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

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

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

Analyses of Phylogenetics and Evolution

v5.5
GPL-2 | GPL-3
Authors
Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)
Initial release
2021-04-24

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