Module: NodeAvailability

The NodeAvailability module subsamples the nodes in the Contact Network (to simulate imperfect epidemiological efforts). See the source code to see what is defined by the abstract class.

List of Implementations

NodeAvailability_Bernoulli

• For each infected Contact Network node, sample from a Bernoulli trial with a user-specified probability of success, and only sample this individual upon success
• Requirements:
  • None
• Config Parameters:
  • node_sample_prob: The probability of success, p, for the Bernoulli trials

NodeAvailability_None

• No infected individuals in the Contact Network are available
• Requirements:
  • Must use NumTimeSample_None module
  • Must use TimeSample_None module
• Config Parameters:
  • None

NodeAvailability_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 NodeAvailability_PANGEA module
  • Must use NodeEvolution_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

NodeAvailability_Perfect

• Perfect sampling of all infected Transmission Network nodes
• Requirements:
  • None
• Config Parameters:
  • None

NodeAvailability_TransmissionWeighted

• The probability that a given ContactNetwork node is sampled is weighted by the number of transmission events in which the node was involved (either as the infector or the infectee)
• Requirements:
  • None
• Config Parameters:
  • node_sample_fraction: The fraction of total infected nodes you wish to sample