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Fix doctests in Algebraic statistics.
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@HechtiDerLachs
HechtiDerLachs committed Sep 30, 2024
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6 changes: 5 additions & 1 deletion experimental/AlgebraicStatistics/src/CI.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,11 @@ julia> ci_statements(["A", "B", "X", "Y"])
[B _||_ Y | {A, X}]
[X _||_ Y | {}]
[X _||_ Y | A]
⋮
[X _||_ Y | B]
[X _||_ Y | {A, B}]
[A _||_ X | {}]
[A _||_ X | B]
[A _||_ X | Y]
[A _||_ X | {B, Y}]
[B _||_ X | {}]
[B _||_ X | A]
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6 changes: 5 additions & 1 deletion experimental/AlgebraicStatistics/src/Markov.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,11 @@ julia> ci_statements(R)
[B _||_ Y | {A, X}]
[X _||_ Y | {}]
[X _||_ Y | A]
⋮
[X _||_ Y | B]
[X _||_ Y | {A, B}]
[A _||_ X | {}]
[A _||_ X | B]
[A _||_ X | Y]
[A _||_ X | {B, Y}]
[B _||_ X | {}]
[B _||_ X | A]
Expand Down
112 changes: 98 additions & 14 deletions experimental/AlgebraicStatistics/src/PhylogeneticParametrization.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -62,22 +62,64 @@ Dict{Tuple{Vararg{Int64}}, QQMPolyRingElem} with 64 entries:
(1, 2, 1) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(3, 1, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(4, 4, 2) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(1, 2, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(1, 2, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 1, 3) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(3, 2, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(3, 2, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(2, 1, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(3, 2, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 2, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 1, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 2, 3) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(2, 1, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 3, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(1, 4, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(2, 1, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(1, 3, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(1, 4, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 1, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 2, 4) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(4, 3, 4) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(2, 2, 1) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(4, 4, 4) => 1//4*a[1]*a[2]*a[3] + 3//4*b[1]*b[2]*b[3]
(4, 3, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(4, 3, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 3, 2) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(4, 1, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(4, 4, 1) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(2, 2, 3) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(3, 4, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(4, 3, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(4, 4, 3) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(4, 2, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 3, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 3, 2) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(1, 4, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 3, 1) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(2, 4, 2) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(1, 1, 2) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(1, 4, 1) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(1, 3, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(3, 3, 4) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(1, 4, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(4, 1, 4) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(3, 4, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(3, 3, 1) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(4, 1, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 2, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(3, 1, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 4, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 3, 3) => 1//4*a[1]*a[2]*a[3] + 3//4*b[1]*b[2]*b[3]
