feat: simplify

docs/src/macro_level/degeneracy.md

@@ -9,4 +9,10 @@
 ```@docs
 isdisconnected
 isdegenerate
-```
+```
+
+## Simplification of networks with disconnected species
+
+```@docs
+simplify
+```

src/SpeciesInteractionNetworks.jl

@@ -90,6 +90,7 @@ export spectralradius
 
 include("macro_level/degeneracy.jl")
 export isdegenerate, isdisconnected
+export simplify
 
 include("meta_level/set.jl")
 include("meta_level/partitions.jl")

src/interfaces/abstractarray.jl

@@ -15,6 +15,9 @@ Base.axes(N::SpeciesInteractionNetwork, i::Integer) = axes(N.edges, i)
 Base.size(E::Interactions) = size(E.edges)
 Base.size(E::Interactions, i::Integer) = size(E.edges, i)
 
+Base.size(E::Bipartite) = (length(E.top), length(E.bottom))
+Base.size(E::Unipartite) = (length(E.margin), length(E.margin))
+
 Base.size(N::SpeciesInteractionNetwork) = size(N.edges)
 Base.size(N::SpeciesInteractionNetwork, i::Integer) = size(N.edges, i)
 

src/macro_level/degeneracy.jl

@@ -81,4 +81,42 @@ end
     @test ~isdisconnected(N, :A, true)
     @test isdisconnected(N, :B, false)
     @test isdisconnected(N, :B, true)
+end
+
+"""
+    simplify(N::SpeciesInteractionNetwork{<:Bipartite, <:Interactions})
+
+Returns a *copy* of a network containing only the species with interactions.
+Internally, this calls [`isdisconnected`](@ref).
+"""
+function simplify(N::SpeciesInteractionNetwork{<:Bipartite, <:Interactions})
+    top_nodes = filter(sp -> !isdisconnected(N, sp), species(N, 1))
+    bot_nodes = filter(sp -> !isdisconnected(N, sp), species(N, 2))
+    return subgraph(N, top_nodes, bot_nodes)
+end
+
+"""
+    simplify(N::SpeciesInteractionNetwork{<:Unipartite, <:Interactions}, allow_self_interactions::Bool=true)
+
+Returns a *copy* of a network containing only the species with interactions.
+Internally, this calls [`isdisconnected`](@ref) -- see this documentation for
+the consequences of `allow_self_interactions`.
+"""
+function simplify(N::SpeciesInteractionNetwork{<:Unipartite, <:Interactions}, allow_self_interactions::Bool=true)
+    nodes = filter(sp -> !isdisconnected(N, sp, allow_self_interactions), species(N))
+    return subgraph(N, nodes)
+end
+
+@testitem "We can simplify a bipartite network" begin
+    nodes = Bipartite([:A, :B, :C], [:a, :b])
+    edges = Binary(zeros(Bool, size(nodes)))
+    N = SpeciesInteractionNetwork(nodes, edges)
+    N[:A, :a] = true
+    N[:A, :b] = true
+    N[:C, :a] = true
+    S = simplify(N)
+    @test richness(S) == 4
+    S[:A, :a] = false
+    @test N[:A, :a] == true
+    @test S[:A, :a] == false
 end