ape: Analyses of Phylogenetics and Evolution

系統学、進化学の解析ツール

• CRAN: http://cran.r-project.org/web/packages/ape/index.html
• URL: http://ape-package.ird.fr/

> library(ape)
> data("bird.families")

バージョン: 3.4

bird.families

鳥類の系統的データ。phyloクラスオブジェクト

> data("bird.families")
> bird.families %>% {
+   class(.) %>% print()
+   str(.) %>% print()
+   .
+ }

[1] "phylo"
List of 4
 $ edge       : int [1:271, 1:2] 138 139 140 141 142 142 141 143 143 140 ...
 $ Nnode      : int 135
 $ tip.label  : chr [1:137] "Struthionidae" "Rheidae" "Casuariidae" "Apterygidae" ...
 $ edge.length: num [1:271] 2.1 4.1 3.9 0.8 17.1 17.1 8.4 9.5 9.5 21.8 ...
 - attr(*, "class")= chr "phylo"
NULL

Phylogenetic tree with 137 tips and 135 internal nodes.

Tip labels:
    Struthionidae, Rheidae, Casuariidae, Apterygidae, Tinamidae, Cracidae, ...

Rooted; includes branch lengths.

collapse.singles

drop.tip

系統樹からtipsを取り除く

Arguments

• phy... phyloクラスオブジェクト
• tip
• trim.internal
• subtree
• root.edge
• rooted
• interactive

> data("bird.families")
> tip <- c(
+ "Eopsaltriidae", "Acanthisittidae", "Pittidae", "Eurylaimidae",
+ "Philepittidae", "Tyrannidae", "Thamnophilidae", "Furnariidae",
+ "Formicariidae", "Conopophagidae", "Rhinocryptidae", "Climacteridae",
+ "Menuridae", "Ptilonorhynchidae", "Maluridae", "Meliphagidae",
+ "Pardalotidae", "Petroicidae", "Irenidae", "Orthonychidae",
+ "Pomatostomidae", "Laniidae", "Vireonidae", "Corvidae",
+ "Callaeatidae", "Picathartidae", "Bombycillidae", "Cinclidae",
+ "Muscicapidae", "Sturnidae", "Sittidae", "Certhiidae",
+ "Paridae", "Aegithalidae", "Hirundinidae", "Regulidae",
+ "Pycnonotidae", "Hypocoliidae", "Cisticolidae", "Zosteropidae",
+ "Sylviidae", "Alaudidae", "Nectariniidae", "Melanocharitidae",
+ "Paramythiidae","Passeridae", "Fringillidae")
> length(tip)

[1] 47

> bird.families %>% {
+   summary(.) %>% print()
+   drop.tip(., tip = tip) %>% summary()
+ }

Phylogenetic tree: . 

  Number of tips: 137 
  Number of nodes: 135 
  Branch lengths:
    mean: 7.413653 
    variance: 38.49237 
    distribution summary:
   Min. 1st Qu.  Median 3rd Qu.    Max. 
   0.10    1.15    9.10   11.50   27.00 
  No root edge.
  First ten tip labels: Struthionidae 
                        Rheidae
                        Casuariidae
                        Apterygidae
                        Tinamidae
                        Cracidae
                        Megapodiidae
                        Phasianidae
                        Numididae
                        Odontophoridae
  No node labels.
NULL

Phylogenetic tree: . 

  Number of tips: 95 
  Number of nodes: 93 
  Branch lengths:
    mean: 8.206952 
    variance: 42.80151 
    distribution summary:
   Min. 1st Qu.  Median 3rd Qu.    Max. 
    0.2     1.5     9.2    12.6    27.0 
  No root edge.
  First ten tip labels: Struthionidae 
                        Rheidae
                        Casuariidae
                        Apterygidae
                        Tinamidae
                        Cracidae
                        Megapodiidae
                        Phasianidae
                        Numididae
                        Odontophoridae
  No node labels.

lmorigin

原点を通る重回帰モデル

Arguments

• formula
• data
• origin
• nperm
• method
• silent

> data("lmorigin.ex1")
> out <- lmorigin.ex1 %>% lmorigin(SO2 ~ ., data = ., origin = FALSE, nperm = 99)

