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:
if(!require(printr)) warning("printr is not installed; displaying the content of 'data(...)' may not work")
data(package="timetrees")
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 .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
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.
Maintainer (temporary): Simon Frost (sdwfrost@gmail.com)
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