Merge pull request #205 from EcoJulia/hotfix-spectral

Spectral radius bug fix

Project.toml

@@ -2,7 +2,7 @@ name = "EcologicalNetworks"
 uuid = "f03a62fe-f8ab-5b77-a061-bb599b765229"
 authors = ["Timothée Poisot <[email protected]>"]
 repo = "https://github.com/EcoJulia/EcologicalNetworks.jl"
-version = "0.5.0"
+version = "0.5.1"
 
 [deps]
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"

src/community/spectralradius.jl

@@ -14,7 +14,7 @@ end
 
 
 ρ_phillips(N::T, v::Float64) where {T <: UnipartiteNetwork}  = v/((links(N)*(richness(N)-1))/richness(N))^0.5
-ρ_ska(N::T, v::Float64) where {T <: UnipartiteNetwork} = v/sqrt(links(N))
+ρ_ska(N::T, v::Float64) where {T <: UnipartiteNetwork} = v/sqrt((links(N)-sum(diag(adjacency(N))))/2.0)
 ρ_raw(N::T, v::Float64) where {T <: UnipartiteNetwork} = v
 
 """
@@ -45,7 +45,7 @@ and S the number of nodes) are:
 1. `EcologicalNetworks.ρ_phillips`: divides by the square root of (2L(S-1))/S,
    as in Phillips (20110)
 1. `EcologicalNetworks.ρ_ska`: divides by the square root of L, as in
-   Staniczenko *et al.* (2013) - this is the **default**
+   Staniczenko *et al.* (2013) - this is the **default**, and has an upper bound of the square root of the number of links
 1. `EcologicalNetworks.ρ_raw`: returns the raw value
 
 #### References

test/community/spectralradius.jl

@@ -20,4 +20,12 @@ A = [1 0 1 1; 1 1 0 1; 1 1 1 0; 1 1 1 0; 1 1 1 0; 0 1 0 1]
 N = BipartiteNetwork(A.>0)
 @test ρ(N; range=EcologicalNetworks.ρ_raw) ≈ 3.595 atol = 0.01
 
+# This specific example was added to catch a bug due to the wrong
+# normalization, see issue #203
+
+A = [1 1 1 1; 1 1 1 0; 1 1 1 0; 1 1 1 0; 1 1 1 0; 1 0 0 0]
+N = BipartiteNetwork(A.>0)
+@test ρ(N, range=EcologicalNetworks.ρ_raw) ≈ 3.943904 atol = 0.01
+@test ρ(N, range=EcologicalNetworks.ρ_ska) ≈ 0.956537 atol = 0.01
+
 end