test.speciation.model not passing

[ArtPoon]

1 Test Suite : 
Kaphi - 29 test functions, 2 errors, 0 failures
ERROR in test.speciation.model: Error in if (V(g1)$production[c1] != V(g2)$production[c2]) { : 
  missing value where TRUE/FALSE needed
DEACTIVATED test.kernel.label: 
ERROR in test.perturb.particles: Error in if (V(g1)$production[c1] != V(g2)$production[c2]) { : 
  missing value where TRUE/FALSE needed

[ArtPoon]

This occurs for computing the kernel score of the tree against itself. n1 and n2 are both 16. This occurs because V(g1)$children[[n1]] returns the value integer(0).

n1 is an internal node. The children vector should have meaningful values for this node, not integer(0). This is happening because the ordering of nodes in children does not match the numbering of nodes in the tree.

> reorder(tree, order='postorder', index.only=T)
 [1] 35 36 34 37 29 30 28 31 24 25 21 22 20 23 19 26 15 16 14 17  9 10  8 11  7
[26] 12  6 13  5 18  4 27  3 32  2 33  1 38
> sapply(.get.children(g), length)
 [1] 2 2 2 2 2 2 2 2 2 0 0 0 0 2 2 0 0 0 2 2 2 0 0 2 0 0 0 2 2 0 0 0 0 2 2 0 0 0
[39] 0

Let's try reordering the tree as the first step in .tree.to.igraph. Then:

> sapply(.get.children(g), length)
 [1] 2 0 0 2 0 2 0 0 2 0 2 0 0 2 0 0 2 2 0 2 0 0 2 0 2 0 0 2 0 2 0 2 2 2 2 0 2 2
[39] 0