OutbreakTools (version 0.1-16)

read annotated trees: Read annotated tree files in Newick or NEXUS format

Description

These functions read annotated trees from files in Newick or NEXUS formats. Except for the annotations, these functions mimic ape's functions read.tree and read.nexus.

Annotations are ordered by edges, i.e. matching the edge.length slot of a phylo object.

Usage

read.annotated.tree(file="", text = NULL, tree.names = NULL, skip = 0,
                      comment.char = "#", keep.multi = FALSE, …)
  read.annotated.nexus(file, tree.names = NULL)

Arguments

file

a file name specified by either a variable of mode character, or a double-quoted string; if <U+2018>file = ""<U+2019> (the default) then the tree is input on the keyboard, the entry being terminated with a blank line

text

alternatively, the name of a variable of mode character which contains the tree(s) in parenthetic format. By default, this is ignored (set to <U+2018>NULL<U+2019>, meaning that the tree is read in a file); if <U+2018>text<U+2019> is not <U+2018>NULL<U+2019>, then the argument <U+2018>file<U+2019> is ignored.

tree.names

if there are several trees to be read, a vector of mode character that gives names to the individual trees; if <U+2018>NULL<U+2019> (the default), the trees are named <U+2018>"tree1"<U+2019>, <U+2018>"tree2"<U+2019>, ...

skip

the number of lines of the input file to skip before beginning to read data (this is passed directly to<U+2018> scan()<U+2019>).

comment.char

a single character, the remaining of the line after this character is ignored (this is passed directly to <U+2018>scan()<U+2019>).

keep.multi

if <U+2018>TRUE<U+2019> and <U+2018>tree.names = NULL<U+2019> then single trees are returned in <U+2018>"multiPhylo"<U+2019> format, with any name that is present (see details). Default is <U+2018>FALSE<U+2019>.

…

further arguments to be passed to <U+2018>scan()<U+2019>.

Value

An object of class "phylo" with an additional slot called annotations. This slot is a list indexed by the nodes.

Details

See read.nexus in the ape package for a specification of NEXUS formatted tree files. This function additionally extracts BEAST annotations for all branches/nodes in the trees and returns these annotations as lists of lists in the resulting "phylo" objects

Examples

# NOT RUN {
## read annotated tree from Nexus file
## (note: do not use 'system file' for your own file!)
tre <- read.annotated.nexus(system.file("files/BEAST-expl.nex", package="OutbreakTools"))

## ladderize the tree
tre <- ladderize(tre)

## this tree has annotations
##
names(tre)
class(tre$annotations)
length(tre$annotations)

## for each edge (each edge is identified by a terminal node), we have:
tre$annotations[[1]]
names(tre$annotations[[1]])

## extract rates from annotations
rates <- unlist(sapply(tre$annotations, function(e) e$rate_median))

## plot tree, show median rates as colors
plot(tre, show.tip=FALSE, edge.col=num2col(rates, col.pal=seasun))

# }