igraph dfs may signal unreachable nodes with 0

* this still seems to be up in the air but at least some preparatory branches
 for igraph 2.0 use a 0 rather than NaN to signal unreachable nodes
* see #517

R/neuron.R

@@ -1411,15 +1411,16 @@ distal_to <- function(x, node.idx=NULL, node.pointno=NULL, root.idx=NULL,
     g=as.directed.usingroot(gorig, root = root.idx)
   }
 
-  #Step3: For each node id, travese the graph from the given node using depth first search and return the visited
+  #Step3: For each node id, traverse the graph from the given node using depth first search and return the visited
   #nodes..
   l=sapply(node.idx, dfs_traversal, g, simplify = FALSE)
   if(length(node.idx)==1) l[[1]] else l
 }
 
 dfs_traversal <- function(x, g) {
   gdfs=igraph::dfs(g, root = x, unreachable = FALSE)
-  as.integer(gdfs$order)[!is.na(gdfs$order)]
+  # nb igraph 2.0 may change signalling for unreached nodes
+  as.integer(gdfs$order)[!(is.na(gdfs$order) | gdfs$order<1)]
 }
 
 

R/ngraph.R

@@ -533,12 +533,14 @@ prune_strahler<-function(x, orderstoprune=1:2, ...) {
 prune_vertices<-function(x, verticestoprune, invert=FALSE, ...) {
   g=as.ngraph(x)
 
-  # because igraph.vs sequences are atttached to a specific graph
+  # because igraph.vs sequences are attached to a specific graph
   if(inherits(verticestoprune, "igraph.vs")) 
     verticestoprune=as.integer(verticestoprune)
   if(invert) {
-    nvertices=nrow(xyzmatrix(x))
+    nvertices=igraph::vcount(g)
     verticestoprune=setdiff(seq_len(nvertices), verticestoprune)
+  } else {
+    verticestoprune=setdiff(verticestoprune, 0)
   }
   dg=igraph::delete.vertices(g, verticestoprune)
   # delete.vertices will return an igraph