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 |
To install the devel version of the package, type:
devtools::install_github("Hackout3/timetrees")Note that this requires the package devtools installed.
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
.RDatafiles in thedata/folder (recommended) - as a text file in the
inst/folder (e.g. as a Newick string) - as a function loading/assembling/simulating a dataset
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:
- disease: mandatory
- location: optional
- year: optional
- sim: mandatory if this is a simulated dataset; otherwise data is assume to be an actual outbreak
- other: (any other relevant information)
Datasets are in the form of a list with three elements:
- tree: phylogeny in
phyloformat - 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. - aln: a multiple sequence alignment in DNAbin matrix format.
- Simon Frost (@sdwfrost)
- Thibaut Jombart (@thibautjombart)
Maintainer (temporary): Simon Frost (sdwfrost@gmail.com)