Module: NumTimeSample

The NumTimeSample module chooses the number of times a given individual in the ContactNetwork will be sampled. See the source code to see what is defined by the abstract class.

List of Implementations

NumTimeSample_File

• Implements the NumTimeSample_File module such that the sample times are read from file
• Requirements:
  • Must use TimeSample_File module
• Config Parameters:
  • sample_time_file: Full path to the file storing the contact network, represented in the FAVITES Sample Time File Format.

NumTimeSample_Fixed

• Each infected individual in the contact network is sampled a fixed user-specified number of times.
• Requirements:
  • None
• Config Parameters:
  • num_sample_times_per_individual: The desired number of times to sample each infected individual

NumTimeSample_None

• No infected individuals are ever sampled
• Requirements:
  • Must use NodeAvailability_None module
  • Must use TimeSample_None module
• Config Parameters:
  • None

NumTimeSample_Once

• Each infected node is sampled exactly once
• Requirements:
  • None
• Config Parameters:
  • None

NumTimeSample_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

NumTimeSample_Poisson

• Each infected individual in the contact network is sampled a number of times that is sampled from a Poisson distribution
• Requirements:
  • NumPy
• Config Parameters:
  • num_time_sample_lambda : The rate of the Poisson distribution from which to sample times to sample each infected individual