Rel 0.1.0

Author: goedman

.travis.yml

@@ -16,8 +16,6 @@ git:
 
 jobs:
   include:
-    - stage: TestPreviousRelease
-      os: linux
     - stage: TestLatestRelease
       julia: 1.5
       os: linux

docs/src/index.md

@@ -15,8 +15,7 @@ DAG(name::AbstractString, d::OrderedDict, df::DataFrame)
 
 ## d_separation
 ```@docs
-d_separation(d::DAG, first::SymbolList, second::SymbolList; debug=false)
-d_separation(d::DAG, first::SymbolList, second::SymbolList, cond::SymbolList; debug=false)
+d_separation(d::DAG, first::SymbolList, second::SymbolList; cond::SymbolListOrNothing, debug=false)
 ```
 
 ## shipley_test

examples/derived/derived.jl

@@ -25,32 +25,31 @@ Wei  27.494715 33.118393  60.609937 24.834038 113.66808
 ";
 
 # A DAG model with a latent variable U
-# G = DAG(Y ~ Z + U, X ~ U + W, Z ~ W)
-dag = DAG("ggm_derived", "DAG(Y ~ Z + U, X ~ U + W, Z ~ W)")
+dag = DAG("ggm_derived", "DAG(y ~ z + u, x ~ u + w, z ~ w)")
 
 to_dagitty(dag.d) |> display
 
 fname = ProjDir * "/derived.dot"
 to_graphviz(dag, fname)
 Sys.isapple() && run(`open -a GraphViz.app $(fname)`)
 
+set_dag_df!(dag, df; force=true)
+
 println("Definition of DAG:")
 display(dag)
 
-println("Adjacency matrix:")
-display(dag.a)
+bs = basis_set(dag; debug=true)
+display(bs)
 
-println("\nAncestral graph:")
-ag = ancestral_graph(dag; m=[:u])
-display(ag)
+#t = shipley_test(dag)
+#display("shipley_test = $t"); println()
 
-println()
-set_dag_df!(dag, df; force=true)
-display(dag.s)
-
-println()
-bs = basis_set(dag)
-display(bs)
+pt = pcor_test(dag, [:w, :y], 1, 44)
+display("pcor_test = $pt"); println()
 
 as = adjustment_sets(dag, :w, :z)
 as |> display
+
+println("\nAncestral graph:")
+ag = ancestral_graph(dag; m=[:u])
+display(ag)

examples/marks/marks.jl

@@ -44,23 +44,19 @@ Sys.isapple() && run(`open -a GraphViz.app $(fname)`)
 
 display(dag.s); println()
 
-#=
-ord = topological_order(dag)
-display(ord); println()
-display(dag.vars[ord]); println()
-=#
-
 bs = basis_set(dag)
 display(bs); println()
 
 t = shipley_test(dag)
-display(t); println()
+display("shipley_test = $t"); println()
+
+pt = pcor_test(dag, [:analysis, :statistics, :mechanics], 1, 88)
+display("pcor_test = $pt"); println()
 
 f = [:statistics]; s = [:mechanics]; sel = vcat(f, s)
-cond = :algebra
 
-e = d_separation(dag, f, s, cond)
-println("d_separation($(dag.name), $f, $s, $cond) = $e")
+e = d_separation(dag, f, s, :algebra)
+println("d_separation($(dag.name), $f, $s, :algebra) = $e")
 
 e = d_separation(dag, f, s)
 println("d_separation($(dag.name), $f, $s) = $e")

src/StructuralCausalModels.jl

@@ -27,8 +27,8 @@ Part of the API, exported.
 """
 scm_path(parts...) = normpath(joinpath(scm_src_path, parts...))
 
-SymbolList = Union{Symbol, Vector{Symbol}, Nothing}
-#SymbolListOrNothing = Union{SymbolList, Nothing}
+SymbolList = Union{Symbol, Vector{Symbol}}
+SymbolListOrNothing = Union{SymbolList, Nothing}
 OrderedDictOrNothing = Union{OrderedDict, Nothing}
 NamedArrayOrNothing = Union{NamedArray, Nothing}
 DataFrameOrNothing = Union{DataFrame, Nothing}

src/methods/d_separation.jl

@@ -16,9 +16,9 @@ d_separation(
 )
 ```
 
-### Optional arguments
+### Keyword arguments
 ```julia
-* `cond::SymbolList`                   : Conditioning set
+* `cond::SymbolListOrNoting=noting`    : Conditioning set
 * `debug=false`                        : Trace execution
 ```
 
@@ -61,19 +61,22 @@ The Julia translation is licenced under: MIT.
 
 Part of the API, exported.
 """
-function d_separation(d::DAG, first::SymbolList, second::SymbolList; debug=false)
+function d_separation(d::DAG, first::SymbolList, second::SymbolList; 
+  cond::SymbolListOrNothing=nothing, debug=false)
 
   e = induced_covariance_graph(d, vcat(first, second), SymbolList[]; debug=debug)
   sum(e[first, second]) == 0
 
 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/pcor.jl

@@ -10,8 +10,8 @@ variables.
 ### Method
 ```julia
 pcor(;
+* `d::DAG`                             : DAG object
 * `u::Vector{Symbol}`                  : Variables used to compute correlation
-* `S::Matrix`                          : Sample covariance matrix
 )
 ```
 where:
@@ -53,9 +53,9 @@ The Julia translation is licenced under: MIT.
 
 Part of the api, not exported.
 """
-function pcor(u::Vector{Symbol}, S::NamedArray)
+function pcor(d:: DAG, u::SymbolList)
   us = String.(u)
-  k = inv(S[us, us])
+  k = inv(d.s[us, us])
   -k[1,2] / sqrt(k[1,1] * k[2,2])
 end
 

src/methods/pcor_test.jl

@@ -51,11 +51,15 @@ The Julia translation is licenced under: MIT.
 
 Part of the api, not exported.
 """
-function pcor_test(r, q, n)
+function pcor_test(d::DAG, u::SymbolList, q, n)
 
+  r = pcor(d, u)
   df = n - 2 - q
   tval = r * sqrt(df) / sqrt(1 - r*r)
-  pv = 2 * pdf(TDist(-abs(tval), df))
+  pv = 2 * cdf(TDist(df), -abs(tval))
   (pv=tval, df=df, pvalue=pv)
 
-end
+end
+
+export
+  pcor_test

src/methods/shipley_test.jl

@@ -103,7 +103,8 @@ function shipley_test(d::DAG)
   p = zeros(k)
   for i in 1:k
     u = append(l[i])
-    r = pcor(u, d.s)
+    println(u)
+    r = pcor(d, u)
     q = length(u) - 2
     p[i] = pval(r, q, n)
   end

src/types/ConditionalIndependence.jl

@@ -1,16 +1,9 @@
 import Base: show, getindex, iterate, HasLength, HasEltype, length
 
-#=
-println("\u2561\u255E")
-println("\u2210")
-println("\u2550\u2550")
-println("\u21d0 \u21d1 \u21d2 \u27f9   \u21e2")
-=#
-
 struct ConditionalIndependency
   f::SymbolList
   s::SymbolList
-  c::SymbolList
+  c::SymbolListOrNothing
 end
 
 ConditionalIndependency(f::SymbolList, s::SymbolList) =
@@ -34,7 +27,7 @@ end
 
 function append(c::ConditionalIndependency)
   v = [c.f, c.s]
-  length(c.c) > 0 && push!(v, c.c...)
+  !isnothing(c.c) && length(c.c) > 0 && push!(v, c.c...)
   v
 end