Utility Modules

• Module simuOpt (function simuOpt.setOptions)
• Module simuPOP.utils
  • Trajectory simulation (classes Trajectory and TrajectorySimulator)
    • Forward-time trajectory simulations (function simulateForwardTrajectory)
    • Backward-time trajectory simulations (function simulateBackwardTrajectory).
  • Graphical or text-based progress bar (class ProgressBar)
  • Display population variables (function viewVars)
  • Import simuPOP population from files in GENEPOP, PHYLIP and FSTAT formats (function importPopulation)
  • Export simuPOP population to files in STRUCTURE, GENEPOP, FSTAT, Phylip, PED, MAP, MS, and CSV formats (function export and operator Exporter)
  • Export simuPOP population in csv format (function saveCSV, deprecated)
• Module simuPOP.demography
  • Predefined migration models
  • Uniform interface of demographic models
  • Demographic models defined by outcomes
  • Demographic models defined by population changes (events)
  • Predefined demographic models for human populations
  • Demographic model without predefined generations to evolve *
• Module simuPOP.sampling
  • Introduction
  • Sampling individuals randomly (class RandomSampler, functions drawRandomSample and drawRandomSamples)
  • Sampling cases and controls (class CaseControlSampler, functions CaseControlSample and CaseControlSamples)
  • Sampling Pedigrees (functions indexToID and plotPedigree)
  • Sampling affected sibpairs (class AffectedSibpairSampler, functions drawAffectedSibpairSample(s))
  • Sampling nuclear families (class NuclearFamilySampler, functions drawNuclearFamilySample and drawNuclearFamilySamples)
  • Sampling three-generation families (class ThreeGenFamilySampler, functions drawThreeGenFamilySample and drawThreeGenFamilySamples)
  • Sampling different types of samples (class CombinedSampler, functions drawCombinedSample and drawCombinedSamples)
  • Sampling from subpopulations and virtual subpopulations *
• Module simuPOP.gsl