nosoi: A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. in prep). 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.

Version: 1.0.1
Depends: data.table (≥ 1.12.0), R (≥ 3.5.0)
Imports: stats (≥ 3.5.2), methods (≥ 3.5.2), dplyr (≥ 0.8.0), magrittr (≥ 1.5), stringr (≥ 1.4.0), reshape2 (≥ 1.4.0), raster (≥ 2.8-19)
Suggests: testthat (≥ 2.1.0), knitr, rmarkdown, igraph, tidyverse, ggplot2, ggnetwork, intergraph, viridis, gifski, png, gganimate, ape (≥ 5.3), tidytree (≥ 0.2.4), treeio (≥ 1.6.2), ggtree (≥ 1.16.0)
Published: 2020-02-19
Author: Sebastian Lequime ORCID iD [aut, cre], Paul Bastide ORCID iD [aut], Simon Dellicour ORCID iD [aut], Philippe Lemey ORCID iD [aut], Guy Baele ORCID iD [aut]
Maintainer: Sebastian Lequime <sebastian.lequime at gmail.com>
License: GPL-3
URL: https://github.com/slequime/nosoi
NeedsCompilation: no
Language: en-US
CRAN checks: nosoi results

Downloads:

Reference manual: nosoi.pdf
Vignettes: Spread of a pathogen in a continuous space
Spread of a pathogen in a discrete structured population
Spread of a pathogen in a homogeneous population
Getting-started
output-summarization
Package source: nosoi_1.0.1.tar.gz
Windows binaries: r-devel: nosoi_1.0.0.zip, r-devel-gcc8: nosoi_1.0.1.zip, r-release: nosoi_1.0.1.zip, r-oldrel: nosoi_1.0.1.zip
OS X binaries: r-release: nosoi_1.0.1.tgz, r-oldrel: nosoi_1.0.1.tgz
Old sources: nosoi archive

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