Package: nosoi 1.1.2

Sebastian Lequime

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-4.5)nosoi_1.1.2.zip(r-4.4)nosoi_1.1.2.zip(r-4.3)
nosoi_1.1.2.tgz(r-4.4-any)nosoi_1.1.2.tgz(r-4.3-any)
nosoi_1.1.2.tar.gz(r-4.5-noble)nosoi_1.1.2.tar.gz(r-4.4-noble)
nosoi_1.1.2.tgz(r-4.4-emscripten)nosoi_1.1.2.tgz(r-4.3-emscripten)
nosoi.pdf |nosoi.html✨
nosoi/json (API)
NEWS

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

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

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

On CRAN:

7.20 score 7 stars 30 scripts 378 downloads 3 mentions 17 exports 6 dependencies

Last updated 1 months agofrom:5db026fe09. Checks:7 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-winOKFeb 13 2025
R-4.5-linuxOKFeb 13 2025
R-4.4-winOKFeb 13 2025
R-4.4-macOKFeb 13 2025
R-4.3-winOKFeb 13 2025
R-4.3-macOKFeb 13 2025

Exports:dualContinuousdualDiscretedualNonegetCumulativegetDynamicgetHostDatagetR0getTableHostsgetTableStategetTransmissionTreenosoiSimnosoiSummarysampleTransmissionTreesampleTransmissionTreeFromExitingsingleContinuoussingleDiscretesingleNone

Dependencies:data.tablelatticerasterRcppspterra

Getting started

Sebastian Lequime

Rendered fromnosoi.Rmdusingknitr::rmarkdownon Feb 13 2025.

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

Output and summarization

Sebastian Lequime

Rendered fromoutput.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2024-02-09
Started: 2019-07-19

Spread of a pathogen in a continuous space

Sebastian Lequime

Rendered fromcontinuous.Rmdusingknitr::rmarkdownon Feb 13 2025.

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

Spread of a pathogen in a discrete structured population

Sebastian Lequime

Rendered fromdiscrete.Rmdusingknitr::rmarkdownon Feb 13 2025.

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

Spread of a pathogen in a homogeneous population

Sebastian Lequime

Rendered fromnone.Rmdusingknitr::rmarkdownon Feb 13 2025.

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