setAs-methods: Converting between phylo4/phylo4d and other phylogenetic tree...

In phylobase: Base package for phylogenetic structures and comparative data

Description

Translation functions to convert between phylobase objects (phylo4 or phylo4d), and objects used by other comparative methods packages in R: ape objects (phylo, multiPhylo), ade4 objects (phylog, now deprecated), and to data.frame representation.

Usage

as(object, class)

Author(s)

Ben Bolker, Thibaut Jombart, Marguerite Butler, Steve Kembel

See Also

generic as, phylo4, phylo4d, extractTree, the original phylog from the ade4 package and as.phylo from the ape package.

Examples

tree.owls <- ape::read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
## 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")

Example output

          label node ancestor edge.length node.type
1   Strix_aluco    1        7         4.2       tip
2     Asio_otus    2        7         4.2       tip
3 Athene_noctua    3        6         7.3       tip
4     Tyto_alba    4        5        13.5       tip
5          <NA>    5        0          NA      root
6          <NA>    6        5         6.3  internal
7          <NA>    7        6         3.1  internal
[1] FALSE
Phylogenetic tree with 4 leaves and 3 nodes
$class: phylog
$call: ade4::newick2phylog(x.tre = xstring)
$tre: (Tyto_alba,(Athene_noctua...aluco,Asio_otus)I1)I2)Root; 

        class   length content                                     
$leaves numeric 4      length of the first preceeding adjacent edge
$nodes  numeric 3      length of the first preceeding adjacent edge
$parts  list    3      subsets of descendant nodes                 
$paths  list    7      path from root to node or leave             
$droot  numeric 7      distance to root                            

         class      dim content                                   
$Wmat    matrix     4-4 W matrix : root to the closest ancestor   
$Wdist   dist       6   Nodal distances                           
$Wvalues numeric    3   Eigen values of QWQ/sum(Q)                
$Wscores data.frame 4-3 Eigen vectors of QWQ '1/n' normed         
$Amat    matrix     4-4 Topological proximity matrix A            
$Avalues numeric    3   Eigen values of QAQ matrix                
$Adim    integer    1   number of positive eigen values of QAQ    
$Ascores data.frame 4-3 Eigen vectors of QAQ '1/n' normed         
$Aparam  data.frame 3-3 Topological indices for nodes             
$Bindica data.frame 4-3 class indicator from nodes                
$Bscores data.frame 4-3 Topological orthonormal basis '1/n' normed
$Blabels character  3   Nodes labelling from orthonormal basis    
Warning message:
In asMethod(object) :
  ade4::phylog objects are deprecated, please use the adephylo package instead
          label node ancestor edge.length node.type
1   Strix_aluco    1        7         4.2       tip
2     Asio_otus    2        7         4.2       tip
3 Athene_noctua    3        6         7.3       tip
4     Tyto_alba    4        5        13.5       tip
5          <NA>    5        0          NA      root
6          <NA>    6        5         6.3  internal
7          <NA>    7        6         3.1  internal

Phylogenetic tree with 4 tips and 3 internal nodes.

Tip labels:
[1] "Strix_aluco"   "Asio_otus"     "Athene_noctua" "Tyto_alba"    

Rooted; includes branch lengths.
No data associated with the tree
          label node ancestor edge.length node.type
1   Strix_aluco    1        7         4.2       tip
2     Asio_otus    2        7         4.2       tip
3 Athene_noctua    3        6         7.3       tip
4     Tyto_alba    4        5        13.5       tip
5          <NA>    5        0          NA      root
6          <NA>    6        5         6.3  internal
7          <NA>    7        6         3.1  internal

phylobase documentation built on May 2, 2019, 6:49 p.m.