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nosoi

Nosoi is a flexible agent-based stochastic transmission chain/epidemiological simulator

https://github.com/slequime/nosoi

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 33 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Nosoi is a flexible agent-based stochastic transmission chain/epidemiological simulator

Basic Info
Statistics
  • Stars: 7
  • Watchers: 4
  • Forks: 4
  • Open Issues: 1
  • Releases: 6
Created over 7 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

nosoi

R-CMD-check codecov CRAN\_Status\_Badge <!-- badges: end -->

The aim of nosoi (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator. It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. nosoi is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

Installation

To get the current released version from CRAN: R install.packages("nosoi")

To get the latest (and possibly unstable) version, you can use the devtools package: R install.packages("devtools") devtools::install_github(repo = "slequime/nosoi")

Documentation

You can find package documentation, with reference, tutorials and examples here: http://slequime.github.io/nosoi/ (built with pkgdown).

Citation

Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey & Guy Baele (2020) nosoi: A stochastic agent-based transmission chain simulation framework in R. Methods in Ecology and Evolution 11:1002-1007 doi:10.1111/2041-210X.13422

nosoi in published manuscripts

  • Lequime et al. (2020) Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of * Aedes albopictus. *PLoS Pathogens** 16(12):e1009068. doi:10.1371/journal.ppat.1009068
  • Aubry, Jacobs & Darmuzey et al. (2021) Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains. Nature Communications 12:916 doi:10.1038/s41467-021-21199-z
  • Giovanetti et al. (2021) SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy. Communications Biology 4:489 doi:10.1038/s42003-021-02025-0
  • Goldstein et al. (2022) Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission. PLoS Computational Biology 18(12): e1010696 doi:10.1371/journal.pcbi.1010696
  • Marini et al. (2022) Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinformatics 38(3):856860 doi:https://doi.org/10.1093/bioinformatics/btab725
  • Vignier et al. (2023) Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barriers permissiveness and supports local epidemic potential. PCI Journal 3:e96 doi:10.24072/pcjournal.326
  • Bastide et al. (2024) Modeling the velocity of evolving lineages and predicting dispersal patterns. Proceedings of the National Academy of Sciences 121(47):e2411582121 doi:10.1073/pnas.2411582121
  • Magalis et al. (2024) Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods Infection, Genetics and Evolution 124:105661 doi:10.1016/j.meegid.2024.105661
  • Sun et al. (2024) DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. PLoS Computational Biology 20(4): e1011351 doi:10.1371/journal.pcbi.1011351
  • Sun et al. (2024) Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics. Bioinformatics Advances 4(1):vbae158 doi:10.1093/bioadv/vbae158

Owner

  • Name: Sebastian Lequime
  • Login: slequime
  • Kind: user
  • Location: Groningen, Netherlands
  • Company: University of Gronignen

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 295
  • Total Committers: 4
  • Avg Commits per committer: 73.75
  • Development Distribution Score (DDS): 0.437
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Sebastian Lequime 3****e 166
Paul Bastide p****e@g****m 111
GuyBaele b****y@g****m 16
Simon Dellicour s****r@g****m 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 12
  • Total pull requests: 12
  • Average time to close issues: 3 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 2.42
  • Average comments per pull request: 0.25
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 29 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • liamxg (4)
  • igoldsteinh (3)
  • rsbivand (2)
  • MichaelChirico (1)
  • krlmlr (1)
  • brmagalis (1)
Pull Request Authors
  • slequime (8)
  • thijsjanzen (2)
  • pbastide (2)
  • olivroy (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 316 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
cran.r-project.org: nosoi

A Forward Agent-Based Transmission Chain Simulator

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 316 Last month
Rankings
Forks count: 21.9%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 30.1%
Dependent repos count: 35.5%
Downloads: 40.9%
Maintainers (1)
sebastian.lequime@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • data.table >= 1.12.0 depends
  • methods >= 3.5.2 imports
  • raster >= 2.8 imports
  • stats >= 3.5.2 imports
  • ape >= 5.3 suggests
  • covr * suggests
  • dplyr >= 0.8.0 suggests
  • gganimate * suggests
  • ggnetwork * suggests
  • ggplot2 * suggests
  • ggtree >= 2.4.0 suggests
  • gifski * suggests
  • igraph * suggests
  • intergraph * suggests
  • knitr * suggests
  • magrittr >= 1.5 suggests
  • png * suggests
  • rmarkdown * suggests
  • testthat >= 2.1.0 suggests
  • tidytree >= 0.3.3 suggests
  • tidyverse * suggests
  • treeio >= 1.14.0 suggests
  • viridis * suggests