proper ancestors and descendants

gui/js/dagitty.js

@@ -4541,7 +4541,7 @@ var GraphTransformer = {
 				}
 			})
 		})
-		
+
 		// Delete all vertices that have not been marked for retention
 		if( opts.direct ){
 			_.each( intermediates_after_source, function(v){ retain[v.id] = true } )
@@ -4551,7 +4551,7 @@ var GraphTransformer = {
 				g_chain.deleteVertex(v)
 			}
 		} )
-		
+
 		// Restore original edge types
 		var edges_to_replace = []
 		_.each( g_chain.edges, function(e){
@@ -4567,7 +4567,8 @@ var GraphTransformer = {
 				g_chain.addEdge( e.v2.id, e.v1.id, Graph.Edgetype.Directed )
 			}
 		} )
-
+
+
 		// Replace dummy nodes from canonical graph with original nodess
 		var Lids = _.pluck(g_canon.L,"id"), Sids = _.pluck(g_canon.S,"id")
 		L=[], S=[]
@@ -4582,17 +4583,25 @@ var GraphTransformer = {
 
 		// For direct effects, add causal paths between mediators
 		if( opts.direct ){
-			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources() ),
+			_.each( Z, Graph.Vertex.markAsVisited )
+			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources(), preserve_previous_visited_information ),
 					g.ancestorsOf( g.getTargets() ) ) )
 			_.each( gind.edges, function(e){
 				if( e.directed == Graph.Edgetype.Directed && !(
 						(gind.isSource(e.v1)||gind.isTarget(e.v1)) && (gind.isSource(e.v2)||gind.isTarget(e.v2))) ){
+					if( !g_chain.getVertex( e.v1.id ) ){
+						g_chain.addVertex( e.v1.id )
+					}
+					if( !g_chain.getVertex( e.v2.id ) ){
+						g_chain.addVertex( e.v2.id )
+					}
 					g_chain.addEdge( e.v1.id, e.v2.id, Graph.Edgetype.Directed )
 				} 
 			})
 		}
 		g = GraphTransformer.decanonicalize( g_chain, L, S )
 		g.setType( in_type )
+
 		return g
 	}, // end of activeBiasGraph
 

jslib/graph/GraphTransformer.js

@@ -764,7 +764,7 @@ var GraphTransformer = {
 				}
 			})
 		})
-		
+
 		// Delete all vertices that have not been marked for retention
 		if( opts.direct ){
 			_.each( intermediates_after_source, function(v){ retain[v.id] = true } )
@@ -774,7 +774,7 @@ var GraphTransformer = {
 				g_chain.deleteVertex(v)
 			}
 		} )
-		
+
 		// Restore original edge types
 		var edges_to_replace = []
 		_.each( g_chain.edges, function(e){
@@ -790,7 +790,8 @@ var GraphTransformer = {
 				g_chain.addEdge( e.v2.id, e.v1.id, Graph.Edgetype.Directed )
 			}
 		} )
-
+
+
 		// Replace dummy nodes from canonical graph with original nodess
 		var Lids = _.pluck(g_canon.L,"id"), Sids = _.pluck(g_canon.S,"id")
 		L=[], S=[]
@@ -805,17 +806,25 @@ var GraphTransformer = {
 
 		// For direct effects, add causal paths between mediators
 		if( opts.direct ){
-			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources() ),
+			_.each( Z, Graph.Vertex.markAsVisited )
+			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources(), preserve_previous_visited_information ),
 					g.ancestorsOf( g.getTargets() ) ) )
 			_.each( gind.edges, function(e){
 				if( e.directed == Graph.Edgetype.Directed && !(
 						(gind.isSource(e.v1)||gind.isTarget(e.v1)) && (gind.isSource(e.v2)||gind.isTarget(e.v2))) ){
+					if( !g_chain.getVertex( e.v1.id ) ){
+						g_chain.addVertex( e.v1.id )
+					}
+					if( !g_chain.getVertex( e.v2.id ) ){
+						g_chain.addVertex( e.v2.id )
+					}
 					g_chain.addEdge( e.v1.id, e.v2.id, Graph.Edgetype.Directed )
 				} 
 			})
 		}
 		g = GraphTransformer.decanonicalize( g_chain, L, S )
 		g.setType( in_type )
+
 		return g
 	}, // end of activeBiasGraph
 

r/R/dagitty.r

@@ -411,6 +411,9 @@ impliedCovarianceMatrix <- function( x, b.default=NULL, b.lower=-.6, b.upper=.6,
 #'
 #' @param x the input graph, of any type.
 #' @param v name(s) of variable(s).
+#' @param proper logical. By default (\code{proper=FALSE}), the \code{descendants} or \code{ancestors}
+#' of a variable include the variable itself. For (\code{proper=TRUE}), the variable itself 
+#' is not included.
 #'
 #' \code{descendants(x,v)} retrieves variables that are are reachable from \code{v} via 
 #' a directed path.
@@ -435,22 +438,35 @@ impliedCovarianceMatrix <- function( x, b.default=NULL, b.lower=-.6, b.upper=.6,
 #'
 #' @examples
 #' g <- dagitty("graph{ a <-> x -> b ; c -- x <- d }")
+#' # Includes "x"
 #' descendants(g,"x")
+#' # Does not include "x"
+#' descendants(g,"x",TRUE)
 #' parents(g,"x")
 #' spouses(g,"x") 
 #' 
 NULL
 
