multiphylo: Manipulating Lists of Trees

In ape: Analyses of Phylogenetics and Evolution

Manipulating Lists of Trees

Description

These are extraction and replacement operators for lists of trees stored in the class "multiPhylo".

Usage

## S3 method for class 'multiPhylo'
x[i]
## S3 method for class 'multiPhylo'
x[[i]]
## S3 method for class 'multiPhylo'
x$name
## S3 replacement method for class 'multiPhylo'
x[i] <- value
## S3 replacement method for class 'multiPhylo'
x[[i]] <- value
## S3 replacement method for class 'multiPhylo'
x$i <- value

Arguments

x, value	an object of class "phylo" or "multiPhylo".
i	index(ices) of the tree(s) to select from a list; this may be a vector of integers, logicals, or names.
name	a character string specifying the tree to be extracted.

Details

The subsetting operator [ keeps the class correctly ("multiPhylo").

The replacement operators check the labels of value if x has a single vector of tip labels for all trees (see examples).

Value

An object of class "phylo" ([[, $) or of class "multiPhylo" ([ and the replacement operators).

Author(s)

Emmanuel Paradis

See Also

summary.phylo, c.phylo

Examples

x <- rmtree(10, 20)
names(x) <- paste("tree", 1:10, sep = "")
x[1:5]
x[1] # subsetting
x[[1]] # extraction
x$tree1 # same than above
x[[1]] <- rtree(20)

y <- .compressTipLabel(x)
## up to here 'x' and 'y' have exactly the same information
## but 'y' has a unique vector of tip labels for all the trees
x[[1]] <- rtree(10) # no error
try(y[[1]] <- rtree(10)) # error

try(x[1] <- rtree(20)) # error
## use instead one of the two:
x[1] <- list(rtree(20))
x[1] <- c(rtree(20))

x[1:5] <- rmtree(5, 20) # replacement
x[11:20] <- rmtree(10, 20) # elongation
x # 20 trees

ape documentation built on May 29, 2024, 10:50 a.m.