Module: TimeSample

The TimeSample module chooses times at which a given individual in the ContactNetwork was sampled (i.e., sequenced). See the source code to see what is defined by the abstract class.

List of Implementations

• TimeSample_End
  • All individuals who are infected at the end of the transmission simulation are sampled (i.e., sequenced) once exactly at the end
  • Requirements:
    • None
  • Config Parameters:
    • None
• TimeSample_PANGEA
  • Wrapper for PANGEA.HIV.sim
  • 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 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
  • 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
• TimeSample_Uniform
  • A given individual is sampled (i.e., sequenced) a user-specified number of times, and each time is chosen from a uniform distribution of the individual's infection time(s)
  • Requirements:
    • None
  • Config Parameters:
    • num_sample_times: The desired number of times to sample (i.e., sequence) each individual