nosoi v1.0.0

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A Forward Agent-Based Transmission Chain Simulator

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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nosoi

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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).

Functions in nosoi

Name Description
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
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Vignettes of nosoi

Name
continuous.Rmd
discrete.Rmd
none.Rmd
nosoi.Rmd
output.Rmd
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