A Forward Agent-Based Transmission Chain Simulator

Documentation for package ‘nosoi’ version 1.1.2

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
getCumulative	Gets the cumulative number of infected hosts for the full length of the simulation
getDynamic	Gets the current number of infected hosts for the full length of the simulation
getHostData	Extracts specific data from a 'nosoiSim' object
getR0	Gets R0 from a 'nosoi' simulation
getTableHosts	Extracts 'table.hosts' from a 'nosoiSim' object
getTableState	Extracts 'table.state' from a 'nosoiSim' object
getTransmissionTree	Gets the full transmission tree (phylogenetic tree-like) from a 'nosoi' simulation
nosoiSim	Top-level function to use 'nosoi'.
nosoiSummary	Summarizes the epidemiological features of a 'nosoi' simulation
sampleTransmissionTree	Sample the transmission tree (phylogenetic tree-like)
sampleTransmissionTreeFromExiting	Sample the transmission tree (phylogenetic tree-like) among the exited hosts
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
summary.nosoiSim	Summarizes the epidemiological features of a 'nosoi' simulation