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nosoi (version 1.0.3)

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

307

Version

1.0.3

License

GPL-3

Issues

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Repository

https://github.com/slequime/nosoi

Maintainer

Sebastian Lequime

Last Published

May 12th, 2020

Functions in nosoi (1.0.3)

Extracts table.hosts from a nosoiSim object

Extracts table.state from a nosoiSim object

keep.tip.treedata

Summarizes the epidemiological features of a nosoi simulation

Extracts specific data from a nosoiSim object

Dual-host pathogen in structured (discrete) hosts populations

Top-level function to use nosoi.

updateHostCount

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

getExitingMoving

Get Exiting or Moving individuals

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

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

Dual-host pathogen in homogeneous hosts populations

getPositionInfected

get Position Infected

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

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

updateTableState

Update table state with exiting individuals

getTransmissionTree

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

Gets R0 from a nosoi simulation

get_other_count

Get host count from table

Number of active infected hosts at time t

Write newly infected function

moveRotateContinuous

Rotates movement in 2D space

paramConstructor

Param concatenator

Generates initial table to start the simulation (internal function)

Get State at sampling time

nosoiSimConstructor

nosoiSim Constructor

progressMessage

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

Make Move function

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

nosoiSimOneConstructor

nosoiSimOne Constructor

Get Position on branch

Should we build the table.host table

Parse function for later use

Meet Transmit function

moveFunction.discrete

Make Discrete Move function

moveFunction.continuous

Make Continuous Move function

sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)

singleContinuous

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

Single-host pathogen in a homogeneous host population

sampleTransmissionTreeFromExiting

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

merge_host_tables

Merge Population Data

numberInfectedStates

Number of active infected hosts at time t

numberInfectedBGW

Number of infected hosts at time t (BGW)

MatrixSanityChecks

Checks if the matrix is properly formatted

Dual-host pathogen in structured (continuous) hosts populations

applyFunctionToHosts

Apply a function to table.host

RasterSanityChecks

Checks if the raster is properly formatted

cumulativeInfected

Cumulative number of infected hosts at time t

Draw newly infected

FunctionSanityChecks

Checks if a function is properly formatted

CoreSanityChecks

Checks if the simulator can start