ojwatson / timetrees

A collection of time-stamped pathogen phylogenies

timetrees: a collection of time-stamped phylogenies

This package compiles a series of time-stamped phylogenies, to be shared during Hackout 3. Data can be provided as R objects (loaded automatically when loading the package), text files distributed alongside the package (e.g. Newick strings), or functions generating a dataset.

The following R datasets are currently available:

data(package="timetrees")

Item	Title
zika.2015	Zika virus, 2015-2016

Installing the package

To install the devel version of the package, type:

devtools::install_github("Hackout3/timetrees")

Note that this requires the package devtools installed.

Add your own data!

How to add data?

We will try to create a better repository and data submission system at a later stage. The purpose of the current package is only to share examplar datasets during the hackathon. Acceptable forms are:

• as a .RData files in the data/ folder (recommended)
• as a text file in the inst/ folder (e.g. as a Newick string)
• as a function loading/assembling/simulating a dataset

Naming Conventions

We use the lower cases and dots to separate words for the files and dataset names, so that for a RData object, a new dataset woud look like: `my.new.data.RData'. Try using informative names, typically using the disease first. Whenever available, order fields as:

1. disease: mandatory
2. location: optional
3. year: optional
4. sim: mandatory if this is a simulated dataset; otherwise data is assume to be an actual outbreak
5. other: (any other relevant information)

Datasets are in the form of a list with three elements:

1. tree: phylogeny in phylo format
2. data: metadata as a dataframe, comprising of the tip labels in the tree (tiplabel) and sampling times (year, month and date as separate columns), plus any additional information.
3. aln: a multiple sequence alignment in DNAbin matrix format.

Contributors (by alphabetic order):

• Simon Frost (@sdwfrost)
• Thibaut Jombart (@thibautjombart)

Maintainer (temporary): Simon Frost ([email protected])