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-4.7-any)nosoi_1.1.2.zip(r-4.6-any)nosoi_1.1.2.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
nosoi/json (API)

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

On CRAN:

Conda:

7.16 score 8 stars 48 scripts 312 downloads 3 mentions 17 exports 6 dependencies

Last updated from:5db026fe09. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK227
source / vignettesOK251
linux-releaseOK214
macos-releaseOK130
macos-oldrelOK140
windows-develOK131
windows-releaseOK95
windows-oldrelOK133
wasm-releaseOK151

Exports:dualContinuousdualDiscretedualNonegetCumulativegetDynamicgetHostDatagetR0getTableHostsgetTableStategetTransmissionTreenosoiSimnosoiSummarysampleTransmissionTreesampleTransmissionTreeFromExitingsingleContinuoussingleDiscretesingleNone

Dependencies:data.tablelatticerasterRcppspterra

Getting started
Introduction | Critical assumption of nosoi | Essential building blocks: 3 probabilities and 2 numbers | What happens at each time step? | Setting up the core functions | Expected output | Functions' arguments | t | prestime | current.in and current.env.value | host.count | Extra Parameters | Combining arguments | Going further
Rendered fromnosoi.Rmdusingknitr::rmarkdown

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

Output and summarization
nosoiSim object | table.hosts | table.state | Epidemiological insights | Epidemiological summary | Epidemiological dynamics | $R_0$ | Transmission chains | Full transmission chain | Sampling the transmission chain | Exporting the Transmission Tree
Rendered fromoutput.Rmdusingknitr::rmarkdown

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

Spread of a pathogen in a continuous space
Structure of the population | Continuous space | Movement kernel | Setting up the simulation | General parameters | Core functions | pExit, param.pExit, timeDep.pExit, diff.pExit and hostCount.pExit | pMove, param.pMove, timeDep.pMove, diff.pMove and hostCount.pMove | sdMove, param.sdMove, timeDep.sdMove, diff.sdMove and hostCount.sdMove | nContact, param.nContact, timeDep.nContact, diff.nContact and hostCount.nContact | pTrans, param.pTrans, timeDep.pTrans,diff.pTrans and hostCount.pTrans | Miscellaneous | Dual host | Running nosoi | Single host | pExit | pMove | sdMove | nContact | pTrans | Running | pExit.B | pMove.B | sdMove.B | nContact.B | pTrans.B | Going further
Rendered fromcontinuous.Rmdusingknitr::rmarkdown

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

Spread of a pathogen in a discrete structured population
Structure of the population | Setting up the simulation | General parameters | Core functions | pExit, param.pExit, timeDep.pExit, diff.pExit and hostCount.pExit | pMove, param.pMove, timeDep.pMove, diff.pMove and hostCount.pMove | nContact, param.nContact, timeDep.nContact, diff.nContact and hostCount.nContact | pTrans, param.pTrans, timeDep.pTrans,diff.pTrans and hostCount.pTrans | Miscellaneous | Dual host | Running nosoi | Single host | pExit | pMove | nContact | pTrans | Running | pExit.B | pMove.B | nContact.B | pTrans.B | Going further
Rendered fromdiscrete.Rmdusingknitr::rmarkdown

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

Spread of a pathogen in a homogeneous population
Setting up the simulation | General parameters | Core functions | pExit, param.pExit and timeDep.pExit | nContact, param.nContact and timeDep.nContact | pTrans, param.pTrans and timeDep.pTrans | Miscellaneous | Dual host | Running nosoi | Single host | pExit | nContact | pTrans | Running | pExit.B | nContact.B | pTrans.B | Going further
Rendered fromnone.Rmdusingknitr::rmarkdown

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