Basic checks on the validity of S4 phylogenetic objects
A prospective phylo4 or phylo4d object
As required by
validObject, returns an error
string (describing problems) or TRUE if everything is OK.
These functions are only intended to be called by other phylobase functions.
checkPhylo4 is an (inflexible) wrapper for
checkTree. The rules for
phylo4 objects essentially
follow those for
phylo objects from the
which are in turn defined in
These are essentially that:
if the tree has edge lengths defined, the number of edge lengths must match the number of edges;
the number of tip labels must match the number of tips;
in a tree with
ntips tips and
(total) nodes, nodes 1 to
ntips must be tips
tree is rooted, the root must be node number
the root node must be the first row of the edge matrix
tip labels, node labels, edge labels, edge lengths must have proper internal names (i.e. internal names that match the node numbers they document)
tip and node labels must be unique
You can alter some of the default options by using the function
checkTree also calls
checkPhylo4Data to check the validity of the data associated with the
tree. It ensures that (1) the data associated with the tree have the correct
dimensions, (2) that the row names for the data are correct.
Ben Bolker, Steven Kembel, Francois Michonneau
phylo4 constructor and
phylo4 class; the
and the phylo4d class do checks for the data
associated with trees. See
translation functions and
phylobase.options to change
some of the default options of the validator.
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