Package: nosoi 1.1.2

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. 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.

Authors:Sebastian Lequime [aut, cre], Paul Bastide [aut], Simon Dellicour [aut], Philippe Lemey [aut], Guy Baele [aut], Thijs Janzen [ctb]

nosoi_1.1.2.tar.gz
nosoi_1.1.2.zip(r-4.7)nosoi_1.1.2.zip(r-4.6)nosoi_1.1.2.zip(r-4.5)
nosoi_1.1.2.tgz(r-4.6-any)nosoi_1.1.2.tgz(r-4.5-any)
nosoi_1.1.2.tar.gz(r-4.7-any)nosoi_1.1.2.tar.gz(r-4.6-any)
nosoi_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nosoi/json (API)
NEWS

# Install 'nosoi' in R:
install.packages('nosoi', repos = c('https://slequime.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/slequime/nosoi/issues

Pkgdown/docs site:https://slequime.github.io

On CRAN:

Conda:

7.11 score 8 stars 43 scripts 247 downloads 3 mentions 17 exports 6 dependencies

Last updated from:2e70670ea0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK194
source / vignettesOK239
linux-release-x86_64OK195
macos-release-arm64OK186
macos-oldrel-arm64OK198
windows-develOK143
windows-releaseOK155
windows-oldrelOK148
wasm-releaseOK130

Exports:dualContinuousdualDiscretedualNonegetCumulativegetDynamicgetHostDatagetR0getTableHostsgetTableStategetTransmissionTreenosoiSimnosoiSummarysampleTransmissionTreesampleTransmissionTreeFromExitingsingleContinuoussingleDiscretesingleNone

Dependencies:data.tablelatticerasterRcppspterra

Getting started

Sebastian Lequime

Rendered fromnosoi.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-02-09
Started: 2019-04-17

Output and summarization

Sebastian Lequime

Rendered fromoutput.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-08-06
Started: 2019-07-19

Spread of a pathogen in a continuous space

Sebastian Lequime

Rendered fromcontinuous.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-02-09
Started: 2019-04-26

Spread of a pathogen in a discrete structured population

Sebastian Lequime

Rendered fromdiscrete.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-02-09
Started: 2019-04-26

Spread of a pathogen in a homogeneous population

Sebastian Lequime

Rendered fromnone.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2020-05-12
Started: 2019-04-26