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Multifractals in ecology using R

Description/Summary

Disclaimer This post is from the link posted by GitHub user lsaravia in this comment. All credit for this post goes to the original author. Multifractals Many natural systems cannot be characterized by a single number such as the fractal dimension. Instead an infinite spectrum of dimensions must be introduced. Multifractal definition Consider a given object $$\Omega$$, its multifractal nature is practically determined by covering the system with a set of boxes $$\{B_i( r)\}$$ with $$(i=1,…, N( r))$$ of side length $$r$$ These boxes are nonoverlaping and such that

Content

Disclaimer
This post is from the link posted by GitHub user lsaravia in this comment. All credit for this post goes to the original author.

Multifractals

• Many natural systems cannot be characterized by a single number such as the fractal dimension. Instead an infinite spectrum of dimensions must be introduced.

Multifractal definition

• Consider a given object $$\Omega$$, its multifractal nature is practically determined by covering the system with a set of boxes $$\{B_i( r)\}$$ with $$(i=1,…, N( r))$$ of side length $$r$$
• These boxes are nonoverlaping and such that

$\Omega = \bigcup_{i=1}^{N( r)} B_i( r)$

This is the box-counting method but now a measure $$\mu(B_n)$$ for each box is computed. This measure corresponds to the total population or biomass contained in $$B_n$$, in general will scale as:

$\mu(B_n) \propto r^\alpha$

The generalized dimensions

• The fractal dimension $$D$$ already defined is actually one of an infinite spectrum of so-called correlation dimension of order $$q$$ or also called Renyi entropies.

$D_q = \lim_{r \to 0} \frac{1}{q-1}\frac{log \left[ \sum_{i=1}^{N( r)}p_i^q \right]}{\log r}$

where $$p_i=\mu(B_i)$$ and a normalization is assumed:

$\sum_{i=1}^{N( r)}p_i=1$

• For $$q=0$$ we have the familiar definition of fractal dimension. To see this we replace $$q=0$$

$D_0 = -\lim_{r \to 0}\frac{N( r)}{\log r}$

Generalized dimensions 1

• It can be shown that the inequality $$D_q’ \leq D_q$$ holds for $$q’ \geq q$$
• The sum

$M_q( r) = \sum_{i=1}^{N( r)}[\mu(B_i( r))]^q = \sum_{i=1}^{N( r)}p_i^q$

is the so-called moment or partition function of order $$q$$.

• Varying q allows to measure the non-homogeneity of the pattern. The moments with larger $$q$$ will be dominated by the densest boxes. For $$q<0$$ will come from small $$p_i$$’s.

• Alternatively we can think that for $$q>0$$, $$D_q$$ reflects the scaling of the large fluctuations and strong singularities. In contrast, for $$q<0$$, $$D_q$$ reflects the scaling of the small fluctuations and weak singularities.

Exercise

• Calculate the partition function for the center and lower images of the figure:

Two important dimensions

• Two particular cases are $$q=1$$ and $$q=2$$. The dimension for $$q=1$$ is the Shannon entropy or also called by ecologist the Shannon’s index of diversity.

$D_1 = -\lim_{r \to 0}\sum_{i=1}^{N( r)} p_i \log p_i$

and the second is the so-called correlation dimension:

$D_2 = -\lim_{r \to 0} \frac{\log \left[ \sum_{i=1}^{N( r)} p_i^2 \right]}{\log r}$

the numerator is the log of the Simpson index.

Application

• Salinity stress in the cladoceran Daphniopsis Australis. Behavioral experiments were conducted on individual males, and their successive displacements analyzed using the generalized dimension function $$D_q$$ and the mass exponent function $$\tau_q$$

both functions indicate that the successive displacements of male D. australis have weaker multifractal properties. This is consistent with and generalizes previous results showing a decrease in the complexity of behavioral sequences under stressful conditions for a range of organisms.

• A shift between multifractal and fractal properties or a change in multifractal properties, in animal behavior is then suggested as a potential diagnostic tool to assess animal stress levels and health.

Mass exponent and Hurst exponent

• The same information contained in the generalized dimensions can be expressed using mass exponents:

$M_q( r) \propto r^{-\tau_q}$

This is the scaling of the partition function. For monofractals $$\tau_q$$ is linear and related to the Hurst exponent:

$\tau_q = q H - 1$

For multifractals we have

$\tau_q = (q -1) D_q$

Note that for $$q=0$$, $$D_q = \tau_q$$ and for $$q=1$$, $$\tau_q=0$$

Paper

1. Kellner JR, Asner GP (2009) Convergent structural responses of tropical forests to diverse disturbance regimes. Ecology Letters 12: 887–897. <10.1111/j.1461-0248.2009.01345.x>.

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