REl 0.1.0

Author: goedman

docs/src/index.md

@@ -51,11 +51,6 @@ adjacency_matrix(e::NamedArray)
 adjacency_matrix_to_dict(ea::NamedArray)
 ancester_graph(e::NamedArray)
 ancestral_graph(a::NamedArray{Int, 2}; m=Symbol[], c=Symbol[])
-DAG(name::AbstractString, d::OrderedDict)
-DAG(name::AbstractString, str::AbstractString, df::DataFrame)
-DAG(name::AbstractString, str::AbstractString)
-DAG(name::AbstractString, a::NamedArray, df::DataFrame)
-DAG(name::AbstractString, a::NamedArray)
 dag_show(io::IO, d::DAG)
 dag_vars(d::OrderedDict)
 edge_matrix(d::OrderedDict)

src/StructuralCausalModels.jl

@@ -32,6 +32,7 @@ SymbolListOrNothing = Union{SymbolList, Nothing}
 OrderedDictOrNothing = Union{OrderedDict, Nothing}
 NamedArrayOrNothing = Union{NamedArray, Nothing}
 DataFrameOrNothing = Union{DataFrame, Nothing}
+ModelDefinition = Union{OrderedDict, AbstractString, NamedArray}
 
 include("types/DAG.jl")
 include("types/Path.jl")

src/methods/d_separation.jl

@@ -18,7 +18,7 @@ d_separation(
 
 ### Keyword arguments
 ```julia
-* `cond::SymbolListOrNoting=noting`    : Conditioning set
+* `cond::SymbolListOrNothing=nothing`  : Conditioning set
 * `debug=false`                        : Trace execution
 ```
 
@@ -69,14 +69,5 @@ function d_separation(d::DAG, first::SymbolList, second::SymbolList;
 
 end
 
-#=
-function d_separation(d::DAG, first::SymbolList, second::SymbolList, cond::SymbolList; debug=false)
-
-  e = induced_covariance_graph(d, vcat(first, second), cond; debug=debug)
-  sum(e[first, second]) == 0
-
-end
-=#
-
 export
   d_separation

src/methods/dag_methods.jl

@@ -135,7 +135,7 @@ Part of the API, exported.
 """
 function adjacency_matrix_to_dict(a::NamedArray)
   vars = names(a, 1)
-  dct = Dict()
+  dct = OrderedDict()
   for (ind, r) in enumerate(eachrow(a))
     rhs = vars[findall(x -> x ==1, r)]
     if length(rhs) == 1

src/types/DAG.jl

@@ -44,13 +44,17 @@ $(SIGNATURES)
 ### Required arguments
 ```julia
 * `name::AbstractString`               : Name for the DAG object
-* `d`                                  : DAG definition as an
-                                           OrderedDict (see extended help)
-                                           AbstractString (as in ggm or dagitty)
-                                           AdjacencyMatrix
+* `d::ModelDefinition`                 : DAG definition
 ```
 
-### Optional positional argument
+where
+```
+ModelDefinition = Union{OrderedDict, AbstractString, NamedArray}
+```
+
+See the extended help for a usage example.
+
+### Keyword arguments
 ```julia
 * `df::DataFrame`                      : DataFrame with observations
 ```
@@ -80,15 +84,15 @@ Coming from R's dagitty:
 amat <- dagitty("dag { {X V} -> U; S1 <- U; {Y V} -> W; S2 <- W}”)
 ```julia
 dag = DAG("my_name", "dag { {X V} -> U; S1 <- U; {Y V} -> W; S2 <- W}”)
-display(dag.a) # Show the adjacency_matrix
+display(dag) # Show the DAG
 ```
 
 Coming from R's ggm:
 
 amat <- DAG(U~X+V, S1~U, W~V+Y, S2~W, order=FALSE)
 ```julia
 dag = DAG("my_name", "DAG(U~X+V, S1~U, W~V+Y, S2~W”)
-display(dag.a) # Show the adjacency_matrix
+display(dag) # Show the DAG
 ```
 
 ### Acknowledgements
@@ -105,121 +109,36 @@ The Julia translation is licenced under: MIT.
 
 Part of API, exported.
 """
-function DAG(name::AbstractString, d::OrderedDict, df::DataFrame)
-
-  vars = dag_vars(d)
-  a = adjacency_matrix(d)
-  e = edge_matrix(d)
-
-  # Compute covariance matrix and store as NamedArray
-
-  @assert length(names(df)) == length(vars) "DataFrame has different number of columns"
-  s = NamedArray(cov(Array(df)), (names(df), names(df)), ("Rows", "Cols"))
-
-  # Create object
-
-  DAG(name, d, a, e, s, df, vars)
-
-end
-
-"""
-
-# `DAG`
-
-$(SIGNATURES)
-
-Part of API, exported.
-"""
-function DAG(name::AbstractString, d::OrderedDict)
-
-  vars = dag_vars(d)
-  a = adjacency_matrix(d)
-  e = edge_matrix(d)
-
-  # Create object
-
-  DAG(name, d, a, e, nothing, nothing, vars)
-end
-
-"""
-
-# `DAG`
-
-$(SIGNATURES)
-
-Part of API, exported.
-"""
-function DAG(name::AbstractString, str::AbstractString, df::DataFrame)
-  ds = strip(str)
-  if ds[1:3] == "DAG"
-    d = from_ggm(ds)
-  elseif ds[1:3] == "dag"
-    d = from_dagitty(ds)
-  else
-    @error "Unrecognized model string: $(ds))"
-  end
+function DAG(name::AbstractString, model::ModelDefinition; df::DataFrameOrNothing=nothing)
+
+  local d
+  if typeof(model) <: OrderedDict
+    d = model
+  elseif typeof(model) <: AbstractString
+    ds = strip(model)
+    if ds[1:3] == "DAG"
+      d = from_ggm(ds)
+    elseif ds[1:3] == "dag"
+      d = from_dagitty(ds)
+    else
+      @error "Unrecognized model string: $(ds))"
+    end
+  elseif typeof(model) <: NamedArray
+    d = adjacency_matrix_to_dict(model)
+  end    
 
   vars = dag_vars(d)
   a = adjacency_matrix(d)
   e = edge_matrix(d)
 
