A Forward Agent-Based Transmission Chain Simulator
Add one tip
Apply a function to table.host
Checks if the simulator can start
Cumulative number of infected hosts at time t
Draw newly infected
Dual-host pathogen in structured (continuous) hosts populations
Dual-host pathogen in structured (discrete) hosts populations
Dual-host pathogen in homogeneous hosts populations
End message
Checks if a function is properly formatted
Get Node
Get host count from table
Get Position on branch
Get State at sampling time
Gets the cumulative number of infected hosts for the full length of th...
Gets the current number of infected hosts for the full length of the s...
Get Exiting or Moving individuals
Extracts specific data from a nosoiSim object
get Position Infected
Gets R0 from a nosoi simulation
Extracts table.hosts from a nosoiSim object
Extracts table.state from a nosoiSim object
Gets the full transmission tree (phylogenetic tree-like) from a `nosoi...
Generates initial table to start the simulation (internal function)
Generates initial movement table to start the simulation (internal fun...
Keep tips
Should we build the table.host table
Make Move function
Checks if the matrix is properly formatted
Meet Transmit function
Merge Population Data
Make Continuous Move function
Make Discrete Move function
Rotates movement in 2D space
Creates a new line to be added to the table when new host is infected ...
Creates a new line to be added to the movement table when hosts moves ...
Top-level function to use nosoi.
nosoiSim Constructor
nosoiSimOne Constructor
Summarizes the epidemiological features of a nosoi simulation
Number of active infected hosts at time t
Number of infected hosts at time t (BGW)
Number of active infected hosts at time t
Param concatenator
Parse function for later use
Progress bar
Checks if the raster is properly formatted
Sample the transmission tree (phylogenetic tree-like)
Sample the transmission tree (phylogenetic tree-like) among the exited...
Single-host pathogen in a structured (continuous) host population
Single-host pathogen in a structured (discrete) host population
Single-host pathogen in a homogeneous host population
Summarise position of hosts in a discrete or discretized (raster) spac...
Update table state with exiting individuals
Write newly infected function
The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). 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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