One feature of EcologicalNetwork which makes the rest of the package works is the type system to represent networks. This is not the most enthralling reading, but this pacge will walk you through the different options, and discuss how and when to use them.

Network representation

All networks types have a field edges to store the sparse adjacency matrix, and fields S, or T and B, for species in unipartite and bipartite networks respectively. edges is always a two-dimensional array (see below for more information), where interactions go from the rows, to the columns. Network types are mutable. Operations that will modify the network end with a !, as is the julian convention.

Fields S, T, and B are one-dimensional arrays of AllowedSpeciesTypes – they currently can be String or Symbol, and represent the species/nodes names. Future allowed types will be added in later releases.

You should never have to manipulate the network by calling its fields directly. The species function will give you access to the species, and the network slicing operations (see later sections) will let you access subset of the network / individual interactions / set of neighbours.

Network types are iterable: this is equivalent to calling the interactions function on a network. On small networks, interactions is faster (but allocates the whole memory at once). On large networks, it can be less true, and using the iteration approach can save some time. The iteration protocol is the same as for all other Julia collections:

for (int_number, interaction) in N
  @info "Interaction $(int_number) -- $(interaction)"
end

The objects returned by the iteration protocol are named tuples with fields to and from (always), and can have additional fields probability and strength.

Partiteness

In unipartite networks, the adjacency matrix edges is square, and has as many rows/columns as there are elements in S. This is always checked and enforced upon construction of the object, so you cannot have a mismatch.

In bipartite networks, the matrix edges is not necessarily square, and has dimensions equal to the lengths of T (rows) and B (columns). This too is checked upon construction.

All elements in S must be unique (no duplicate node names). In addition, all names in the union of T and B must be unique too (so that when a bipartite network is cast to a unipartite one, the constraint on unique names in S is respected). These constraints are enforced when constructing the object, and will return explicit error messages if not met.

Type of information

At all points, you can have a look at the types of the interactions and the species objects – the next entries in this documentation give additional information about the types allowed.

Missing docstring.

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

Union types

All networks are grouped upon the AbstractEcologicalNetwork type:

EcologicalNetworks.AbstractEcologicalNetworkType

All networks in the package belong to the AbstractEcologicalNetwork type. They all have a field A to represent interactions as a matrix, and a number of fields for species. See the documentation for AbstractBipartiteNetwork and AbstractUnipartiteNetwork, as well as AllowedSpeciesTypes for the allowed types for species.

Note that all species in a network (including both levels of a bipartite network) must have the same type. For example, ["a", :b, "c"] is not a valid array of species, as not all its elements have the same type.

source

The type of nodes that are allowed is determined by the non-exported EcologicalNetworks._check_species_validity function. To allow an additional type of node, you can write the following:


struct Foo
  name::AbstractString
  bar::AbstractFloat
end

import EcologicalNetworks
function EcologicalNetworks._check_species_validity(::Type{Foo})
end

Note that integers are never valid species identifiers. By default, String and Symbol are used. The function _check_species_validity should do nothing for an accepted type (and it will throw an error for any other type).

By partiteness

EcologicalNetworks.AbstractBipartiteNetworkType

This abstract type groups all bipartite networks, regardless of the type of information. Bipartite networks have two fields for species, named T (for top, corresponding to matrix rows), and B (for bottom, matrix columns).

Any bipartite network can be declared (we'll use the example of a binary network) either using BipartiteNetwork(A, T, B) (assuming A is a matrix of interactions and T and B are vectors of species names for the top and bottom level), or BipartiteNetwork(A), in which case the species will be named automatically.

source
EcologicalNetworks.AbstractUnipartiteNetworkType

This abstract type groups all unipartite networks, regardless of the type of information. Unipartite networks have a single field for species, named S, which has the same number of elements as the size of the matrix.

Any unipartite network can be declared (we'll use the example of a binary network) either using UnipartiteNetwork(A, S) (assuming A is a matrix of interactions and S is a vector of species names), or UnipartiteNetwork(A), in which case the species will be named automatically.

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By interaction type

EcologicalNetworks.BinaryNetworkConstant

This is a union type for both Bipartite and Unipartite deterministic networks. All networks from these class have adjacency matrices represented as arrays of Boolean values.

source
EcologicalNetworks.QuantitativeNetworkConstant

This is a union type for both unipartite and bipartite quantitative networks. All networks of this type have adjancency matrices as two-dimensional arrays of numbers.

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List of available types

These are the types that you actually declare and use. They are presented last because it is easier to understand what they are when you get a sense for the different union types.