Man pages for nosoi
A Forward Agent-Based Transmission Chain Simulator

add_node_tipAdd one tip
applyFunctionToHostsApply a function to
CoreSanityChecksChecks if the simulator can start
cumulativeInfectedCumulative number of infected hosts at time t
drawBernouilliDraw newly infected
dualContinuousDual-host pathogen in structured (continuous) hosts...
dualDiscreteDual-host pathogen in structured (discrete) hosts populations
dualNoneDual-host pathogen in homogeneous hosts populations
endMessageEnd message
FunctionSanityChecksChecks if a function is properly formatted
getCumulativeGets the cumulative number of infected hosts for the full...
getDynamicGets the current number of infected hosts for the full length...
getExitingMovingGet Exiting or Moving individuals
getHostDataExtracts specific data from a 'nosoiSim' object
get_nodeGet Node
get_other_countGet host count from table
get_positionGet Position on branch
getPositionInfectedget Position Infected
getR0Gets R0 from a 'nosoi' simulation
get_stateGet State at sampling time
getTableHostsExtracts 'table.hosts' from a 'nosoiSim' object
getTableStateExtracts 'table.state' from a 'nosoiSim' object
getTransmissionTreeGets the full transmission tree (phylogenetic tree-like) from...
iniTableGenerates initial table to start the simulation (internal...
iniTableStateGenerates initial movement table to start the simulation...
keepStateShould we build the table
keep.tip.treedataKeep tips
makeMovesMake Move function
MatrixSanityChecksChecks if the matrix is properly formatted
meetTransmitMeet Transmit function
merge_host_tablesMerge Population Data
moveFunction.continuousMake Continuous Move function
moveFunction.discreteMake Discrete Move function
moveRotateContinuousRotates movement in 2D space
newLineCreates a new line to be added to the table when new host is...
newLineStateCreates a new line to be added to the movement table when...
nosoiSimTop-level function to use 'nosoi'.
nosoiSimConstructornosoiSim Constructor
nosoiSimOneConstructornosoiSimOne Constructor
nosoiSummarySummarizes the epidemiological features of a 'nosoi'...
numberInfectedNumber of active infected hosts at time t
numberInfectedBGWNumber of infected hosts at time t (BGW)
numberInfectedStatesNumber of active infected hosts at time t
paramConstructorParam concatenator
parseFunctionParse function for later use
progressMessageProgress bar
RasterSanityChecksChecks if the raster is properly formatted
sampleTransmissionTreeSample the transmission tree (phylogenetic tree-like)
sampleTransmissionTreeFromExitingSample the transmission tree (phylogenetic tree-like) among...
singleContinuousSingle-host pathogen in a structured (continuous) host...
singleDiscreteSingle-host pathogen in a structured (discrete) host...
singleNoneSingle-host pathogen in a homogeneous host population
updateHostCountSummarise position of hosts in a discrete or discretized...
updateTableStateUpdate table state with exiting individuals
writeInfectedWrite newly infected function
nosoi documentation built on Aug. 17, 2021, 5:09 p.m.