CRAN/E | nosoi

nosoi

A Forward Agent-Based Transmission Chain Simulator

Installation

About

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). 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.

Citation nosoi citation info
github.com/slequime/nosoi
slequime.github.io/nosoi/
Bug report File report

Key Metrics

Version 1.1.2
R ≥ 3.5.0
Published 2024-02-09 49 days ago
Needs compilation? no
License GPL-3
CRAN checks nosoi results
Language en-US

Downloads

Yesterday 21 0%
Last 7 days 77 -11%
Last 30 days 353 -26%
Last 90 days 1.311 +50%
Last 365 days 3.951 +6%

Maintainer

Maintainer

Sebastian Lequime

sebastian.lequime@gmail.com

Authors

Sebastian Lequime

aut / cre

Paul Bastide

aut

Simon Dellicour

aut

Philippe Lemey

aut

Guy Baele

aut

Thijs Janzen

ctb

Material

NEWS
Reference manual
Package source

In Views

Epidemiology

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 and summarization

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

nosoi archive

Depends

data.table ≥ 1.12.0
R ≥ 3.5.0

Imports

stats ≥ 3.5.2
methods ≥ 3.5.2
raster ≥ 2.8-19

Suggests

testthat ≥ 2.1.0
knitr
rmarkdown
igraph
ggplot2
ggnetwork
intergraph
viridis
gifski
png
gganimate
ape ≥5.3
tidytree ≥ 0.3.3
treeio ≥ 1.14.0
ggtree ≥2.4.0
magrittr ≥ 1.5
dplyr ≥ 0.8.0
covr