Description Usage Author(s) See Also Examples
Translation functions to convert between phylobase objects
(phylo4
or phylo4d
), and objects used by other
comparative methods packages in R: ape
objects
(phylo
, multiPhylo
), RNeXML
object
(nexml
), ade4
objects (phylog
, now
deprecated), and to data.frame
representation.
as(object, class)
Ben Bolker, Thibaut Jombart, Marguerite Butler, Steve Kembel, Francois Michonneau
generic as
,
phylo4-methods
, phylo4d-methods
,
extractTree
, nexml
class from the
RNeXML
package, phylog
from the
ade4
package and as.phylo
from the
ape
package.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | tree_string <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
tree.owls <- ape::read.tree(text=tree_string)
## round trip conversion
tree_in_phylo <- tree.owls # tree is a phylo object
(tree_in_phylo4 <- as(tree.owls,"phylo4")) # phylo converted to phylo4
identical(tree_in_phylo,as(tree_in_phylo4,"phylo"))
## test if phylo, and phylo4 converted to phylo are identical
## (no, because of dimnames)
## Conversion to phylog (ade4)
as(tree_in_phylo4, "phylog")
## Conversion to data.frame
as(tree_in_phylo4, "data.frame")
## Conversion to phylo (ape)
as(tree_in_phylo4, "phylo")
## Conversion to phylo4d, (data slots empty)
as(tree_in_phylo4, "phylo4d")
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