Merge branch 'louvain_mod' of github.com:PoisotLab/EcologicalNetwork.…

…jl into louvain_mod

.travis.yml

@@ -4,6 +4,10 @@ os:
   - linux
 julia:
   - 0.5
+  - 0.6
+matrix:
+  allow_failures:
+    - julia: 0.6
 script:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
   - julia --check-bounds=yes -e 'Pkg.clone(pwd()); Pkg.build("EcologicalNetwork"); Pkg.test("EcologicalNetwork"; coverage=true)'

docs/src/species/foodweb.md

@@ -1,5 +1,30 @@
 # Food-web specific measures
 
+## Measures of trophic level
+
+These measure work by counting the distance to a primary producer -- where
+"primary producer" is defined as the fact of not having outgoing interactions.
+Primary producers have a trophic level of 1, and species that consume primary
+producers have trophic levels of 2, etc. This represents a species' *fractional*
+trophic level.
+
+~~~@docs
+fractional_trophic_level
+~~~
+
+Because some species higher-up the food chain eat preys at various fractional
+trophic levels, there is also a more integrative measure -- the trophic level of
+a species is the weighted average of the fractional trophic level of its preys:
+
+~~~@docs
+trophic_level
+~~~
+
+## Measures of trophic positions
+
+For every species in a food web, this will return an array with its overall
+position:
+
 ~~~@docs
 foodweb_position
 ~~~

test/foodwebs.jl

@@ -24,4 +24,10 @@ module TestFoodWebs
   @test foodweb_position(s1)[2] == :intermediate
   @test foodweb_position(s1)[3] == :bottom
 
+
+  # test that the results are the same with and without loops
+  A = unipartitemotifs()[:S1]
+  @test foodweb_position(A, loops=false)[1] == :top
+  @test foodweb_position(A, loops=true)[1] == :top
+
 end

test/types.jl

@@ -42,7 +42,6 @@ A = BipartiteNetwork([0 1; 0 0])
 A = UnipartiteNetwork([0 1; 0 0])
 @test typeof(A) <: DeterministicNetwork
 
-
 # Is there an interaction?
 A = UnipartiteNetwork([false true; true false])
 @test has_interaction(A, 1, 2)