seraphim

seraphim is a R package for investigating the impact of environmental factors on the dispersal history and dynamics of viral lineages. The package can also be used to estimate dispersal statistics and mapping continuous phylogeographic trees.

References

• Dellicour S, Rose R, Faria N, Lemey P, Pybus OG (2016). SERAPHIM: studying environmental rasters and phylogenetically-informed movements. Bioinformatics 32: 3204-3206.
• Dellicour S, Rose R, Pybus OG (2016). Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. BMC Bioinformatics 17: 82.

Stay tuned!

If you want to remain informed about last updates or improvements, just send an e-mail to simon.dellicour[at]ulb[dot]be with "seraphim mailing list" in the object.

Installation

In R, seraphim can be installed with the devtools package:

install.packages("devtools"); library(devtools)
install_github("sdellicour/seraphim/unix_OS") # (for a Unix OS)
install_github("sdellicour/seraphim/windows") # (for a Windows OS)

Using seraphim with the command line version of the program Circuitscape can sometimes be challenging as the later requires specific Python 2 settings. To facilitate its installation and subsequent application, users can now use Conda to install the appropriate environment specified in the seraphim.yaml file. Conda is an open source package/environment management system that can be installed following the instructions available here.

Once Conda is installed, the installation of the seraphim environment can be performed in a Terminal using the following command:

sudo conda env create -f seraphim.yaml --force

And the Conda environment can then be activated as follows:

conda activate seraphim

Within this environment, the command line version of Circuitscape running on Python 2 can subsequently be installed as follows:

sudo -H pip install -U --upgrade circuitscape

Always within the dedicated Conda environment, seraphim can finally be installed in R as described above:

library(devtools)
install_github("sdellicour/seraphim/unix_OS")