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nosoi (version 1.1.2)

A Forward Agent-Based Transmission Chain Simulator

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.

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Install

install.packages('nosoi')

Monthly Downloads

276

Version

1.1.2

License

GPL-3

Issues

Pull Requests

Stars

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Repository

https://github.com/slequime/nosoi

Homepage

https://slequime.github.io/nosoi/

Maintainer

Sebastian Lequime

Last Published

February 9th, 2024

Functions in nosoi (1.1.2)

Top-level function to use nosoi.

Extracts specific data from a nosoiSim object

Make Move function

Single-host pathogen in a structured (discrete) host population

Extracts table.hosts from a nosoiSim object

sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)

sampleTransmissionTreeFromExiting

Sample the transmission tree (phylogenetic tree-like) among the exited hosts

singleContinuous

Single-host pathogen in a structured (continuous) host population

Write newly infected function

Generates initial table to start the simulation (internal function)

Meet Transmit function

Generates initial movement table to start the simulation (internal function)

Dual-host pathogen in structured (discrete) hosts populations

moveRotateContinuous

Rotates movement in 2D space

updateHostCount

Summarise position of hosts in a discrete or discretized (raster) space

progressMessage

Creates a new line to be added to the table when new host is infected (internal function)

Parse function for later use

getPositionInfected

get Position Infected

get_other_count

Get host count from table

Summarizes the epidemiological features of a nosoi simulation

Dual-host pathogen in homogeneous hosts populations

updateTableState

Update table state with exiting individuals

Extracts table.state from a nosoiSim object

nosoiSimOneConstructor

nosoiSimOne Constructor

Number of active infected hosts at time t

moveFunction.discrete

Make Discrete Move function

Creates a new line to be added to the movement table when hosts moves (internal function)

nosoiSimConstructor

nosoiSim Constructor

getTransmissionTree

Gets the full transmission tree (phylogenetic tree-like) from a nosoi simulation

numberInfectedBGW

Number of infected hosts at time t (BGW)

merge_host_tables

Merge Population Data

moveFunction.continuous

Make Continuous Move function

paramConstructor

Param concatenator

numberInfectedStates

Number of active infected hosts at time t

Single-host pathogen in a homogeneous host population

Draw newly infected

FunctionSanityChecks

Checks if a function is properly formatted

Dual-host pathogen in structured (continuous) hosts populations

RasterSanityChecks

Checks if the raster is properly formatted

CoreSanityChecks

Checks if the simulator can start

MatrixSanityChecks

Checks if the matrix is properly formatted

cumulativeInfected

Cumulative number of infected hosts at time t

applyFunctionToHosts

Apply a function to table.host

Gets R0 from a nosoi simulation

Gets the cumulative number of infected hosts for the full length of the simulation

Gets the current number of infected hosts for the full length of the simulation

getExitingMoving

Get Exiting or Moving individuals

keep.tip.treedata

Get State at sampling time

Get Position on branch

Should we build the table.host table