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
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nosoi_1.1.2.tgz(r-4.4-any)nosoi_1.1.2.tgz(r-4.3-any)
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nosoi.pdf |nosoi.html✨
nosoi/json (API)
NEWS

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

Peer review:

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

On CRAN:

7.20 score 7 stars 30 scripts 305 downloads 3 mentions 17 exports 6 dependencies

Last updated 4 months agofrom:e2b8bc7964. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:dualContinuousdualDiscretedualNonegetCumulativegetDynamicgetHostDatagetR0getTableHostsgetTableStategetTransmissionTreenosoiSimnosoiSummarysampleTransmissionTreesampleTransmissionTreeFromExitingsingleContinuoussingleDiscretesingleNone

Dependencies:data.tablelatticerasterRcppspterra

Getting started

Sebastian Lequime

Rendered fromnosoi.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Output and summarization

Sebastian Lequime

Rendered fromoutput.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Spread of a pathogen in a continuous space

Sebastian Lequime

Rendered fromcontinuous.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Spread of a pathogen in a discrete structured population

Sebastian Lequime

Rendered fromdiscrete.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Spread of a pathogen in a homogeneous population

Sebastian Lequime

Rendered fromnone.Rmdusingknitr::rmarkdownon Nov 06 2024.

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