-  # Compute covariance matrix and store as NamedArray
-
-  @assert length(names(df)) == length(vars) "DataFrame has different number of columns"
-  s = NamedArray(cov(Array(df)), (names(df), names(df)), ("Rows", "Cols"))
-
-  # Create object
-
-  DAG(name, d, a, e, s, df, vars)
-
-end
-
-"""
-
-# `DAG`
-
-$(SIGNATURES)
-
-Part of API, exported.
-"""
-function DAG(name::AbstractString, str::AbstractString)
-  ds = strip(str)
-  if ds[1:3] == "DAG"
-    d = from_ggm(ds)
-  elseif ds[1:3] == "dag"
-    d = from_dagitty(ds)
+  if isnothing(df)
+    s = nothing
   else
-    @error "Unrecognized model string: $(ds))"
+    # Compute covariance matrix and store as NamedArray
+    @assert length(names(df)) == length(vars) "DataFrame has different number of columns"
+    s = NamedArray(cov(Array(df)), (names(df), names(df)), ("Rows", "Cols"))
   end
 
-  vars = dag_vars(d)
-  a = adjacency_matrix(d)
-  e = edge_matrix(d)
-
-  # Create object
-
-  DAG(name, d, a, e, nothing, nothing, vars)
-end
-
-"""
-
-# `DAG`
-
-$(SIGNATURES)
-
-Part of API, exported.
-"""
-function DAG(name::AbstractString, a::NamedArray, df::DataFrame)
-
-  vars = names(a, 1)
-  d = adjacency_matrix_to_dict(a)
-  e = StructuralCausalModels.edge_matrix(a)
-
-  # Compute covariance matrix and store as NamedArray if df is present
-
-  @assert length(names(df)) == length(vars) "DataFrame has different number of columns"
-  s = NamedArray(cov(Array(df)), (names(df), names(df)), ("Rows", "Cols"))
-
   # Create object
 
   DAG(name, d, a, e, s, df, vars)
@@ -228,26 +147,6 @@ end
 
 """
 
-# `DAG`
-
-$(SIGNATURES)
-
-Part of API, exported.
-"""
-function DAG(name::AbstractString, a::NamedArray)
-
-  vars = names(a, 1)
-  d = adjacency_matrix_to_dict(a)
-  e = StructuralCausalModels.edge_matrix(a)
-
-  # Create object
-
-  DAG(name, d, a, e, nothing, nothing, vars)
-
-end
-
-"""
-
 # `set_dag_df!`
 
 Set or update Dataframe associated to DAG

test/runtests.jl

@@ -14,6 +14,7 @@ using Test
   include("test_sr6_4_2a.jl")
   @test adjustmentsets == [[:a], [:c]]
   =#
+  println("\n")
 
 end
 
@@ -28,6 +29,7 @@ end
   @test show_dag_path(dag, allpaths[1]) == ":w ⇒ :s ⇐ :a ⇐ :d"
   @test adjustmentsets == Array{Symbol,1}[]
   =#
+  println("\n")
 
 end 
 
@@ -40,6 +42,7 @@ end
   include("test_dagitty_conversion.jl")
   include("test_ggm_conversion.jl")
   include("test_graphviz_conversions.jl")
+  println("\n")
 
 end
 
@@ -57,5 +60,6 @@ end
   @test show_dag_path(dag, allpaths[1]) == ":w ⇒ :s ⇐ :a ⇐ :d"
   @test adjustmentsets == Array{Symbol,1}[]
   =#
-end 
+  println("\n")
 
+end 

test/test_ag.jl

@@ -42,7 +42,11 @@ fr1 = ancestral_graph(a; m=m, c=c)
 @test all(fr .== fr1)
 
 fr2 = test_ag(dag.a; m=m, c=c)
-@test all(fr .== fr2);
+for i in names(fr, 1)
+  for j in names(fr, 1)
+    @test fr[i, j] == fr2[i, j]
+  end
+end
 
 println()
 display(fr)

test/test_graphviz_conversions.jl

@@ -25,7 +25,7 @@ d = from_ggm("DAG(
     analysis ~ algebra)"
 );
 
-dag = DAG("marks", d, df);
+dag = DAG("marks", d, df=df);
 show(dag)
 
 fn = joinpath(mktempdir(), "marks.dot")

test/test_sr6_4_2.jl

@@ -30,7 +30,7 @@ d = OrderedDict(
   :u => :a
   )
 
-dag = DAG("sr6_4_2", d, df);
+dag = DAG("sr6_4_2", d, df=df);
 
 fn = joinpath(mktempdir(), "sr6_4_2.dot")
 to_graphviz(dag, fn)

test/test_sr6_4_2a.jl

@@ -29,7 +29,7 @@ d = OrderedDict(
 );
 u = [:u]
 
-dag = DAG("sr6_4_2a", d, df);
+dag = DAG("sr6_4_2a", d; df=df);
 show(dag)
 
 fn = joinpath(mktempdir(), "sr6_4_2a.dot")