bat_rodent_tolerance
Data and code to reproduce the analyses in "Experimental infections reveal unexceptional viral tolerance in bats"
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: wiley.com, plos.org -
○Academic email domains
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary
Repository
Data and code to reproduce the analyses in "Experimental infections reveal unexceptional viral tolerance in bats"
Basic Info
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- Releases: 2
Metadata Files
README.md
Experimental infections reveal unexceptional viral tolerance in bats
Data and code to reproduce the analyses in "Experimental infections reveal unexceptional viral tolerance in bats"
Package Management
Run renv:restore() (see packages.R) in the root directory to load the correct package versions.
Then set working directory to scripts and run scripts in the following order:
Data Preprocessing
virus_taxize.R- grabs virus higher level taxonomy from NCBIvirus_traits_merge.R- merges reservoir and fatality data from Mollentze and Guth papershost_specificity.R- gets host range data from VIRION and calculates host specificity metrics and host evolutionary isolationsymptoms_harmonize.R- cleans raw data on organs damaged, behavioural changes, and symptoms. Creates severity scores. Note that species only and individual level data are merged in the output (Individual level data have values in the IndividualID column; species only data have NA). Makes summary plots for individuals.dose_harmonize.R- cleans dose volume, dose unit, and inocculation route for individual data. Marges with body size data from COMBINE to calculate dose/mass. Makes summary plots.
Data Summaries
data_summaries.R- calculates simple quantiateive measures for reporting in the paper. Creates heatmap of host x virus severity.phylo_plot_sampling.R- generates descriptive figures for phylogenetic sampling, host traits, and numbers of described and experimental hosts per virus.
Analyses
brms_models.rmd- conducts Bayesian hierarchical models via brms + Stan and outputsbrms_models.html
Data
raw_data contains untransformed original data from this manuscript (article_metadata.csv, primary_screen.csv, species_only_data.csv, individual_data.csv), taxonomic name translation tables, and published data (e.g. VIRION, Guth et al. (2022), Mollentze & Streicker (2020), Upham et al. 2019, COMBINE), and Web of Science search results and relevant CLOVER articles included in the primaty literature search.
clean_data contains cleaned and summarized versions of the raw_data files, including harmonized dose and severity measures, host range data, viral traits, and virus taxonomy.
Note: output .rds files in fit_models are not included to reduce repository size, but will be re-fit and saved when brms_models.rmd is compiled.
Owner
- Name: Maxwell J Farrell
- Login: maxfarrell
- Kind: user
- Company: University of Toronto
- Website: individual.utoronto.ca/maxfarrell
- Repositories: 3
- Profile: https://github.com/maxfarrell
EEB Postdoctoral Fellow
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Maxwell
given-names: Farrell
orcid: https://orcid.org/0000-0003-0452-6993
title:maxfarrell/bat_rodent_tolerance: Data and code to reproduce the analyses in "Limited evidence for unique viral tolerance in bats"
version: initial_submission
date-released: 2025-04-11
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- Release event: 3
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