This is my reading notes for Functional and Phylogenetic Ecology in R by Nathan Swenson. All credits go to Nathan.
This post will be updated later when I learn more about this topic.

Chapter 2: Reading and plotting tree.

Possible packages needed.

install.packages(c("picante", "phylobase", "phylotools", "ecodist", "FD", 
"adephylo", "geiger"))
lapply(c("picante", "phylobase", "phylotools", "ecodist", "FD", "adephylo", 
    "geiger"), library, character.only = T)

Data reading

Get data at here.

library(ape)
my.phylo = read.tree("data/my.phylo.newick.file.txt")  # read.tree()
my.phylo
is.ultrametric(my.phylo)  # is.ultrametric()
plot(my.phylo, cex = 0.5)
add.scale.bar(length = 0.1)
plot.phylo(my.phylo, type = "fan")  # plot.phylo()
nodelabels(frame = "none", cex = 0.8)
tiplabels()

Prun tree

my.subtrees = subtrees(my.phylo)  # subtrees() to subset
my.subtrees[[15]]
# subtreeplot(my.phylo)
plot(my.subtrees[[15]])
drop.tree = drop.tip(my.phylo, c("e", "j"))  # drop.tip() to prun tree
plot(drop.tree)
# extract.clade(my.phylo, interactive = T)

Polynomy

my.poly.phylo = read.tree("data/example.poly.txt")
my.poly.phylo
plot(my.poly.phylo)
my.di.phylo = multi2di(my.poly.phylo)  # multi2di() 
my.di.phylo
plot(my.di.phylo)

multi2di() solves the polynomy by randomly add a zero length branch within the polynomy.

Branching time

branching.times(my.phylo)

branching.times() returns branch times for all internodes, ordered from root to tips.

Phylo distance between pairs of terminal taxa

p.dist.mat = cophenetic(my.phylo)
vcv(my.phylo)

cophenetic() returns a phylogenetic distance species by species matrix. Values in the matrix are the sum of the branch lengths separating each pair of species.
vcv() returns a species by species matrix also. But it is a phylogenetic variance-covariance (VCV) matrix. Diagonal values are the distance from the root to the tip; off-diagonal values are the amount of shared branch length between pairs of species. Or you can think it as a correlation matrix. The larger the values, the closer the species.

Simulating phylogenies in R

There are two common methods. Consider the assumptions when choose simulation method.

Randomly split the edges. Begin with a single branch that randomly splits into two daughter branches, and the daughter branches may then branch into two, and so on.

new.tree = rtree(n = 40, rooted = T)  # can provide tip.label=c(sp, sp,...)
plot(new.tree)

Randomly cluster the tips.

new.ultra.tree = rcoal(40)
plot(new.ultra.tree)
write.tree(new.ultra.tree, "name.txt")

Reading and plotting phylogenetic data in R