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
• NodeEvolution_PANGEA
  • Wrapper for PANGEA.HIV.sim
  • Requirements:
    • 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)
    • pangea_yr.start: See PANGEA.HIV.sim help ("" for default)
    • pangea_yr.end: See PANGEA.HIV.sim help ("" for default)
    • pangea_seed: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.INC.recent: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.INC.recent.len: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.PREV.min: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.PREV.max: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.PREV.base: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.INTERVENTION.start: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.INTERVENTION.mul: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.ARCHIVAL.n: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.MODEL: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.PREV.max.n: See PANGEA.HIV.sim help ("" for default)
    • pangea_s.INTERVENTION.prop: See PANGEA.HIV.sim help ("" for default)
    • pangea_epi.model: See PANGEA.HIV.sim help ("" for default)
    • pangea_epi.acute: See PANGEA.HIV.sim help ("" for default)
    • pangea_epi.intervention: See PANGEA.HIV.sim help ("" for default)
    • pangea_epi.dt: See PANGEA.HIV.sim help ("" for default)
    • pangea_epi.import: See PANGEA.HIV.sim help ("" for default)
    • pangea_root.edge.fixed: See PANGEA.HIV.sim help ("" for default)
    • pangea_v.N0tau: See PANGEA.HIV.sim help ("" for default)
    • pangea_v.r: See PANGEA.HIV.sim help ("" for default)
    • pangea_v.T50: See PANGEA.HIV.sim help ("" for default)
    • pangea_wher.mu: See PANGEA.HIV.sim help ("" for default)
    • pangea_wher.sigma: See PANGEA.HIV.sim help ("" for default)
    • pangea_bwerm.mu: See PANGEA.HIV.sim help ("" for default)
    • pangea_bwerm.sigma: See PANGEA.HIV.sim help ("" for default)
    • pangea_er.gamma: See PANGEA.HIV.sim help ("" for default)
    • pangea_er.gtr: See PANGEA.HIV.sim help ("" for default)
    • pangea_sp.prop.of.sexactive: See PANGEA.HIV.sim help ("" for default)
    • pangea_report.prop.recent: See PANGEA.HIV.sim help ("" for default)
    • pangea_dbg.GTRparam: See PANGEA.HIV.sim help ("" for default)
    • pangea_dbg.rER: See PANGEA.HIV.sim help ("" for default)
    • pangea_index.starttime.mode: See PANGEA.HIV.sim help ("" for default)
    • pangea_startseq.mode: See PANGEA.HIV.sim help ("" for default)
    • pangea_seqtime.mode: See PANGEA.HIV.sim help ("" for default)
• NodeEvolution_Yule
  • Evolves viral phylogenetic trees based on the Yule model
  • Requirements:
    • NumPy
  • Config Parameters:
    • yule_rate: The Yule rate, λ