Map Inf path lengths to zero (#117)

* Map Inf path lengths to zero

* Use FW paths to calculate rna[:averagepath]

* Add disconnected graph test for rna

* Move :averagepath calculation to separate function

* Bump version to v1.5.2

Author: gerrygralton

NEWS.md

@@ -1,5 +1,8 @@
 # RecurrenceAnalysis.jl News
 
+## v1.5.2
+- New, faster formula for `rna[:averagepath]` allowing disconnected graphs.
+
 ## v1.5.1
 - Minor documentation fixes.
 

Project.toml

@@ -1,7 +1,7 @@
 name = "RecurrenceAnalysis"
 uuid = "639c3291-70d9-5ea2-8c5b-839eba1ee399"
 repo = "https://github.com/JuliaDynamics/RecurrenceAnalysis.jl.git"
-version = "1.5.1"
+version = "1.5.2"
 
 [deps]
 DelayEmbeddings = "5732040d-69e3-5649-938a-b6b4f237613f"

src/rna.jl

@@ -43,7 +43,22 @@ function rna(args...; kwargs...)
     return Dict{Symbol, Float64}(
         :density => density(graph),
         :transitivity => global_clustering_coefficient(graph),
-        :averagepath => mean(1 ./ closeness_centrality(graph)),
+        :averagepath => averagepath(graph),
         :diameter => diameter(graph)
     )
 end
+
+"""
+    averagepath(graph)
+
+Calculates average minimum path length for a SimpleGraph.
+Uses Donner, 2010, Eq. 26 on pg. 18.
+"""
+function averagepath(graph::SimpleGraph)
+    num_verts = nv(graph)
+
+    dist_mat = floyd_warshall_shortest_paths(graph).dists
+    @. dist_mat[dist_mat == typemax(dist_mat)] = 0.
+
+    return sum(dist_mat) / (num_verts * (num_verts - 1))
+end

test/smallmatrix.jl

@@ -184,4 +184,27 @@ end
     @test rna_dict[:transitivity] ≈ sum(triangles) / sum(triples)
     @test rna_dict[:averagepath] ≈ sum(dismat9) / (9*8)
     @test rna_dict[:diameter] == maximum(dismat9)
+    adjmat11 = [0 0 0 1 0 0 0 1 0 0
+                0 0 0 0 1 0 0 0 1 0
+                0 0 0 0 0 1 0 0 0 0
+                1 0 0 0 0 0 1 0 0 0
+                0 1 0 0 0 0 0 1 0 0
+                0 0 1 0 0 0 0 0 1 0
+                0 0 0 1 0 0 0 0 0 0
+                1 0 0 0 1 0 0 0 0 0
+                0 1 0 0 0 1 0 0 0 0
+                0 0 0 0 0 0 0 0 0 0]
+    dismat11 =  [0 3 6 1 2 5 2 1 4 Inf
+                 3 0 3 4 1 2 5 2 1 Inf
+                 6 3 0 7 4 1 8 5 2 Inf
+                 1 4 7 0 3 6 1 2 5 Inf
+                 2 1 4 3 0 3 4 1 2 Inf
+                 5 2 1 6 3 0 7 4 1 Inf
+                 2 5 8 1 4 7 0 3 6 Inf
+                 1 2 5 2 1 4 3 0 3 Inf
+                 4 1 2 5 2 1 6 3 0 Inf
+                 Inf Inf Inf Inf Inf Inf Inf Inf Inf 0]
+    rna_dict = rna(RecurrenceMatrix(adjmat11))
+    @test !isinf(rna_dict[:averagepath])
+    @test rna_dict[:averagepath] ≈ sum(dismat11[1:9,1:9]) / (9*10)
 end