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:
  • Dual-Birth Simulator
  • TreeSwift
• 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_File

• The phylogenetic tree(s) is/are loaded from file
• Requirements:
  • None
• Config Parameters:
  • tree_file: The Newick tree file in unit of time

NodeEvolution_None

• Speciations only occur at transmission events
• Requirements:
  • None
• Config Parameters:
  • None

NodeEvolution_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

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:
  • Java
  • TreeSwift
• 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
  • vts_max_attempts: The maximum number of attempts to coalesce a single tree (e.g. 100) before FAVITES kills VirusTreeSimulator (otherwise it can run infinitely)

NodeEvolution_Yule

• Evolves viral phylogenetic trees based on the Yule model
• Requirements:
  • Dual-Birth Simulator
  • TreeSwift
• 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