tdata {phylobase}R Documentation

Retrieving or updating tip and node data in phylo4d objects

Description

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

Usage

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

Arguments

x A phylo4d object
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?
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?
... For the tipData and nodeData accessors, further arguments to be used by tdata. For the replacement forms, further arguments to be used by formatData (e.g. match.data), see formatData for more details.
value a data frame (or object to be coerced to one) to replace the values associated with the nodes specified by the argument type

Value

tdata returns a data frame

Methods

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

Author(s)

Ben Bolker, Thibaut Jombart, Francois Michonneau

See Also

phylo4d

Examples

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

[Package phylobase version 0.5 Index]