The phylogenetic range of bacterial and viral pathogens of vertebrates: dataset and supplementary material
datasetposted on 17.01.2020, 12:42 authored by Liam ShawLiam Shaw
[N.B. This is an archived version of the code and data repository available at https://github.com/liampshaw/Pathogen-host-range.]
Associated preprint: The phylogenetic range of bacterial and viral pathogens of vertebrates
Authors: Liam P. Shaw*, Alethea Wang*, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux (* co-first authors)
This repository contains code to reproduce all figures and analyses in the associated paper analysing the host range of pathogen species. This is bundled together in the Rmarkdown notebook (Supplementary Text 1 of the manuscript). It also contains several data files. The image above is a schematic for the manual literature review used to construct the database of host-pathogen associations. For more information on the dataset collection methods and analysis, please see the preprint.
The main dataset contains a human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species.
Code can be altered to change any of the figures. Some explanatory text is provided, but not much. Any questions can be addressed via email (liam.philip.shaw at gmail dot com).
Unless otherwise stated, data related to viruses is plotted in red and bacteria in black. The code should take <10 minutes to run on a standard laptop.
Note: At several points code is adapted/reused from the supplementary code repository made available by Olival et. al. (2017):
- Olival et al. (2017) paper: Host and viral traits predict zoonotic spillover from mammals https://doi.org/10.1038/nature22975
- Code repository: https://github.com/ecohealthalliance/HP3
- MIT License: https://opensource.org/licenses/MIT
This mainly applies to several scripts in the `scripts' directory relating to the fitting and plotting of generalized additive models (GAMs) - more information is included where appropriate. All code here is also made available under the MIT License.