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nosoi (version 1.0.2)

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. bioRxiv 2020.03.03.973107). 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

1.0.2

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/slequime/nosoi

Maintainer

Sebastian Lequime

Last Published

April 3rd, 2020

Functions in nosoi (1.0.2)

CoreSanityChecks

Checks if the simulator can start

getExitingMoving

Get Exiting or Moving individuals

Dual-host pathogen in structured (discrete) hosts populations

Extracts table.state from a nosoiSim object

moveRotateContinuous

Rotates movement in 2D space

sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)

sampleTransmissionTreeFromExiting

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

Extracts specific data from a nosoiSim object

Make Move function

Get State at sampling time

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

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

Should we build the table.host table

Draw newly infected

Gets R0 from a nosoi simulation

keep.tip.treedata

moveFunction.discrete

Make Discrete Move function

Meet Transmit function

getTransmissionTree

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

getPositionInfected

get Position Infected

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

merge_host_tables

Merge Population Data

Generates initial table to start the simulation (internal function)

numberInfectedBGW

Number of infected hosts at time t (BGW)

Parse function for later use

moveFunction.continuous

Make Continuous Move function

updateTableState

Update table state with exiting individuals

paramConstructor

Param concatenator

Top-level function to use nosoi.

progressMessage

get_other_count

Get host count from table

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

Single-host pathogen in a homogeneous host population

Summarizes the epidemiological features of a nosoi simulation

Get Position on branch

nosoiSimOneConstructor

nosoiSimOne Constructor

Number of active infected hosts at time t

singleContinuous

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

Write newly infected function

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

updateHostCount

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

nosoiSimConstructor

nosoiSim Constructor

RasterSanityChecks

Checks if the raster is properly formatted

Dual-host pathogen in structured (continuous) hosts populations

cumulativeInfected

Cumulative number of infected hosts at time t

FunctionSanityChecks

Checks if a function is properly formatted

Dual-host pathogen in homogeneous hosts populations

MatrixSanityChecks

Checks if the matrix is properly formatted

applyFunctionToHosts

Apply a function to table.host

Extracts table.hosts from a nosoiSim object