general markov tests

Author: antonydellavecchia

experimental/AlgebraicStatistics/src/PhylogeneticModels.jl

@@ -1094,7 +1094,6 @@ end
 
   hyb = hybrids(N)
   R, dict_maps, rv, Dict{Edge, MPolyRingElem}(hyb[h_nodes[i]][j] => l[i,j] for i in 1:length(h_nodes) for j in 1:2)
-
 end
 
 @attr Tuple{
@@ -1167,15 +1166,12 @@ end
 
   R, l, x... = polynomial_ring(base_field(PM), :l => (1:length(h_nodes),1:2), edge_gens...; cached=cached)
 
-
   hyb = hybrids(N)
   R, Dict{Tuple{VarName, Edge}, MPolyRingElem}(
      (vars[i], e) => x[i][j] for i in 1:length(vars), (j,e) in enumerate(sort_edges(N, sorted_edges))),
      Dict{Edge, MPolyRingElem}(hyb[h_nodes[i]][j] => l[i,j] for i in 1:length(h_nodes) for j in 1:2)
-
 end
 
-
 ###################################################################################
 #
 #       Model Ring & Parametrizations

experimental/AlgebraicStatistics/test/PhylogeneticModels.jl

@@ -143,8 +143,21 @@
       @test allunique([entry_transition_matrix(model, i, j, Edge(4,3)) for i in 1:4 for j in 1:4])
 
       # Polynomial rings
-      @test ngens(parameter_ring(model)[1]) ==  4 + 16(n_edges(tree))
-      @test ngens(full_model_ring(model)[1]) == n_states(model)^(n_leaves(tree))
+      PR, pv, rv = parameter_ring(model)
+      @test ngens(PR) == 16(n_edges(tree))
+      @test ngens(coefficient_ring(PR)) == 4
+      @test ngens(full_model_ring(model)) == n_states(model)^(n_leaves(tree))
+
+      phi = parametrization(model)
+      MR, mr_gens = model_ring(model)
+      π1*m11[1]*m11[3]*m12[2] + π2*m21[1]*m21[3]*m22[2] + π3*m31[1]*m31[3]*m32[2] + π4*m41[1]*m41[3
+]*m42[2]
+
+      @test phi(mr_gens[1, 2, 1]) == ( rv[1] * pv[:m11, 4, 1] * pv[:m11, 4, 3] * pv[:m12, 4, 2]
+                                       + rv[2] * pv[:m21, 4, 1] * pv[:m21, 4, 3] * pv[:m22, 4, 2] 
+                                       + rv[3] * pv[:m31, 4, 1] * pv[:m31, 4, 3] * pv[:m32, 4, 2] 
+                                       + rv[4] * pv[:m41, 4, 1] * pv[:m41, 4, 3] * pv[:m42, 4, 2] )
+      
     end
 
     # Test parametrizations for a specific tree and model