View source: R/summary.phylo.R
c.phylo | R Documentation |
These functions help to build lists of trees of class "multiPhylo"
.
## S3 method for class 'phylo'
c(..., recursive = TRUE)
## S3 method for class 'multiPhylo'
c(..., recursive = TRUE)
.compressTipLabel(x, ref = NULL)
.uncompressTipLabel(x)
... |
one or several objects of class |
recursive |
see details. |
x |
an object of class |
ref |
an optional vector of mode character to constrain the order of the tips. By default, the order from the first tree is used. |
These c
methods check all the arguments, and return by default
a list of single trees unless some objects are not trees or lists of
trees, in which case recursive
is switched to FALSE and a
warning message is given. If recursive = FALSE
, the objects are
simply concatenated into a list. Before ape 4.0, recursive
was always set to FALSE.
.compressTipLabel
transforms an object of class
"multiPhylo"
by checking that all trees have the same tip
labels and renumbering the tips in the edge
matrix so that the
tip numbers are also the same taking the first tree as the reference
(duplicated labels are not allowed). The returned object has a unique
vector of tip labels (attr(x, "TipLabel")
).
.uncompressTipLabel
does the reverse operation.
An object of class "multiPhylo"
.
Emmanuel Paradis
summary.phylo
, multiphylo
x <- c(rtree(4), rtree(2))
x
y <- c(rtree(4), rtree(4))
z <- c(x, y)
z
print(z, TRUE)
try(.compressTipLabel(x)) # error
a <- .compressTipLabel(y)
.uncompressTipLabel(a) # back to y
## eventually compare str(a) and str(y)
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