Description Usage Arguments Value Note Author(s) See Also
Basic checks on the validity of S4 phylogenetic objects
1 | checkPhylo4(object)
|
object |
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 ape
package, which are in turn defined in
http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf. 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 nnodes
(total) nodes, nodes 1 to ntips
must be tips
if the tree is rooted, the root must be node number ntips+1
and
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
phylobase.options
.
For phylo4d
objects, 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
the phylo4
constructor and phylo4
class; formatData
, the phylo4d
constructor and
the phylo4d class do checks for the data associated with
trees. See coerce-methods
for translation functions and
phylobase.options to change some of the default options of the
validator.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.