Module: SeedSelection

The SeedSelection module chooses which nodes in the ContactNetwork object to be initially infected. See the source code to see what is defined by the abstract class.

List of Implementations

• SeedSelection_ClustersBernoulli
  • There will be k seed clusters with m total seed individuals that are chosen as follows:
    • k initial seeds are chosen in an edge-weighted manner
    • For each of the k initial seeds, a random walk is performed starting at the initial seed
      • At each non-seed node in the walk, the node is chosen as a seed with probability p
      • The random walk ends when m/k nodes are chosen to be seeds in this cluster
  • Requirements:
    • None
  • Config Parameters:
    • seed_k: The desired number of seed clusters
    • seed_m: The desired total number of seed nodes
    • seed_p: The Bernoulli probability of selecting a given non-seed node during a walk
• SeedSelection_CommunityRandomConstant
  • The same number of seed nodes are selected uniformly from each community
  • Requirements:
    • None
  • Config Parameters:
    • num_seeds_per_cluster: The desired number of seed nodes in each community
• SeedSelection_EdgeWeighted
  • The probability at which a node is chosen is weighted by its degree
  • Requirements:
    • None
  • Config Parameters:
    • num_seeds: The desired number of seed nodes
• SeedSelection_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 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
  • 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
• SeedSelection_Random
  • Seed nodes are selected from the set of all nodes in the contact network with equal probability
  • Requirements:
    • None
  • Config Parameters:
    • num_seeds: The desired number of seed nodes
• SeedSelection_TransmissionFile
  • Transmission network is read from file
  • Requirements:
    • Must use EndCriteria_TransmissionFile module
    • Must use TransmissionNodeSample_TransmissionFile module
    • Must use TransmissionTimeSample_TransmissionFile module
  • Config Parameters:
    • transmission_network_file: The desired transmission network, represented in the FAVITES Transmission Network File Format
    • seed_file: The desired seed nodes, represented in the FAVITES Seed File Format