Merge c8d2143 into 721b707

src/make_parameters.jl

@@ -250,6 +250,7 @@ function model_parameters(A;
     parameters[:extinctions] = []
     parameters[:extinctionstime] = []
     parameters[:tmpA] = []
+    adbm_trigger == :interval ? parameters[:rewiretime] = [] : Nothing
  else
     error("Invalid method for rewiring -- must be :DO (alternatively :stan), :ADBM, :DS (alternatively :Gilljam) or :none")
  end

src/rewiring/parameters/checkParameters.jl

@@ -19,21 +19,32 @@ function check_rewiring_parameters(rewireP,rewireMethod)
     :Nmethod,
     :Hmethod,
     :rewire_method,
-    :costMat]
+    :adbm_trigger,
+    :costMat,
+    :extinctions,
+    :extinctionstime,
+    :tmpA]
+    if rewireP[:adbm_trigger] == :interval
+      append!(required_keys, [:adbm_interval, :rewiretime])
+    end
   elseif rewireMethod ∈ [:Gilljam, :DS]
     required_keys = [
     :rewire_method,
     :similarity,
     :specialistPrefMag,
     :extinctions,
+    :extinctionstime,
+    :tmpA,
     :preferenceMethod,
     :cost,
     :costMat,
     :specialistPref]
   elseif rewireMethod ∈ [:stan, :DO]
     required_keys = [
     :rewire_method,
-    :extinctions]
+    :extinctions,
+    :extinctionstime,
+    :tmpA]
   end
 
   if rewireMethod ∈ [:Gilljam, :ADBM, :stan, :DO, :DS]

src/rewiring/parameters/updateParameters.jl

@@ -2,18 +2,27 @@ function update_rewiring_parameters(parameters::Dict{Symbol,Any}, biomass, t)
   S = size(parameters[:A], 1)
 
   if parameters[:rewire_method] == :ADBM
+    # Is there any extinction and/or rewiring happening?
+    A = parameters[:A] #interaction matrix
+    Anew = ADBM(S,parameters,biomass) #potentially new interaction  matrix
+    if A != Anew #different matrices => rewired
+      append!(parameters[:tmpA], [parameters[:A]]) #store the old matrix
+      if parameters[:adbm_trigger] == :interval
+        append!(parameters[:rewiretime], t) #store the time t whichrewiring happened
+      end
+    end
+    #Is there any extinction?
     extinct = findall(biomass .< 100*eps())
     for i in extinct
       if i ∉ parameters[:extinctions]
         append!(parameters[:extinctions], i) ;
         append!(parameters[:extinctionstime], [(t, i)])
-        append!(parameters[:tmpA], [parameters[:A]])
       end
     end
     sort!(parameters[:extinctions])
 
     #assign new array
-    parameters[:A] = ADBM(S,parameters,biomass)
+    parameters[:A] = Anew
 
     #update the parameters
     get_herbivores(parameters) #

test/rewiring/ADBM.jl

@@ -111,5 +111,17 @@ module TestADBM_interval
 
     @test p[:extinctions] == [1,2]
     @test p[:extinctionstime] == [(0.0, 2), (100.0, 1)]
-    @test p[:tmpA] == [A, [0 0 0 ; 0 0 0 ; 0 0 0]]
+    @test p[:tmpA] == [convert(Array{Any, 2}, A)]
+    @test length(p[:rewiretime]) != 0
+
+    A = [0 1 0 0; 0 0 0 1 ; 0 0 0 1 ; 0 0 0 0]
+    p = model_parameters(A, rewire_method = :ADBM, adbm_trigger = :interval, adbm_interval = 1, Z = 10.0)
+    b = [0.8, 2e-6, 0.8, 0.5]
+    s = simulate(p, b, stop = 10)
+
+    @test p[:extinctions] == [2]
+    @test length(p[:extinctionstime]) != 0
+    @test p[:tmpA] == map(x -> convert(Array{Any, 2}, x),[A, [0 1 1 1; 0 0 0 1; 0 0 0 1; 0 0 0 0]])
+    @test length(p[:rewiretime]) != 0
+
 end