Null models

Randomization of networks is mostly used to perform null hypothesis significance testing, or to draw random realizations of a probabilistic network. There are two ways to perform networks randomization: either by shuffling interactions within the networks while enforcing some constraints (shuffle) or by drawing random samples from a probabilistic network (rand).

Draw a network from a probabilistic network

Base.rand — Function

rand(N::ProbabilisticNetwork)

Converts a probabilistic network into a deterministic one by performing random draws. All interactions are treated as independent Bernoulli events. Note that this network is not checked for degeneracy, i.e. species can end up with no interactions.

References

Poisot, T., Cirtwill, A.R., Cazelles, K., Gravel, D., Fortin, M.-J., Stouffer, D.B., 2016. The structure of probabilistic networks. Methods in Ecology and Evolution 7, 303–312. https://doi.org/10.1111/2041-210X.12468

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rand(N::ProbabilisticNetwork, n::T) where {T<:Integer}

Generates a number of random deterministic networks based on a probabilistic network.

References

Poisot, T., Cirtwill, A.R., Cazelles, K., Gravel, D., Fortin, M.-J., Stouffer, D.B., 2016. The structure of probabilistic networks. Methods in Ecology and Evolution 7, 303–312. https://doi.org/10.1111/2041-210X.12468

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rand(N::ProbabilisticNetwork, S::Tuple{Int64,Int64})

Generates a number of random deterministic networks based on a probabilistic network, and returns them as a matrix.

References

Poisot, T., Cirtwill, A.R., Cazelles, K., Gravel, D., Fortin, M.-J., Stouffer, D.B., 2016. The structure of probabilistic networks. Methods in Ecology and Evolution 7, 303–312. https://doi.org/10.1111/2041-210X.12468

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Generate probabilistic networks from deterministic networks

These functions generate a probabilistic network from a deterministic network, where the probability of every interaction is determined by the degree distribution (or connectance) of the network.

EcologicalNetworks.null1 — Function

null1(N::BinaryNetwork)

Given a network N, null1(N) returns a network with the same dimensions, where every interaction happens with a probability equal to the connectance of N.

Note that this does not guarantee that the network is not degenerate, so the output of this analysis should be filtered using is_degenerate, or passed to simplify. The output of this approach is always a probabilistic network of the same partiteness as the original network.

References

Fortuna, M.A., Bascompte, J., 2006. Habitat loss and the structure of plantanimal mutualistic networks. Ecol. Lett. 9, 281–286. https://doi.org/10.1111/j.1461-0248.2005.00868.x

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EcologicalNetworks.null2 — Function

null2(N::BinaryNetwork)

Given a network N, null2(N) returns a network with the same dimensions, where every interaction happens with a probability equal to the degree of each species.

References

Bascompte, J., Jordano, P., Melian, C.J., Olesen, J.M., 2003. The nested assembly of plant-animal mutualistic networks. PNAS 100, 9383–9387. https://doi.org/10.1073/pnas.1633576100

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EcologicalNetworks.null3 — Function

null3(N::BinaryNetwork; dims::Integer=1)

Given a network N, null3(N) returns a matrix with the same dimensions, where every interaction happens with a probability equal to the out-degree (dims=1) or to the in-degree (dims=2, number of predecessors) of each species, divided by the total number of possible predecessors/successors.

References

Poisot, T., Stanko, M., Miklisová, D., Morand, S., 2013. Facultative and obligate parasite communities exhibit different network properties. Parasitology 140, 1340–1345. https://doi.org/10.1017/S0031182013000851

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Random Dot Product Graph model

The interaction probability in a Random Dot Product Graphs model are given by the dot product of species representations in two metric spaces of a given dimension (one describing species as consumers, one as producers – or predators and preys).

EcologicalNetworks.RDPG — Function

RDPG(N::BinaryNetwork; rank::Integer=3)

Given a binary network N, RDPG(N) returns a probabilistic network with the same number of species, where every interaction happens with a probability equal to the dot product of species representation in the network N's RDPG space of rank rank.

Because the pairwise dot product obtained by the matrix multiplication of the two spaces Left * Right are not granted to be bounded between 0 and 1 (for numerical and theoric reasons), we bound the entries to be in the [0,1] range.

References

Dalla Riva, G.V. and Stouffer, D.B., 2016. Exploring the evolutionary signature of food webs' backbones using functional traits. Oikos, 125(4), pp.446-456. https://doi.org/10.1111/oik.02305

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The Random Dot Product Graph spaces are computed via a truncated Singular Value Decomposition of the food web adjacency matrix.

Missing docstring.

Missing docstring for svd_truncated. Check Documenter's build log for details.

Shuffle interactions

Random.shuffle! — Function

shuffle!(N::BinaryNetwork; constraint::Symbol=:degree)

Shuffles interactions inside a network (the network is modified), under the following constraint:

:degree, which keeps the degree distribution intact
:generality, which keeps the out-degree distribution intact
:vulnerability, which keeps the in-degree distribution intact
:fill, which moves interactions around freely

The function will take two interactions, and swap the species establishing them. By repeating the process a large enough number of times, the resulting network should be relatively random. Note that this function will conserve the degree (when appropriate under the selected constraint) of every species. Calling the function will perform a single shuffle. If you want to repeat the shuffling a large enough number of times, you can use something like:

[shuffle!(n) for i in 1:10_000]

If the keyword arguments are invalid, the function will throw an ArgumentError.

References

Fortuna, M.A., Stouffer, D.B., Olesen, J.M., Jordano, P., Mouillot, D., Krasnov, B.R., Poulin, R., Bascompte, J., 2010. Nestedness versus modularity in ecological networks: two sides of the same coin? Journal of Animal Ecology 78, 811–817. https://doi.org/10.1111/j.1365-2656.2010.01688.x

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Random.shuffle — Function

shuffle(N::BinaryNetwork; constraint::Symbol=:degree)

Return a shuffled copy of the network (the original network is not modified). See shuffle! for a documentation of the keyword arguments.

References

Fortuna, M.A., Stouffer, D.B., Olesen, J.M., Jordano, P., Mouillot, D., Krasnov, B.R., Poulin, R., Bascompte, J., 2010. Nestedness versus modularity in ecological networks: two sides of the same coin? Journal of Animal Ecology 78, 811–817. https://doi.org/10.1111/j.1365-2656.2010.01688.x

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