomas Rajala, University of Jyväskylä, Finland 24/24

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