Node and Edge look-up functions
Functions for retrieving node and edge IDs (possibly with corresponding labels) from a phylogenetic tree.
getNode(
x,
node,
type = c("all", "tip", "internal"),
missing = c("warn", "OK", "fail")
)
## S4 method for signature 'phylo4'
getNode(
x,
node,
type = c("all", "tip", "internal"),
missing = c("warn", "OK", "fail")
)
getEdge(
x,
node,
type = c("descendant", "ancestor"),
missing = c("warn", "OK", "fail")
)
## S4 method for signature 'phylo4'
getEdge(
x,
node,
type = c("descendant", "ancestor"),
missing = c("warn", "OK", "fail")
)x |
a phylo4 object (or one inheriting from phylo4, e.g. a phylo4d object) |
node |
either an integer vector corresponding to node ID numbers, or a
character vector corresponding to node labels; if missing, all nodes
appropriate to the specified type will be returned by |
type |
( |
missing |
what to do if some requested node IDs or names are not in the tree: warn, do nothing, or stop with an error |
getNode and getEdge are primarily intended for looking up the
IDs either of nodes themselves or of edges associated with those nodes. Note
that they behave quite differently. With getNode, any input nodes are
looked up against tree nodes of the specified type, and those that match are
returned as numeric node IDs with node labels (if they exist) as element
names. With getEdge, any input nodes are looked up against edge ends
of the specified type, and those that match are returned as character edge
IDs with the corresponding node ID as element names.
If missing is “warn” or “OK”, NA is returned for
any nodes that are unmatched for the specified type. This can provide a
mechanism for filtering a set of nodes or edges.
nodeId provides similar output to getNode in the case when no
node is supplied, but it is faster and returns an unnamed vector of the
numeric IDs of all nodes of the specified node type. Similarly,
edgeId simply returns an unnamed vector of the character IDs of all
edges for which the descendant node is of the specified node type.
list("getNode") |
returns a named integer vector of node IDs, in the order of input nodes if provided, otherwise in nodeId order |
list("getEdge") |
returns a named character vector of edge IDs, in the order of input nodes if provide, otherwise in nodeId order |
list("nodeId") |
returns an unnamed integer vector of node IDs, in ascending order |
list("getEdge") |
returns an unnamed character vector of edge IDs, in edge matrix order |
data(geospiza)
nodeLabels(geospiza) <- LETTERS[1:nNodes(geospiza)]
plot(as(geospiza, "phylo4"), show.node.label=TRUE)
getNode(geospiza, 18)
getNode(geospiza, "D")
getEdge(geospiza, "D")
getEdge(geospiza, "D", type="ancestor")
## match nodes only to tip nodes, flagging invalid cases as NA
getNode(geospiza, c(1, 18, 999), type="tip", missing="OK")
## get all edges that descend from internal nodes
getEdge(geospiza, type="ancestor")
## identify an edge from its terminal node
getEdge(geospiza, c("olivacea", "B", "fortis"))
getNode(geospiza, c("olivacea", "B", "fortis"))
edges(geospiza)[c(26, 1, 11),]
## quickly get all tip node IDs and tip edge IDs
nodeId(geospiza, "tip")
edgeId(geospiza, "tip")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.