addData-methods: Adding data to a phylo4 or a phylo4d object

In phylobase: Base package for phylogenetic structures and comparative data

Description

addData adds data to a phylo4 (converting it in a phylo4d object) or to a phylo4d object

Usage

addData(x, ...)

## S4 method for signature 'phylo4d'
addData(x, tip.data = NULL, node.data = NULL,
  all.data = NULL, merge.data = TRUE, pos = c("after", "before"), ...)

## S4 method for signature 'phylo4'
addData(x, tip.data = NULL, node.data = NULL,
  all.data = NULL, merge.data = TRUE, pos = c("after", "before"), ...)

Arguments

x	a phylo4 or a phylo4d object
tip.data	a data frame (or object to be coerced to one) containing only tip data
node.data	a data frame (or object to be coerced to one) containing only node data
all.data	a data frame (or object to be coerced to one) containing both tip and node data
merge.data	if both tip.data and node.data are provided, it 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.data and node.data have no column names in common.
pos	should the new data provided be bound before or after the pre-existing data?
...	additional arguments to be passed to formatData

Details

Rules for matching data to tree nodes are identical to those used by the phylo4d constructor.

If any column names in the original data are the same as columns in the new data, ".old" is appended to the former column names and ".new" is appended to the new column names.

The option pos is ignored (silently) if x is a phylo4 object. It is provided for compatibility reasons.

Value

addData returns a phylo4d object.

Author(s)

Francois Michonneau

See Also

tdata for extracting or updating data and phylo4d constructor.

Examples

data(geospiza)
  nDt <- data.frame(a=rnorm(nNodes(geospiza)), b=1:nNodes(geospiza),
                    row.names=nodeId(geospiza, "internal"))
  t1 <- addData(geospiza, node.data=nDt)

phylobase documentation built on May 2, 2019, 6:49 p.m.