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:
    • DendroPy
    • Dual-Birth Simulator
  • Config Parameters:
    • dualbirth_path: The path to your dualbirth executable (or simply "dualbirth" if it is in your PATH variable)
    • 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:
    • 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
• NodeEvolution_VirusTreeSimulator
  • Evolves viral phylogenetic trees under a coalescent model with various effective population growth models:
    • Constant effective population growth (i.e., viral populations remain constant over time)
    • Exponential effective population growth (i.e., viral populations experience exponential growth after infection)
    • Logistic effective population growth (i.e., viral populations experience logistic growth after infection)
  • Requirements:
    • DendroPy
    • Java
  • Config Parameters:
    • java_path : The path to your java executable (or simply "java" if it is in your PATH variable)
    • vts_model: The desired viral population growth model to use
      • Options are constant, exponential, and logistic
    • vts_n0: The desired effective population size at time zero (used in all models)
      • It makes sense to use a value of 1 for viruses if you assume a single viral family was transmitted
    • vts_growthRate: The desired effective population size growth rate (used in exponential and logistic models)
    • vts_t50: The time point, relative to the time of infection in backwards time, at which the population is equal to half its final asymptotic value, in the logistic model
• NodeEvolution_Yule
  • Evolves viral phylogenetic trees based on the Yule model
  • Requirements:
    • DendroPy
    • Dual-Birth Simulator
  • Config Parameters:
    • dualbirth_path: The path to your dualbirth executable (or simply "dualbirth" if it is in your PATH variable)
    • yule_rate: The Yule rate, λ