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_CommunityRandom

• A user-specified number of seed nodes are selected from each community
  • The user must specify a separate number of seeds for each community
• Requirements:
  • Must use a ContactNetworkGenerator module that creates communities
• Config Parameters:
  • num_seeds_each_community: The desired number of seed nodes for each community (a list of integers)

SeedSelection_CommunityRandomConstant

• The same number of seed nodes are selected uniformly from each community
• Requirements:
  • Must use a ContactNetworkGenerator module that creates communities
• Config Parameters:
  • num_seeds_per_community: The desired number of seed nodes per community (a single integer)

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
• 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

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