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nosoi

nosoi (pronounced no.so.i) is a flexible agent-based stochastic transmission chain/epidemic simulator in R, named after the daimones of plague, sickness and disease that escaped Pandora's jar in Greek mythology. nosoi is able to take into account the impact of multiple variables 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.

Installation

To get the current released version from CRAN:

install.packages("nosoi")

To get the latest (and possibly unstable) version, you can use the devtools package:

install.packages("devtools")
devtools::install_github(repo = "slequime/nosoi")

Documentation

You can find package documentation, with reference, tutorials and examples here: http://slequime.github.io/nosoi/ (built with pkgdown).

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Version

Install

install.packages('nosoi')

Monthly Downloads

322

Version

1.0.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Sebastian Lequime

Last Published

January 14th, 2020

Functions in nosoi (1.0.0)

dualDiscrete

Dual-host pathogen in structured (discrete) hosts populations
getDynamic

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

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

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

Gets the cumulative number of infected hosts for the full length of the simulation
moveFunction.discrete

Make Discrete Move function
get_state

Get State at sampling time
singleContinuous

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

Make Continuous Move function
CoreSanityChecks

Checks if the simulator can start
nosoiSimOneConstructor

nosoiSimOne Constructor
dualNone

Dual-host pathogen in homogeneous hosts populations
getPositionInfected

get Position Infected
getExitingMoving

Get Exiting or Moving individuals
get_other_count

Get host count from table
nosoiSimConstructor

nosoiSim Constructor
get_position

Get Position on branch
getTransmissionTree

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

Checks if the raster is properly formatted
MatrixSanityChecks

Checks if the matrix is properly formatted
cumulativeInfected

Cumulative number of infected hosts at time t
makeMoves

Make Move function
nosoiSim

Top-level function to use nosoi.
newLineState

Creates a new line to be added to the movement table when hosts moves (internal function)
getR0

Gets R0 from a nosoi simulation
keepState

Should we build the table.host table
sampleTransmissionTreeFromExiting

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

Number of infected hosts at time t (BGW)
get_node

Get Node
FunctionSanityChecks

Checks if a function is properly formatted
drawBernouilli

Draw newly infected
endMessage

End message
singleNone

Single-host pathogen in a homogeneous host population
getHostData

Extracts specific data from a nosoiSim object
nosoiSummary

Summarizes the epidemiological features of a nosoi simulation
updateTableState

Update table state with exiting individuals
paramConstructor

Param concatenator
writeInfected

Write newly infected function
sampleTransmissionTree

Sample the transmission tree (phylogenetic tree-like)
numberInfected

Number of active infected hosts at time t
moveRotateContinuous

Rotates movement in 2D space
newLine

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

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

Progress bar
meetTransmit

Meet Transmit function
getTableHosts

Extracts table.hosts from a nosoiSim object
applyFunctionToHosts

Apply a function to table.host
merge_host_tables

Merge Population Data
add_node_tip

Add one tip
parseFunction

Parse function for later use
getTableState

Extracts table.state from a nosoiSim object
iniTableState

Generates initial movement table to start the simulation (internal function)
keep.tip.treedata

Keep tips
dualContinuous

Dual-host pathogen in structured (continuous) hosts populations