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Spatial point processes in aid of rainforest ecology

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.

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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...
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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,...

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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

λôֵ

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.
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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

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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)

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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.
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