Rel 0.1.0

Author: goedman

README.md

@@ -14,7 +14,7 @@
 
 # Introduction
 
-StructuralCausalModels.jl is part of the StatisticalRethinkingJulia eco system and, for now, containg functionality to analyse directed acyclic graph (DAG) based causal models as described in [StatisticalRethinking](https://xcelab.net/rm/statistical-rethinking/),[Causal Inference in Statistics](http://bcs.wiley.com/he-bcs/Books?action=index&bcsId=10288&itemId=1119186846) and [Cause and Correlation in Biology](https://www.cambridge.org/core/books/cause-and-correlation-in-biology/247799189B31939D24BC0F61FD59E9BB#).
+StructuralCausalModels.jl is part of the StatisticalRethinkingJulia eco system and contains functionality to analyse directed acyclic graph (DAG) based causal models as described in [StatisticalRethinking](https://xcelab.net/rm/statistical-rethinking/), [Causal Inference in Statistics](http://bcs.wiley.com/he-bcs/Books?action=index&bcsId=10288&itemId=1119186846) and [Cause and Correlation in Biology](https://www.cambridge.org/core/books/cause-and-correlation-in-biology/247799189B31939D24BC0F61FD59E9BB#).
 
 My initial goal for this package is to have a way to apply SCM ideas to the examples in [StatisticalRethinking.jl](https://github.com/StatisticalRethinkingJulia), i.e. a working version of `basis_set()`, `d_separation()` and `adjustment_sets()`.
 
@@ -37,7 +37,9 @@ Important links are:
 4. Sadeghi, K. (2011). Stable classes of graphs containing directed acyclic
 graphs, implementation as included in ggm.
 
-The latter two have been used for the Julia implementations of `basis_set()`, `d_separation()`, `shipley_test()`, `pcor_test()` and `ancestral_graph`.
+The latter two have been used for the Julia implementations of most fuctions
+in this package, e.g. `basis_set()`, `d_separation()`, `m_separation`,
+`shipley_test()`, `pcor_test()` and `ancestral_graph`.
 
 
 # References

docs/src/index.md

@@ -14,7 +14,12 @@ DAG(name::AbstractString, model::ModelDefinition; df::DataFrameOrNothing=nothing
 
 ## d_separation
 ```@docs
-d_separation(d::DAG, first::SymbolList, second::SymbolList; cond::SymbolListOrNothing, debug=false)
+d_separation(d::DAG, f::SymbolList, s::SymbolList; c::SymbolListOrNothing, debug=false)
+```
+
+## m_separation
+```@docs
+m_separation(d::DAG, f::SymbolList, s::SymbolList; c::SymbolListOrNothing, debug=false)
 ```
 
 ## shipley_test
@@ -32,6 +37,11 @@ basis_set(dag::DAG)
 ancestral_graph(d::DAG; m=Symbol[], c=Symbol[])
 ```
 
+## ribbbon_graph
+```@docs
+ribbon_graph(d::DAG; m=Symbol[], c=Symbol[])
+```
+
 ## adjustment_sets
 ```@docs
 adjustment_sets(d::DAG, f::Symbol, l::Symbol; debug=false)

examples/SR/SR6.4.2/sr6.4.2.jl

@@ -54,8 +54,8 @@ display(t); println()
 
 f = [:a]; s = [:b]; conditioning_set = [:u, :c]
 
-e = d_separation(dag, f, s, cset=conditioning_set)
-println("d_separation($(dag.name), $f, $s, cset=$conditioning_set) = $e")
+e = d_separation(dag, f, s, c=conditioning_set)
+println("d_separation($(dag.name), $f, $s, c=$conditioning_set) = $e")
 println()
 
 adjustmentsets = adjustment_sets(dag, :x, :y)

examples/SR/SR6.4.3/sr6.4.3.jl

@@ -44,8 +44,8 @@ display(t); println()
 
 f = :w; s = :d;
 
-e = d_separation(dag, [f], [s], cset=[:m, :a])
-println("d_separation($(dag.name), $f, $s, cset=[:m, :a]) = $e\n")
+e = d_separation(dag, [f], [s], c=[:m, :a])
+println("d_separation($(dag.name), $f, $s, c=[:m, :a]) = $e\n")
 
 #ap = all_paths(dag, f, s)
 ap = all_paths(dag, f, s)

examples/SR/chain/AMD.jl

@@ -46,10 +46,10 @@ end
 println()
 
 f = [:A]; s = [:D]; sel = vcat(f, s)
-cset = [:M]
+c = [:M]
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s; cset=cset)
-println("d_separation($(dag.name), $f, $s; cset=$cset) = $e")
+e = d_separation(dag, f, s; c=c)
+println("d_separation($(dag.name), $f, $s; c=$c) = $e")

examples/SR/fork/AMD.jl

@@ -44,13 +44,13 @@ end
 println()
 
 f = [:M]; s = [:D]; sel = vcat(f, s)
-cset = [:A]
+c = [:A]
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s, cset=cset)
-println("d_separation($(dag.name), $f, $s, cset=$cset) = $e")
+e = d_separation(dag, f, s, c=c)
+println("d_separation($(dag.name), $f, $s, c=$c) = $e")
 println()
 N = 100
 df = DataFrame();
@@ -94,13 +94,13 @@ end
 println()
 
 f = :M; s = :D; sel = vcat(f, s)
-cset = :A
+c = :A
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s, cset=cset)
-println("d_separation($(dag.name), $f, $s, cset=$cset) = $e")
+e = d_separation(dag, f, s, c=c)
+println("d_separation($(dag.name), $f, $s, c=$c) = $e")
 
