tree.plot {ouch} | R Documentation |
Validate or plot the phylogenetic tree in ouch format.
is.valid.ouch.tree(node, ancestor, times, regimes = NULL) tree.plot(node, ancestor, times, names = NULL, regimes = NULL)
node |
A character vector giving the name of each node. |
ancestor |
Specification of the topology of the phylogenetic tree. This is in the form of a character vector naming the immediate ancestor of each node. In particular, the i-th name is that of the ancestor of the i-th node. The root node is distinguished by having no ancestor (i.e., NA). |
times |
A vector of nonnegative numbers, one per node in the tree, specifying the time at which each node is located. The root node should be assigned time 0. |
names |
Optional vector of species names. |
regimes |
A vector of codes, one for each node in the tree, specifying the selective regimes hypothesized to have been operative. Corresponding to each node, enter the code of the regime hypothesized for the branch segment terminating in that node. For the root node, because it has no branch segment terminating on it, the regime specification is irrelevant. |
tree.plot
makes a simple plot of the phylogenetic tree. Labels
and/or a selective-regime-based coloring scheme are optional.
is.valid.ouch.tree
performs several checks to make sure that
the tree is valid. These include checks to ensure that all the vector
arguments are of the same length, that the nodes have unique names,
that there is a unique root, that there is at least one terminal node,
that every node's ancestor is in fact part of the tree, that there are
no cycles in the 'tree', and that the tree is connected. It returns
TRUE if the tree is valid, FALSE otherwise and gives diagnostic
warnings.
Aaron A. King <kingaa at umich dot edu>
data(bimac) attach(bimac) is.valid.ouch.tree(node,ancestor,time,OU.LP) tree.plot(node,ancestor,time,species,OU.LP)