Data and code repository for Gibb et al., "Mammal virus diversity estimates are unstable due to accelerating discovery effort"

This repository contains the data and code for Gibb et al., 2021, 'Mammal virus diversity estimates are unstable due to accelerating discovery effort' (Biology Letters). The contents and organisation of the repository are described below:

VIRION database (public release v0.2.1; https://github.com/viralemergence/virion/) and host-virus metadata:

↳ data → virion → Virion.csv.gz (host-virus database)

↳ data → clovert → domestic_status (list of domestication status for species)

↳ data → speciesrichness (csvs of order and family-level species richness calculated from IUCN data)

Analysis scripts (numbered in order of use in the study pipeline). Each script is annotated at the top to describe its use.

↳ scripts

Analysis outputs:

↳ output → figures_2021 (main text and supp. figures)

↳ output → host_effort (citation counts for hosts as scraped from PubMed)

↳ output → host_synonyms (all known synonyms for hosts as scraped from PubMed)

For any enquiries please contact Rory Gibb (rory.j.gibb at gmail.com) or Colin Carlson (Colin.Carlson at georgetown.edu).