 as = adjustment_sets(dag, :A, :D)
 as |> display

examples/SR/waffledivorce/AMD_Dag_1.jl

@@ -42,13 +42,13 @@ end
 println()
 
 f = [:A]; s = [:D]; sel = vcat(f, s)
-cset = [:M]
+c = [:M]
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s, cset=cset)
-println("d_separation($(dag.name), $f, $s, cset=$cset) = $e\n")
+e = d_separation(dag, f, s, c=c)
+println("d_separation($(dag.name), $f, $s, c=$c) = $e\n")
 
 bs = basis_set(dag)
 display(bs)

examples/SR/waffledivorce/AMD_Dag_2.jl

@@ -36,13 +36,13 @@ end
 println()
 
 f = [:A]; s = [:D]; sel = vcat(f, s)
-cset = [:M]
+c = [:M]
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s, cset=cset)
-println("d_separation($(dag.name), $f, $s, cset=$cset) = $e\n")
+e = d_separation(dag, f, s, c=c)
+println("d_separation($(dag.name), $f, $s, c=$c) = $e\n")
 
 bs = basis_set(dag)
 display(bs)

examples/SR/waffledivorce/AMD_Dag_3.jl

@@ -36,13 +36,13 @@ end
 println()
 
 f = [:M]; s = [:D]; sel = vcat(f, s)
-cset = [:A]
+c = [:A]
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")
 
-e = d_separation(dag, f, s, cset=cset)
-println("d_separation($(dag.name), $f, $s, cset=$cset) = $e\n")
+e = d_separation(dag, f, s, c=c)
+println("d_separation($(dag.name), $f, $s, c=$c) = $e\n")
 
 bs = basis_set(dag)
 display(bs)

examples/Shipley/fig2.6/fig2.6.a.jl

@@ -18,40 +18,40 @@ show(dag)
 f = [:x]; s = [:v]
 g1 = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) == $g1")
-g1 = d_separation(dag, f, s; cset=[:u])
-println("d_separation($(dag.name), $f, $s; cset=[:u) == $g1")
-g1 = d_separation(dag, f, s; cset=[:s1])
-println("d_separation($(dag.name), $f, $s; cset=[:s1]) == $g1\n")
+g1 = d_separation(dag, f, s; c=[:u])
+println("d_separation($(dag.name), $f, $s; c=[:u) == $g1")
+g1 = d_separation(dag, f, s; c=[:s1])
+println("d_separation($(dag.name), $f, $s; c=[:s1]) == $g1\n")
 
 f = [:x]; s = [:w]
 g2 = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) == $g2")
-g2 = d_separation(dag, f, s; cset=[:u])
-println("d_separation($(dag.name), $f, $s; cset=[:u]) == $g2")
-g2 = d_separation(dag, f, s; cset=[:v])
-println("d_separation($(dag.name), $f, $s; cset=[:v]) == $g2")
-g2 = d_separation(dag, f, s; cset=[:u, :v])
-println("d_separation($(dag.name), $f, $s; cset=[:u, :v]) == $g2\n")
+g2 = d_separation(dag, f, s; c=[:u])
+println("d_separation($(dag.name), $f, $s; c=[:u]) == $g2")
+g2 = d_separation(dag, f, s; c=[:v])
+println("d_separation($(dag.name), $f, $s; c=[:v]) == $g2")
+g2 = d_separation(dag, f, s; c=[:u, :v])
+println("d_separation($(dag.name), $f, $s; c=[:u, :v]) == $g2\n")
 
 f = [:x]; s = [:y]
 g3 = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) == $g3")
-g3 = d_separation(dag, f, s; cset=[:u, :w])
-println("d_separation($(dag.name), $f, $s; cset=[:u, :w]) == $g3")
-g3 = d_separation(dag, f, s; cset=[:s1, :s2])
-println("d_separation($(dag.name), $f, $s; cset=[:s1, :s2]) == $g3")
-g3 = d_separation(dag, f, s; cset=[:u, :v, :w])
-println("d_separation($(dag.name), $f, $s; cset=[:u, :v, :w]) == $g3")
-g3 = d_separation(dag, f, s; cset=[:s1, :s2, :u])
-println("d_separation($(dag.name), $f, $s; cset=[:s1, :s2, :u]) == $g3")
-g3 = d_separation(dag, f, s; cset=[:s1])
-println("d_separation($(dag.name), $f, $s; cset=[:s1]) == $g3\n")
+g3 = d_separation(dag, f, s; c=[:u, :w])
+println("d_separation($(dag.name), $f, $s; c=[:u, :w]) == $g3")
+g3 = d_separation(dag, f, s; c=[:s1, :s2])
+println("d_separation($(dag.name), $f, $s; c=[:s1, :s2]) == $g3")
+g3 = d_separation(dag, f, s; c=[:u, :v, :w])
+println("d_separation($(dag.name), $f, $s; c=[:u, :v, :w]) == $g3")
+g3 = d_separation(dag, f, s; c=[:s1, :s2, :u])
+println("d_separation($(dag.name), $f, $s; c=[:s1, :s2, :u]) == $g3")
+g3 = d_separation(dag, f, s; c=[:s1])
+println("d_separation($(dag.name), $f, $s; c=[:s1]) == $g3\n")
 
 f = [:u]; s = [:w]
 g4 = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) == $g4"), [:s1]
-g4 = d_separation(dag, f, s; cset=[:v])
-println("d_separation($(dag.name), $f, $s; cset=[:v]) == $g4\n")
+g4 = d_separation(dag, f, s; c=[:v])
+println("d_separation($(dag.name), $f, $s; c=[:v]) == $g4\n")
 
 bs = basis_set(dag)
 bs |> display