R: A Forward Agent-Based Transmission Chain Simulator

# A Forward Agent-Based Transmission Chain Simulator

## Documentation for package ‘nosoi’ version 1.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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