Module: TransmissionNodeSample

The TransmissionNodeSample module chooses two nodes to be involved in a given transmission event. See the source code to see what is defined by the abstract class.

List of Implementations

TransmissionNodeSample_GEMF

• For use with a GEMF TransmissionTimeSample module
• Requirements:
  • Must use EndCriteria_GEMF module
  • Must use a GEMF TransmissionTimeSample module
• Config Parameters:
  • gemf_path: The path to your GEMF executable (or simply "GEMF" if it is in your PATH variable)

TransmissionNodeSample_PANGEA

• Wrapper for PANGEA.HIV.sim
• This is not supported in the Docker/Singularity images from FAVITES 1.1.11 onward
• Requirements:
  • R
  • PANGEA.HIV.sim
  • Must use ContactNetwork_PANGEA module
  • Must use ContactNetworkGenerator_PANGEA module
  • Must use EndCriteria_Instant module
  • Must use NodeEvolution_PANGEA module
  • Must use NodeSample_PANGEA module
  • Must use NumBranchSample_All module
  • Must use NumTimeSample_PANGEA module
  • Must use PostValidation_Dummy module
  • Must use SeedSelection_PANGEA module
  • Must use SeedSequence_PANGEA module
  • Must use SequenceEvolution_PANGEA module
  • Must use SourceSample_PANGEA module
  • Must use TimeSample_PANGEA module
  • Must use TransmissionNodeSample_PANGEA module
  • Must use TransmissionTimeSample_PANGEA module
  • Must use TreeUnit_Same module
• Config Parameters
  • Rscript_path: The path to your Rscript executable (or simply "Rscript" if it is in your PATH variable)
  • All pangea_ parameters, which correspond to PANGEA.HIV.sim parameters (see entry in FAVITES_ModuleList.json for complete list, and see PANGEA.HIV.sim help for details)
    • Use "" for default

TransmissionNodeSample_RandomMultiInfection

• For each transmission, the source node is selected from the set of all infected nodes in the Contact Network with equal probability, and the destination node is selected from the set of all of the source's neighbors with equal probability
  • In other words, multi-infections are allowed
• Requirements:
  • None
• Config Parameters:
  • None

TransmissionNodeSample_RandomSingleInfection

• For each transmission, the source node is selected from the set of all infected nodes in the Contact Network with equal probability, and the destination node is selected from the set of all of the source's uninfected neighbors with equal probability
• Requirements:
  • None
• Config Parameters:
  • None

TransmissionNodeSample_SI

• Transmission network is simulated via the SI model
• Requirements:
  • Must use TransmissionTimeSample_SI module
• Config Parameters:
  • infection_rate: The rate at which susceptible individuals are infected (per infected and time)

TransmissionNodeSample_TransmissionFile

• Transmission network is read from file
• Requirements:
  • Must use EndCriteria_TransmissionFile module
  • Must use SeedSelection_TransmissionFile module
  • Must use TransmissionTimeSample_TransmissionFile module
• Config Parameters:
  • transmission_network_file: The desired transmission network, represented in the FAVITES Transmission Network File Format