Reference

Simulation function These functions are called by nosoiSim and are specific to the type of simulations your run.
nosoiSim()	Top-level function to use nosoi.
singleNone()	Single-host pathogen in a homogeneous host population
singleContinuous()	Single-host pathogen in a structured (continuous) host population
singleDiscrete()	Single-host pathogen in a structured (discrete) host population
dualContinuous()	Dual-host pathogen in structured (continuous) hosts populations
dualDiscrete()	Dual-host pathogen in structured (discrete) hosts populations
dualNone()	Dual-host pathogen in homogeneous hosts populations
Output: data extraction These functions are used to get information on your nosoi output.
getHostData()	Extracts specific data from a nosoiSim object
getTableHosts()	Extracts table.hosts from a nosoiSim object
getTableState()	Extracts table.state from a nosoiSim object
Output: epidemiology These functions are used to get information on your nosoi output.
nosoiSummary() summary(<nosoiSim>)	Summarizes the epidemiological features of a nosoi simulation
getR0()	Gets R0 from a nosoi simulation
getDynamic()	Gets the current number of infected hosts for the full length of the simulation
getCumulative()	Gets the cumulative number of infected hosts for the full length of the simulation
Output: transmission chains These functions are used to get information on your nosoi output.
getTransmissionTree()	Gets the full transmission tree (phylogenetic tree-like) from a nosoi simulation
sampleTransmissionTree()	Sample the transmission tree (phylogenetic tree-like)
sampleTransmissionTreeFromExiting()	Sample the transmission tree (phylogenetic tree-like) among the exited hosts