Multiple regression with estimation of intercept 
Permutation method = residuals of full model 
Computation time = 0.427000  sec

> out

Multiple regression with estimation of intercept 

Call:
lmorigin(formula = SO2 ~ ., data = ., origin = FALSE, nperm = 99) 

Coefficients and parametric test results 

                   Coefficient Std_error t-value   Pr(>|t|)    
(Intercept)          58.195935 20.487894  2.8405    0.00728 ** 
Mean_Annual_Temp_F   -0.587145  0.371008 -1.5826    0.12203    
No_manufactures       0.071225  0.016060  4.4349 0.00007955 ***
Population_x_1000    -0.046648  0.015372 -3.0346    0.00439 ** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Two-tailed tests of regression coefficients

                   Coefficient p-param p-perm   
(Intercept)          58.195935  0.0073     NA   
Mean_Annual_Temp_F   -0.587145  0.1220   0.17   
No_manufactures       0.071225  0.0001   0.01 **
Population_x_1000    -0.046648  0.0044   0.02 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

One-tailed tests of regression coefficients: 
test in the direction of the sign of the coefficient

                   Coefficient p-param p-perm   
(Intercept)          58.195935  0.0036     NA   
Mean_Annual_Temp_F   -0.587145  0.0610   0.07 . 
No_manufactures       0.071225  0.0000   0.01 **
Population_x_1000    -0.046648  0.0022   0.01 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 15.19126 on 37 degrees of freedom 
Multiple R-square: 0.6125468   Adjusted R-square: 0.5811317 

F-statistic: 19.49847 on 3 and 37 DF:
   parametric p-value   : 0.0000000948852 
   permutational p-value: 0.01 
after 99 permutations of residuals of full model

pic

系統独立対比の実施

> tree.primates <- c("((((Homo:0.21,Pongo:0.21):0.28,","Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);") %>%
+   read.tree(text = .)
> X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
> Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
> names(X) <- names(Y) <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
> (pic.X <- pic(X, tree.primates))

        6         7         8         9 
3.3583189 1.1929263 1.5847416 0.7459333

> (pic.Y <- pic(Y, tree.primates))

        6         7         8         9 
0.8970604 0.8678969 0.7176125 2.1798897

> cor.test(pic.X, pic.Y)

    Pearson's product-moment correlation

data:  pic.X and pic.Y
t = -0.85623, df = 2, p-value = 0.4821
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.9874751  0.8823934
sample estimates:
       cor 
-0.5179156

read.tree

系統樹ファイルの読み込み

> library(adephylo)

Loading required package: ade4

Attaching package: 'adephylo'

The following object is masked from 'package:ade4':

    orthogram

> data("ungulates")
> read.tree(text = ungulates$tre) %>%  {
+   print(.)
+   plot(.)
+ }

Phylogenetic tree with 18 tips and 13 internal nodes.

Tip labels:
    Antilocapra_americana, Gorgon_taurinus, Oryx_leucoryx, Taurotragus_livingstoni, Tautragus_oryx, Gazella_thompsoni, ...
Node labels:
    Root, W11, W10, W1, W2, W7, ...

Rooted; no branch lengths.

rtree

ランダムな系統樹データを生成

rtree, rcoal, rmtree

Arguments

• n
• rooted
• tip.label
• br
• ...
• N

> rtree(n = 20)

Phylogenetic tree with 20 tips and 19 internal nodes.

Tip labels:
    t8, t20, t9, t3, t11, t7, ...

Rooted; includes branch lengths.

write.tree

Newickファイルの書き出し

> set.seed(100)
> rtree(n = 20) %>% 
+   write.tree(phy = ., file = "../inst/ape_write_tree.tre")
> 
> read.tree(file = "../inst/ape_write_tree.tre") %>% {
+   print(.)
+   is.binary.tree(.)
+ }

Phylogenetic tree with 20 tips and 19 internal nodes.

Tip labels:
    t6, t8, t14, t12, t4, t20, ...

Rooted; includes branch lengths.

[1] TRUE