Man pages for nosoi
A Forward Agent-Based Transmission Chain Simulator
| add_node_tip | Add one tip |
| applyFunctionToHosts | Apply a function to table.host |
| CoreSanityChecks | Checks if the simulator can start |
| cumulativeInfected | Cumulative number of infected hosts at time t |
| drawBernouilli | Draw newly infected |
| dualContinuous | Dual-host pathogen in structured (continuous) hosts... |
| dualDiscrete | Dual-host pathogen in structured (discrete) hosts populations |
| dualNone | Dual-host pathogen in homogeneous hosts populations |
| endMessage | End message |
| FunctionSanityChecks | Checks if a function is properly formatted |
| getCumulative | Gets the cumulative number of infected hosts for the full... |
| getDynamic | Gets the current number of infected hosts for the full length... |
| getExitingMoving | Get Exiting or Moving individuals |
| getHostData | Extracts specific data from a 'nosoiSim' object |
| get_node | Get Node |
| get_other_count | Get host count from table |
| get_position | Get Position on branch |
| getPositionInfected | get Position Infected |
| getR0 | Gets R0 from a 'nosoi' simulation |
| get_state | Get State at sampling time |
| 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... |
| iniTable | Generates initial table to start the simulation (internal... |
| iniTableState | Generates initial movement table to start the simulation... |
| keepState | Should we build the table.host table |
| keep.tip.treedata | Keep tips |
| makeMoves | Make Move function |
| MatrixSanityChecks | Checks if the matrix is properly formatted |
| meetTransmit | Meet Transmit function |
| merge_host_tables | Merge Population Data |
| moveFunction.continuous | Make Continuous Move function |
| moveFunction.discrete | Make Discrete Move function |
| moveRotateContinuous | Rotates movement in 2D space |
| newLine | Creates a new line to be added to the table when new host is... |
| newLineState | Creates a new line to be added to the movement table when... |
| nosoiSim | Top-level function to use 'nosoi'. |
| nosoiSimConstructor | nosoiSim Constructor |
| nosoiSimOneConstructor | nosoiSimOne Constructor |
| nosoiSummary | Summarizes the epidemiological features of a 'nosoi'... |
| numberInfected | Number of active infected hosts at time t |
| numberInfectedBGW | Number of infected hosts at time t (BGW) |
| numberInfectedStates | Number of active infected hosts at time t |
| paramConstructor | Param concatenator |
| parseFunction | Parse function for later use |
| progressMessage | Progress bar |
| RasterSanityChecks | Checks if the raster is properly formatted |
| sampleTransmissionTree | Sample the transmission tree (phylogenetic tree-like) |
| sampleTransmissionTreeFromExiting | Sample the transmission tree (phylogenetic tree-like) among... |
| singleContinuous | Single-host pathogen in a structured (continuous) host... |
| singleDiscrete | Single-host pathogen in a structured (discrete) host... |
| SingleNone | Single-host pathogen in a homogeneous host population |
| updateHostCount | Summarise position of hosts in a discrete or discretized... |
| updateTableState | Update table state with exiting individuals |
| writeInfected | Write newly infected function |
