feat: bipartite motifs

docs/SpeciesInteractionNetworks.bib

@@ -565,4 +565,17 @@ @Article{Poisot2023Network
   publisher = {Elsevier {BV}},
 }
 
+@Article{Simmons2018Motifs,
+  author    = {Benno I. Simmons and Alyssa R. Cirtwill and Nick J. Baker and Hannah S. Wauchope and Lynn V. Dicks and Daniel B. Stouffer and William J. Sutherland},
+  journal   = {Oikos},
+  title     = {Motifs in bipartite ecological networks: uncovering indirect interactions},
+  year      = {2018},
+  month     = {oct},
+  number    = {2},
+  pages     = {154--170},
+  volume    = {128},
+  doi       = {10.1111/oik.05670},
+  publisher = {Wiley},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}

docs/mkdocs.yml

@@ -46,6 +46,7 @@ nav:
     - Specificity: micro_level/specificity.md
     - Centrality: micro_level/centrality.md
   - Meso:
+    - Motifs: meso_level/motifs.md
     - Paths: meso_level/paths.md
   - Macro:
     - Links counting: macro_level/links.md

docs/src/meso_level/motifs.md

@@ -0,0 +1,11 @@
+# Motifs
+
+!!! abstract
+
+    ya
+
+## List of motifs
+
+```@docs
+motifs
+```

src/SpeciesInteractionNetworks.jl

@@ -93,6 +93,9 @@ export ShortestPathMethod
 export normalize
 export shortestpath, pathbetween
 
+include("meso_level/motifs.jl")
+export motifs
+
 include("meso_level/paths/BellmanFord.jl")
 export BellmanFord
 

src/meso_level/motifs.jl

@@ -0,0 +1,48 @@
+"""
+    motifs(::Type{Bipartite}, nodes::Integer)
+
+Returns a list of bipartite motifs with the specified number of nodes. The list
+of motifs for each richness are from [Simmons2018Motifs](@citet).
+
+###### References
+
+[Simmons2018Motifs](@citet*)
+"""
+function motifs(::Type{Bipartite}, nodes::Integer)
+    A = Matrix{Bool}[]
+    if nodes == 2
+        A = [ones(Bool, 1,1)]
+    end
+    if nodes == 3
+        A = Matrix{Bool}[
+            Bool[1 1;],
+            reshape(Bool[1; 1], (2,1))
+        ]
+    end
+    if nodes == 4
+        A = Matrix{Bool}[
+            Bool[1 1 1;],
+            Bool[1 1; 0 1],
+            Bool[1 1; 1 1],
+            reshape(Bool[1; 1; 1], (3,1)),
+        ]
+    end
+    if nodes == 5
+        A = Matrix{Bool}[
+            Bool[1 1 1 1;],
+            Bool[1 0; 1 0; 1 1;],
+            Bool[1 0; 1 1; 0 1;],
+            Bool[1 0; 1 1; 1 1;],
+            Bool[1 1; 1 1; 1 1;],
+            Bool[1 0 0; 1 1 1;],
+            Bool[1 1 0; 0 1 1;],
+            Bool[1 1 0; 1 1 1;],
+            Bool[1 1 1; 1 1 1],
+            reshape(Bool[1; 1; 1; 1;], (4, 1)),
+        ]
+    end
+    if isempty(A)
+        throw("Bipartite motifs with $(nodes) nodes are not supported")
+    end
+    return SpeciesInteractionNetwork{Bipartite, Binary}.(A)
+end