Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies
testEdgeMat is a small simple function which tests the $edge matrix of 'phylo' objects for
inconsistencies that can cause downstream analytical problems.
The associated function,
cleanNewPhylo puts an input
phylo object, presumably freshly created or reconstituted by some function, through a series
of post-processing, This includes having singles collapsed,
nodes reordered and being written out as a Newick string and read back in,
to ensure functionality with ape functions
and ape-derived functions.
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A phylogeny object of type phylo
Useful when doing complex manipulations and reconstitutions of 'phylo' objects (or their de novo construction), and thus is used by a number of paleotree functions.
testEdgeMat, if all the checks in the function pass correctly, the logical TRUE is returned.
cleanNewPhylo, an object of class 'phylo' is returned.
David W. Bapst, with a large number of tests incorporated from Emmanuel Paradis's checkValidPhylo function, provided at his github repo here, which was released GPL v>2:
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set.seed(444) tree<-rtree(10) # should return TRUE testEdgeMat(tree) # should also work on star trees testEdgeMat(stree(10)) # should also work on trees with two taxa testEdgeMat(rtree(2)) # should also work on trees with one taxon testEdgeMat(stree(1)) #running cleanNewPhylo on this tree should have little effect #beyond ladderizing it... tree1<-cleanNewPhylo(tree) #compare outputs layout(1:2) plot(tree) plot(tree1) layout(1)
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