SIMPLICITY documentation

Welcome to the documentation for SIMPLICITY.

Contents:

• setup module
• SIMPLICITY
  • setup module
  • simplicity package
• simplicity package
  • Subpackages
  • Submodules
  • simplicity.dir_manager module
  • simplicity.extrande module
  • simplicity.intra_host_model module
  • simplicity.output_manager module
  • simplicity.plots_manager module
  • simplicity.population module
  • simplicity.population_model module
  • simplicity.random_gen module
  • simplicity.runme module
  • simplicity.settings_manager module
  • simplicity.simulation module
  • Module contents
• simplicity.evolution package
  • Submodules
  • simplicity.evolution.decoder module
  • simplicity.evolution.mutations module
  • simplicity.evolution.reference module
  • Module contents
• simplicity.phenotype package
  • Submodules
  • simplicity.phenotype.consensus module
  • simplicity.phenotype.distance module
  • simplicity.phenotype.update module
  • simplicity.phenotype.weight module
  • Module contents
• simplicity.runners package
  • Submodules
  • simplicity.runners.multiprocessing module
  • simplicity.runners.serial module
  • simplicity.runners.slurm module
  • simplicity.runners.unit_run module
  • Module contents
• simplicity.tree package
  • Submodules
  • simplicity.tree.filtered_infection_tree module
  • simplicity.tree.json_tree module
  • simplicity.tree.newick module
  • simplicity.tree.nexus module
  • simplicity.tree.tree_builder module
  • Module contents
• simplicity.tuning package
  • Submodules
  • simplicity.tuning.diagnosis_rate module
  • simplicity.tuning.evolutionary_rate module
  • Module contents