tdata: Retrieving or updating tip and node data in phylo4d objects

Description

Methods to retrieve or update tip, node or all data associated with a phylogenetic tree stored as a phylo4d object

Usage

tdata(x, ...)
# S4 method for phylo4d
tdata(
  x,
  type = c("all", "tip", "internal"),
  label.type = c("row.names", "column"),
  empty.columns = TRUE
)
tdata(x, ...) <- value
# S4 method for phylo4d
tdata(
  x,
  type = c("all", "tip", "internal"),
  merge.data = TRUE,
  clear.all = FALSE,
  ...
) <- value
tipData(x, ...)
# S4 method for phylo4d
tipData(x, ...)
tipData(x, ...) <- value
# S4 method for phylo4d
tipData(x, ...) <- value
nodeData(x, ...)
# S4 method for phylo4d
nodeData(x, ...)
nodeData(x, ...) <- value
# S4 method for phylo4d
nodeData(x, ...) <- value

Value

tdata returns a data frame

Arguments

x: A phylo4d object
...: For the tipData and nodeData accessors, further arguments to be used by tdata. For the replacement forms, further arguments to be used to control matching between tree and data (see Details section of phylo4d-methods).
type: The type of data to retrieve or update: “all” (default) for data associated with both tip and internal nodes, “tip” for data associated with tips only, “internal” for data associated with internal nodes only.
label.type: How should the tip/node labels from the tree be returned? “row.names” returns them as row names of the data frame, “column” returns them in the first column of the data frame. This options is useful in the case of missing (NA) or non-unique labels.
empty.columns: Should columns filled with NA be returned?
value: a data frame (or object to be coerced to one) to replace the values associated with the nodes specified by the argument type
merge.data: if tip or internal node data are provided and data already exists for the other type, this determines whether columns with common names will be merged together (default TRUE). If FALSE, columns with common names will be preserved separately, with “.tip” and “.node” appended to the names. This argument has no effect if tip and node data have no column names in common, or if type=“all”.
clear.all: If only tip or internal node data are to be replaced, should data of the other type be dropped?

Methods

tdata: signature(object="phylo4d"): retrieve or update data associated with a tree in a phylo4d object

Author

Ben Bolker, Thibaut Jombart, Francois Michonneau

Examples

Run this code

   data(geospiza)
   tdata(geospiza)
   tipData(geospiza) <- 1:nTips(geospiza)
   tdata(geospiza)

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