Pruning a phylogeny for taxa

require(picante)

## Loading required package: picante
## Loading required package: ape
## Loading required package: vegan
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.0-9
## Loading required package: nlme

library(PhyloOrchard)

data(BinindaEmondsEtAl2007)
plot(BinindaEmondsEtAl2007[[1]], show.node.label = TRUE)

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tree <- BinindaEmondsEtAl2007[[1]]

tree

## 
## Phylogenetic tree with 4510 tips and 2108 internal nodes.
## 
## Tip labels:
##  Tachyglossus_aculeatus, Zaglossus_bruijni, Ornithorhynchus_anatinus, Anomalurus_beecrofti, Anomalurus_derbianus, Anomalurus_pelii, ...
## 
## Rooted; includes branch lengths.


which(tree$tip.label %in% "Dipodomys_merriami")

## [1] 1407

which(tree$tip.label %in% "Chaetodipus_baileyi")

## [1] 1391


# get distance matrix
trx <- cophenetic(tree)

# distance between taxa
trx["Dipodomys_merriami", "Chaetodipus_baileyi"]

## [1] 69


# see prune.sample, normally this takes in a siteXspp matrix, have to fool
# it a bit here
d <- matrix(nrow = 1, ncol = 4)
colnames(d) <- c("Dipodomys_merriami", "Chaetodipus_baileyi", "Peromyscus_eremicus", 
    "Dipodomys_ordii")

# prune the tree
tree.p <- prune.sample(phylo = tree, samp = d)
plot(tree.p)

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