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nosoi (version 1.0.1)

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. in prep). 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

1.0.1

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/slequime/nosoi

Maintainer

Sebastian Lequime

Last Published

February 19th, 2020

Functions in nosoi (1.0.1)

RasterSanityChecks

Checks if the raster is properly formatted

Dual-host pathogen in structured (continuous) hosts populations

Draw newly infected

applyFunctionToHosts

Apply a function to table.host

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

Dual-host pathogen in structured (discrete) hosts populations

FunctionSanityChecks

Checks if a function is properly formatted

Extracts table.hosts from a nosoiSim object

Extracts table.state from a nosoiSim object

getTransmissionTree

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

getExitingMoving

Get Exiting or Moving individuals

getPositionInfected

get Position Infected

Get State at sampling time

Top-level function to use nosoi.

sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)

sampleTransmissionTreeFromExiting

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

Dual-host pathogen in homogeneous hosts populations

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

Gets R0 from a nosoi simulation

get_other_count

Get host count from table

Generates initial table to start the simulation (internal function)

Meet Transmit function

Extracts specific data from a nosoiSim object

singleContinuous

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

Make Move function

nosoiSimOneConstructor

nosoiSimOne Constructor

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

nosoiSimConstructor

nosoiSim Constructor

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

Should we build the table.host table

Summarizes the epidemiological features of a nosoi simulation

merge_host_tables

Merge Population Data

keep.tip.treedata

moveFunction.discrete

Make Discrete Move function

Single-host pathogen in a homogeneous host population

Get Position on branch

moveRotateContinuous

Rotates movement in 2D space

numberInfectedBGW

Number of infected hosts at time t (BGW)

Parse function for later use

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

Number of active infected hosts at time t

paramConstructor

Param concatenator

Write newly infected function

updateHostCount

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

moveFunction.continuous

Make Continuous Move function

updateTableState

Update table state with exiting individuals

progressMessage

cumulativeInfected

Cumulative number of infected hosts at time t

CoreSanityChecks

Checks if the simulator can start

MatrixSanityChecks

Checks if the matrix is properly formatted