phylobase: Base package for phylogenetic structures and comparative data

系統比較のための基本的なパッケージ

> library(phylobase)

バージョン: 0.8.0

関数名 概略
addData Adding data to a phylo4 or a phylo4d object
as Converting between phylo4/phylo4d and other phylogenetic tree formats
checkPhylo4 Validity checking for phylo4 objects
children tree traversal and utility functions
extractTree Get tree from tree+data object
formatData Format data for use in phylo4d objects
geospiza Data from Darwin's finches
getNode node and edge look-up functions
hasNodeData Tests for presence of data associated with
trees stored as phylo4d objects
hasSingle Test trees for polytomies, inline nodes, or reticulation
labels<- Labels for phylo4/phylo4d objects
multiPhylo-class multiPhylo4 and extended classes
nData Retrieves the number of datasets in phylo4d objects
nNodes Methods for S4 phylogeny classes
owls4 'Owls' data from ape
pdata Constructor for pdata (phylogenetic data) class
pdata-class Class "pdata"
phylo4-class The phylo4 class
phylo4-methods Create a phylogenetic tree
phylo4d Combine a phylogenetic tree with data
phylo4d-class phylo4d class
phylo4vcov-class matrix classes for phylobase
phyloXXYY Calculate node x and y coordinates
phylobase-package Utilities and Tools for Phylogenetics
phylobase.options Set or return options of phylobase
phylobubbles Bubble plots for phylo4d objects
phylog-class Class "phylog"
plotOneTree Plot a phylo4 object
print,phylo4-method Displaying phylo4 object
printphylo4 print a phylogeny
readNexus Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file
reorder-methods reordering trees within phylobase objects show,phylo4d-method Display methods for phylo4d objects
subset-methods Methods for creating subsets of phylogenies
tdata Retrieving or updating tip and node data in phylo4d objects
tip.data.plot Plotting trees and associated data
treePlot Phylogeny plotting

as

phyloクラス等への変換。

変換できるクラスの例（{phylobase}, {ape}, {ade4}）...phylo4, phylo4d, phylo, multiPhylo, multiPhylo4, phylog, data.frame

> trString <- "(((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 = trString))


Phylogenetic tree with 4 tips and 3 internal nodes.

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

Rooted; includes branch lengths.

> class(tree.owls)

[1] "phylo"

> as(object = tree.owls, Class = "phylo4") %>% class()

[1] "phylo4"
attr(,"package")
[1] "phylobase"

> as(object = tree.owls, Class = "phylo4") %>% as(., "phylo4d") %>% class()

[1] "phylo4d"
attr(,"package")
[1] "phylobase"

> as(object = tree.owls, Class = "phylo4") %>% as(., "data.frame") %>% class()

[1] "data.frame"

checkPhylo4

phylo4オブジェクトの確認

> trString <- "(((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 = trString))


Phylogenetic tree with 4 tips and 3 internal nodes.

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

Rooted; includes branch lengths.

> # 変換には`as()`を使う
> as(object = tree.owls, Class = "phylo4") %>% checkPhylo4() # checkTree(), checkPhylo4Data()

[1] TRUE

extractTree

phylo4dオブジェクト（系統樹とデータ）から系統樹オブジェクトを抽出する

> tree.phylo <- ape::read.tree(text = "((a,b),c);")
> tree <- as(tree.phylo, "phylo4") # phylo4 オブジェクトに変換（dataスロットなし）
> tip.data <- data.frame(size = c(1, 2, 3), row.names = c("a", "b", "c"))
> (treedata <- phylo4d(tree, tip.data)) # phylo4オブジェクト（dataスロットなし）とデータを結合

  label node ancestor edge.length node.type size
1     a    1        5          NA       tip    1
2     b    2        5          NA       tip    2
3     c    3        4          NA       tip    3
4  <NA>    4        0          NA      root   NA
5  <NA>    5        4          NA  internal   NA

> extractTree(treedata)

  label node ancestor edge.length node.type
1     a    1        5          NA       tip
2     b    2        5          NA       tip
3     c    3        4          NA       tip
4  <NA>    4        0          NA      root
5  <NA>    5        4          NA  internal

geospiza

ダーウィンフィンチのデータ（phylo4dクラス）

> data(geospiza)
> class(geospiza)

[1] "list"

> names(geospiza)

[1] "geospiza.tree" "geospiza.data" "phy"           "dat"

> dplyr::glimpse(geospiza@data)

Error in nrow(tbl): trying to get slot "data" from an object of a basic class ("list") with no slots