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nosoi  

A Forward Agent-Based Transmission Chain Simulator
View on CRAN: Click here


Download and install nosoi package within the R console
Install from CRAN:
install.packages("nosoi")

Install from Github:
library("remotes")
install_github("cran/nosoi")

Install by package version:
library("remotes")
install_version("nosoi", "1.1.2")



Attach the package and use:
library("nosoi")
Maintained by
Sebastian Lequime
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-01-14
Latest Update: 2024-02-09
Description:
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.
How to cite:
Sebastian Lequime (2020). nosoi: A Forward Agent-Based Transmission Chain Simulator. R package version 1.1.2, https://cran.r-project.org/web/packages/nosoi. Accessed 25 Jun. 2026.
Previous versions and publish date:
1.0.0 (2020-01-14 11:30), 1.0.1 (2020-02-19 18:20), 1.0.2 (2020-04-03 16:10), 1.0.3 (2020-05-12 23:30), 1.1.0 (2021-08-17 18:20)
Other packages that cited nosoi R package
View nosoi citation profile
Other R packages that nosoi depends, imports, suggests or enhances
Complete documentation for nosoi
Functions, R codes and Examples using the nosoi R package
Some associated functions: CoreSanityChecks . FunctionSanityChecks . MatrixSanityChecks . RasterSanityChecks . add_node_tip . applyFunctionToHosts . cumulativeInfected . drawBernouilli . dualContinuous . dualDiscrete . dualNone . endMessage . getCumulative . getDynamic . getExitingMoving . getHostData . getPositionInfected . getR0 . getTableHosts . getTableState . getTransmissionTree . get_node . get_other_count . get_position . get_state . iniTable . iniTableState . keep.tip.treedata . keepState . makeMoves . meetTransmit . merge_host_tables . moveFunction.continuous . moveFunction.discrete . moveRotateContinuous . newLine . newLineState . nosoiSim . nosoiSimConstructor . nosoiSimOneConstructor . nosoiSummary . numberInfected . numberInfectedBGW . numberInfectedStates . paramConstructor . parseFunction . progressMessage . sampleTransmissionTree . sampleTransmissionTreeFromExiting . singleContinuous . singleDiscrete . singleNone . updateHostCount . updateTableState . writeInfected . 
Some associated R codes: dual-continuous.R . dual-discrete.R . dual-none.R . nosoiSim.R . nosoi_sanityChecks-Messages.R . nosoi_step1-makeMoves.R . nosoi_step2-MeetTransmit.R . nosoi_tablesManagment.R . nosoi_utilityFunctions.R . output_nosoiSummary.R . output_utilityFunctions.R . single-continuous.R . single-discrete.R . single-none.R .  Full nosoi package functions and examples
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