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.

singleContinuous()

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

singleDiscrete()

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

singleNone()

Single-host pathogen in a homogeneous 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