Module: NodeEvolution

The NodeEvolution module evolves the phylogenetic trees of the viruses within a specified node until a specified time. See the source code to see what is defined by the abstract class.

List of Implementations

• NodeEvolution_BirthDeath
  • Evolves viral phylogenetic trees based on a Birth-Death process using DendroPy's birth_death_tree function
  • Requirements:
    • DendroPy
  • Config Parameters:
    • bd_birth: The birth rate
    • bd_birth_sd: The standard deviation of the normally-distributed mutation added to the birth rate as it is inherited by daughter nodes
      • If 0, birth rate does not evolve on the tree
    • bd_death: The death rate
    • bd_death_sd: The standard deviation of the normally-distributed mutation added to the death rate as it is inherited by daughter nodes
      • If 0, death rate does not evolve on the tree
• NodeEvolution_DualBirth
  • Evolves viral phylogenetic trees based on the Dual-Birth model
  • Requirements:
    • NumPy
  • Config Parameters:
    • rate_A: The Dual-Birth activation rate, λ_a
    • rate_B: The Dual-Birth birth rate, λ_b
• NodeEvolution_None
  • No speciations or deaths (the root simply propagates through time)
    • The result is a phylogenetic tree containing a single leaf
  • Requirements:
    • None
  • Config Parameters:
    • None
• TransmissionTimeSample_PANGEA
  • Wrapper for PANGEA.HIV.sim
  • Requirements:
    • R
    • PANGEA.HIV.sim
    • Must use ContactNetwork_PANGEA module
    • Must use ContactNetworkEdge_PANGEA module
    • Must use ContactNetworkGenerator_PANGEA module
    • Must use ContactNetworkNode_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 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
• NodeEvolution_Yule
  • Evolves viral phylogenetic trees based on the Yule model
  • Requirements:
    • NumPy
  • Config Parameters:
    • yule_rate: The Yule rate, λ