tdata {phylobase} | R Documentation |
Method to retrieve or update tip, node or all data associated with a phylogenetic tree stored as a phylo4d object
## 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
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 |
tdata
returns a data frame
signature(object="phylo4d")
: retrieve or update
data associated with a tree in a phylo4d
objectBen Bolker, Thibaut Jombart, Francois Michonneau
data(geospiza) tdata(geospiza) tipData(geospiza) <- 1:nTips(geospiza) tdata(geospiza)