 #' @rdname AncestralRelations
 #' @export
-descendants <- function( x, v ){
-	.kins( x, v, "descendants" )
+descendants <- function( x, v, proper=FALSE ){
+	r <- .kins( x, v, "descendants" )
+	if( proper ){
+		setdiff( r, v )
+	} else {
+		r
+	}
 }
 
 #' @rdname AncestralRelations
 #' @export
-ancestors <- function( x, v ){
-	.kins( x, v, "ancestors" )
+ancestors <- function( x, v, proper=FALSE ){
+	r <- .kins( x, v, "ancestors" )
+	if( proper ){
+		setdiff( r, v )
+	} else {
+		r
+	}
 }
 
 #' @rdname AncestralRelations

r/inst/js/dagitty-alg.js

@@ -4536,7 +4536,7 @@ var GraphTransformer = {
 				}
 			})
 		})
-		
+
 		// Delete all vertices that have not been marked for retention
 		if( opts.direct ){
 			_.each( intermediates_after_source, function(v){ retain[v.id] = true } )
@@ -4546,7 +4546,7 @@ var GraphTransformer = {
 				g_chain.deleteVertex(v)
 			}
 		} )
-		
+
 		// Restore original edge types
 		var edges_to_replace = []
 		_.each( g_chain.edges, function(e){
@@ -4562,7 +4562,8 @@ var GraphTransformer = {
 				g_chain.addEdge( e.v2.id, e.v1.id, Graph.Edgetype.Directed )
 			}
 		} )
-
+
+
 		// Replace dummy nodes from canonical graph with original nodess
 		var Lids = _.pluck(g_canon.L,"id"), Sids = _.pluck(g_canon.S,"id")
 		L=[], S=[]
@@ -4577,17 +4578,25 @@ var GraphTransformer = {
 
 		// For direct effects, add causal paths between mediators
 		if( opts.direct ){
-			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources() ),
+			_.each( Z, Graph.Vertex.markAsVisited )
+			var gind = this.inducedSubgraph( g, _.intersection( g.descendantsOf( g.getSources(), preserve_previous_visited_information ),
 					g.ancestorsOf( g.getTargets() ) ) )
 			_.each( gind.edges, function(e){
 				if( e.directed == Graph.Edgetype.Directed && !(
 						(gind.isSource(e.v1)||gind.isTarget(e.v1)) && (gind.isSource(e.v2)||gind.isTarget(e.v2))) ){
+					if( !g_chain.getVertex( e.v1.id ) ){
+						g_chain.addVertex( e.v1.id )
+					}
+					if( !g_chain.getVertex( e.v2.id ) ){
+						g_chain.addVertex( e.v2.id )
+					}
 					g_chain.addEdge( e.v1.id, e.v2.id, Graph.Edgetype.Directed )
 				} 
 			})
 		}
 		g = GraphTransformer.decanonicalize( g_chain, L, S )
 		g.setType( in_type )
+
 		return g
 	}, // end of activeBiasGraph
 

r/tests/testthat/testBasics.R

@@ -86,3 +86,9 @@ test_that("children and parents of nothing", {
 	expect_equal( length(parents("a->b",c())), 0 )
 } )
 
+test_that("proper and non-proper ancestors ",{
+	expect_equal( "x" %in% ancestors(dagitty("graph{a <-> x -> b ; c -- x <- d}"), "x"), TRUE )
+	expect_equal( "x" %in% ancestors(dagitty("graph{a <-> x -> b ; c -- x <- d}"), "x",TRUE), FALSE )
+	expect_equal( "x" %in% descendants(dagitty("graph{a <-> x -> b ; c -- x <- d}"), "x"), TRUE )
+	expect_equal( "x" %in% descendants(dagitty("graph{a <-> x -> b ; c -- x <- d}"), "x",TRUE), FALSE )
+} )

test/test/biasing-paths.js

@@ -66,11 +66,17 @@ assert.equal((function(){
 	return $es(GraphTransformer.activeBiasGraph(g))
 })(), "" )
 
-
 assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->m->y z->{x y}"), { X:["x"] , Y:["y"] } ).edges.length, 2 )
 
 assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->m->y"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 2 )
 
+assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->m->y"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 2 )
+
+assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->m->y"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 2 )
+assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->{m[a]}->y"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 0 )
+assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->{{m[a]}->y}<-z"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 3 )
+assert.equal( GraphTransformer.activeBiasGraph( new Graph("x->{{m[a]}->y}<-{z[a]}"), {direct : true, X:["x"], Y:["y"] } ).edges.length, 0 )
+
 
 });