(4, 1, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(4, 2, 4) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(3, 4, 3) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(4, 2, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(3, 2, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(2, 3, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(4, 2, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 3, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(2, 4, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 1, 4) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(2, 1, 2) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(2, 4, 1) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(1, 1, 1) => 1//4*a[1]*a[2]*a[3] + 3//4*b[1]*b[2]*b[3]
(2, 3, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(2, 4, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(1, 1, 3) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
(1, 2, 4) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
⋮ => ⋮
```
"""
Expand Down Expand Up @@ -155,6 +197,48 @@ Dict{Tuple{Vararg{Int64}}, QQMPolyRingElem} with 64 entries:
(4, 4, 4) => 0
(4, 3, 1) => 0
(3, 3, 2) => 0
(4, 1, 2) => 0
(4, 4, 1) => x[3, 1]*x[1, 2]*x[2, 2]
(2, 2, 3) => 0
(3, 4, 2) => x[1, 2]*x[2, 2]*x[3, 2]
(4, 3, 3) => 0
(4, 4, 3) => 0
(4, 2, 2) => 0
(1, 3, 4) => 0
(2, 3, 2) => 0
(1, 4, 4) => x[1, 1]*x[2, 2]*x[3, 2]
(1, 3, 1) => 0
(2, 4, 2) => 0
(1, 1, 2) => 0
(1, 4, 1) => 0
(1, 3, 3) => x[1, 1]*x[2, 2]*x[3, 2]
(3, 3, 4) => 0
(1, 4, 3) => 0
(4, 1, 4) => x[2, 1]*x[1, 2]*x[3, 2]
(3, 4, 4) => 0
(3, 3, 1) => x[3, 1]*x[1, 2]*x[2, 2]
(4, 1, 1) => 0
(1, 2, 2) => x[1, 1]*x[2, 2]*x[3, 2]
(3, 1, 2) => 0
(3, 4, 1) => 0
(3, 3, 3) => 0
(4, 1, 3) => 0
(4, 2, 4) => 0
(3, 4, 3) => 0
(4, 2, 1) => 0
(3, 2, 2) => 0
(2, 3, 4) => x[1, 2]*x[2, 2]*x[3, 2]
(4, 2, 3) => x[1, 2]*x[2, 2]*x[3, 2]
(2, 3, 1) => 0
(2, 4, 4) => 0
(1, 1, 4) => 0
(2, 1, 2) => x[2, 1]*x[1, 2]*x[3, 2]
(2, 4, 1) => 0
(1, 1, 1) => x[1, 1]*x[2, 1]*x[3, 1]
(2, 3, 3) => 0
(2, 4, 3) => x[1, 2]*x[2, 2]*x[3, 2]
(1, 1, 3) => 0
(1, 2, 4) => 0
⋮ => ⋮
```
"""
Expand Down Expand Up @@ -192,16 +276,16 @@ Dict{Tuple{Vararg{Int64}}, QQMPolyRingElem} with 5 entries:
(1, 2, 1) => 1//4*a[1]*a[3]*b[2] + 1//4*a[2]*b[1]*b[3] + 1//2*b[1]*b[2]*b[3]
(1, 1, 1) => 1//4*a[1]*a[2]*a[3] + 3//4*b[1]*b[2]*b[3]
(1, 2, 2) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*a[3]*b[1] + 1//2*b[1]*b[2]*b[3]
(1, 2, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] …
(1, 2, 3) => 1//4*a[1]*b[2]*b[3] + 1//4*a[2]*b[1]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//4*b[1]*b[2]*b[3]
(1, 1, 2) => 1//4*a[1]*a[2]*b[3] + 1//4*a[3]*b[1]*b[2] + 1//2*b[1]*b[2]*b[3]
julia> p_equivclasses.classes
Dict{Tuple{Vararg{Int64}}, Vector{Tuple{Vararg{Int64}}}} with 5 entries:
(1, 2, 1) => [(1, 2, 1), (1, 3, 1), (1, 4, 1), (2, 1, 2), (2, 3, 2), (2, 4, 2…
(1, 2, 1) => [(1, 2, 1), (1, 3, 1), (1, 4, 1), (2, 1, 2), (2, 3, 2), (2, 4, 2), (3, 1, 3), (3, 2, 3), (3, 4, 3), (4, 1, 4), (4, 2, 4), (4, 3, 4)]
(1, 1, 1) => [(1, 1, 1), (2, 2, 2), (3, 3, 3), (4, 4, 4)]
(1, 2, 2) => [(1, 2, 2), (1, 3, 3), (1, 4, 4), (2, 1, 1), (2, 3, 3), (2, 4, 4…
(1, 2, 3) => [(1, 2, 3), (1, 2, 4), (1, 3, 2), (1, 3, 4), (1, 4, 2), (1, 4, 3…
(1, 1, 2) => [(1, 1, 2), (1, 1, 3), (1, 1, 4), (2, 2, 1), (2, 2, 3), (2, 2, 4…
(1, 2, 2) => [(1, 2, 2), (1, 3, 3), (1, 4, 4), (2, 1, 1), (2, 3, 3), (2, 4, 4), (3, 1, 1), (3, 2, 2), (3, 4, 4), (4, 1, 1), (4, 2, 2), (4, 3, 3)]
(1, 2, 3) => [(1, 2, 3), (1, 2, 4), (1, 3, 2), (1, 3, 4), (1, 4, 2), (1, 4, 3), (2, 1, 3), (2, 1, 4), (2, 3, 1), (2, 3, 4) … (3, 2, 1), (3, 2, 4), (3, 4, 1), (3, 4, 2), (4, 1, 2), (4, 1, 3), (4, 2, 1), (4, …
(1, 1, 2) => [(1, 1, 2), (1, 1, 3), (1, 1, 4), (2, 2, 1), (2, 2, 3), (2, 2, 4), (3, 3, 1), (3, 3, 2), (3, 3, 4), (4, 4, 1), (4, 4, 2), (4, 4, 3)]
julia> q_equivclasses = compute_equivalent_classes(q);
Expand Down Expand Up @@ -251,7 +335,7 @@ Dict{Tuple{Int64, Int64, Int64}, QQMPolyRingElem} with 5 entries:
(1, 2, 1) => 3*a[1]*a[3]*b[2] + 3*a[2]*b[1]*b[3] + 6*b[1]*b[2]*b[3]
(1, 1, 1) => a[1]*a[2]*a[3] + 3*b[1]*b[2]*b[3]
(1, 2, 2) => 3*a[1]*b[2]*b[3] + 3*a[2]*a[3]*b[1] + 6*b[1]*b[2]*b[3]
(1, 2, 3) => 6*a[1]*b[2]*b[3] + 6*a[2]*b[1]*b[3] + 6*a[3]*b[1]*b[2] + 6*b[1]*…
(1, 2, 3) => 6*a[1]*b[2]*b[3] + 6*a[2]*b[1]*b[3] + 6*a[3]*b[1]*b[2] + 6*b[1]*b[2]*b[3]
(1, 1, 2) => 3*a[1]*a[2]*b[3] + 3*a[3]*b[1]*b[2] + 6*b[1]*b[2]*b[3]
```
"""
Expand Down

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