ape (version 5.5)

multiphylo: Manipulating Lists of Trees

Description

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

Usage

# S3 method for multiPhylo
[(x, i)
# S3 method for multiPhylo
[[(x, i)
# S3 method for multiPhylo
$(x, name)
# S3 method for multiPhylo
[(x, ...) <- value
# S3 method for multiPhylo
[[(x, ...) <- value
# S3 method for multiPhylo
$(x, ...) <- 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.

…

index(ices) of the tree(s) to replace; this may be a vector of integers, logicals, or names.

Value

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

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).

See Also

summary.phylo, c.phylo

Examples

# NOT RUN {
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
# }