added functions for getting edge sets

caseywdunn · Apr 12, 2017 · 0585b48 · 0585b48
1 parent 26f9066
commit 0585b48
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Showing 28 changed files with 126 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,4 +22,4 @@ Suggests:
     roxygen2,
     knitr
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,9 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export(ancestral_edges)
 export(are_bipartitions_compatible)
 export(bipartition_for_edge)
 export(bipartition_for_edge_by_label)
 export(compatible_edges)
+export(connecting_edges)
 export(cut_tree)
 export(decompose_tree)
 export(descendants)

diff --git a/R/utility_functions.R b/R/utility_functions.R
@@ -414,3 +414,53 @@ distance_from_tip = function(phy){
 
 	return(ages)
 }	
+
+#' For a node in a tree, get a vector of the edges between the 
+#' node and the root
+#' 
+#' @param phy A phylo object
+#' @param node A node number
+#' @return A vector of edge numbers
+#' @export
+ancestral_edges = function(phy, node){
+	edges = c()
+	focal_node = node
+
+	# While there is an edge with child focal node, 
+	# add the edge and then sqitch the focal node to its
+	#parent.
+	while( focal_node %in% phy$edge[ ,2 ] ){
+		new_edge = which( phy$edge[ ,2 ] == focal_node )
+		edges = c( edges, new_edge )
+		focal_node = phy$edge[ new_edge, 1 ]
+	}
+
+	return(edges)
+}
+
+#' For two nodes in a tree, get a vector of the edges that 
+#' connect them
+#' 
+#' @param phy A phylo object
+#' @param node_a Number of the first node
+#' @param node_b Number of the second node
+#' @return A vector of edge numbers
+#' @export
+connecting_edges = function(phy, node_a, node_b){
+
+	# For each node, get the set of edges that connect
+	# it to the root
+	edges_a = ancestral_edges( phy, node_a )
+	edges_b = ancestral_edges( phy, node_b )
+
+	# The path between the nodes is the set of edges that
+	# are present in one but not the other, ie xor. This 
+	# can be obtained by taking the union and then removing
+	# the intersection
+	edges = setdiff(
+			union( edges_a, edges_b ),
+			intersect( edges_a, edges_b )
+		)
+
+	return(edges)
+}
diff --git a/man/ancestral_edges.Rd b/man/ancestral_edges.Rd
diff --git a/man/are_bipartitions_compatible.Rd b/man/are_bipartitions_compatible.Rd
diff --git a/man/bipartition_for_edge.Rd b/man/bipartition_for_edge.Rd
diff --git a/man/bipartition_for_edge_by_label.Rd b/man/bipartition_for_edge_by_label.Rd
diff --git a/man/compatible_edges.Rd b/man/compatible_edges.Rd
diff --git a/man/connecting_edges.Rd b/man/connecting_edges.Rd
diff --git a/man/cut_tree.Rd b/man/cut_tree.Rd
diff --git a/man/decompose_tree.Rd b/man/decompose_tree.Rd
diff --git a/man/descendants.Rd b/man/descendants.Rd
diff --git a/man/difference_from_calibrated.Rd b/man/difference_from_calibrated.Rd
diff --git a/man/distance_from_tip.Rd b/man/distance_from_tip.Rd
diff --git a/man/flip_bipartition.Rd b/man/flip_bipartition.Rd
diff --git a/man/get_bipartitions.Rd b/man/get_bipartitions.Rd
diff --git a/man/get_corresponding_nodes.Rd b/man/get_corresponding_nodes.Rd
diff --git a/man/hutan.Rd b/man/hutan.Rd
diff --git a/man/is_compatible_with_set.Rd b/man/is_compatible_with_set.Rd
diff --git a/man/is_monophyletic.Rd b/man/is_monophyletic.Rd
diff --git a/man/safe.drop.tip.Rd b/man/safe.drop.tip.Rd
diff --git a/man/siphonophore_constraint.Rd b/man/siphonophore_constraint.Rd
diff --git a/man/siphonophore_ml.Rd b/man/siphonophore_ml.Rd
diff --git a/man/slide_root_edges.Rd b/man/slide_root_edges.Rd
diff --git a/man/tip_descendants.Rd b/man/tip_descendants.Rd
diff --git a/man/tips.Rd b/man/tips.Rd
diff --git a/man/zero_constrained.Rd b/man/zero_constrained.Rd
diff --git a/tests/testthat/test_general.R b/tests/testthat/test_general.R
@@ -56,3 +56,32 @@ test_that("the correct number of depths are produced",{
 	expect_equal( length(depths), 11 )
 })
 
+test_that("can get the edges that connect a tip to the root",{
+	edges = ancestral_edges( siphonophore_ml, 2 )
+	expect_true( setequal( edges, c( 3, 2 ) ) )
+})
+
+test_that("can get the edges that connect a tip to the root",{
+	edges = ancestral_edges( siphonophore_ml, 10 )
+	expect_true( setequal( edges, c( 30, 29, 28, 26, 24, 23, 22, 12, 11, 10, 9, 8, 7, 6, 5, 4, 2 ) ) )
+})
+
+test_that("can get the edges that connect an internal node to the root",{
+	edges = ancestral_edges( siphonophore_ml, 65 )
+	expect_true( setequal( edges, c( 10, 9, 8, 7, 6, 5, 4, 2 ) ) )
+})
+
+test_that("can get the connecting edges for sister species",{
+	edges = connecting_edges( siphonophore_ml, 31, 32)
+	expect_true( setequal( edges, c( 71, 72 ) ) )
+})
+
+test_that("can get the connecting edges for tips that span root",{
+	edges = connecting_edges( siphonophore_ml, 1, 32)
+	expect_true( setequal( edges, c( 1, 72, 70, 69, 67, 66, 58, 57, 11, 10, 9, 8, 7, 6, 5, 4, 2 ) ) )
+})
+
+test_that("can get the connecting edges for ancestor and descendent nodes",{
+	edges = connecting_edges( siphonophore_ml, 65, 67)
+	expect_true( setequal( edges, c( 11, 12 ) ) )
+})